@article{EndresKneitzOrthetal.2016, author = {Endres, Marcel and Kneitz, Susanne and Orth, Martin F. and Perera, Ruwan K. and Zernecke, Alma and Butt, Elke}, title = {Regulation of matrix metalloproteinases (MMPs) expression and secretion in MDA-MB-231 breast cancer cells by LIM and SH3 protein 1 (LASP1)}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {39}, doi = {10.18632/oncotarget.11720}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176920}, pages = {64244-64259}, year = {2016}, abstract = {The process of tumor invasion requires degradation of extracellular matrix by proteolytic enzymes. Cancer cells form protrusive invadopodia, which produce and release matrix metalloproteinases (MMPs) to degrade the basement membrane thereby enabling metastasis. We investigated the effect of LASP1, a newly identified protein in invadopodia, on expression, secretion and activation of MMPs in invasive breast tumor cell lines. By analyzing microarray data of in-house generated control and LASP1-depleted MDA-MB-231 breast cancer cells, we observed downregulation of MMP1, -3 and -9 upon LASP1 depletion. This was confirmed by Western blot analysis. Conversely, rescue experiments restored in part MMP expression and secretion. The regulatory effect of LASP1 on MMP expression was also observed in BT-20 breast cancer cells as well as in prostate and bladder cancer cell lines. In line with bioinformatic FunRich analysis of our data, which mapped a high regulation of transcription factors by LASP1, public microarray data analysis detected a correlation between high LASP1 expression and enhanced c-Fos levels, a protein that is part of the transcription factor AP-1 and known to regulate MMP expression. Compatibly, in luciferase reporter assays, AP-1 showed a decreased transcriptional activity after LASP1 knockdown. Zymography assays and Western blot analysis revealed an additional promotion of MMP secretion into the extracellular matrix by LASP1, thus, most likely, altering the microenvironment during cancer progression. The newly identified role of LASP1 in regulating matrix degradation by affecting MMP transcription and secretion elucidated the migratory potential of LASP1 overexpressing aggressive tumor cells in earlier studies.}, language = {en} } @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} } @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} } @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} } @phdthesis{Pasch2016, author = {Pasch, Elisabeth}, title = {The role of SUN4 and related proteins in sperm head formation and fertility}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139092}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Spermiogenesis describes the differentiation of haploid germ cells into motile, fertilization-competent spermatozoa. During this fundamental transition the species-specific sperm head is formed, which necessitates profound nuclear restructuring coincident with the assembly of sperm-specific structures and chromatin compaction. In the case of the mouse, it is characterized by reshaping of the early round spermatid nucleus into an elongated sickle-shaped sperm head. This tremendous shape change requires the transduction of cytoskeletal forces onto the nuclear envelope (NE) or even further into the nuclear interior. LINC (linkers of nucleoskeleton and cytoskeleton) complexes might be involved in this process, due to their general function in bridging the NE and thereby physically connecting the nucleus to the peripheral cytoskeleton. LINC complexes consist of inner nuclear membrane integral SUN-domain proteins and outer nuclear membrane KASH-domain counterparts. SUN- and KASH-domain proteins are directly connected to each other within the perinuclear space, and are thus capable of transferring forces across the NE. To date, these protein complexes are known for their essential functions in nuclear migration, anchoring and positioning of the nucleus, and even for chromosome movements and the maintenance of cell polarity and nuclear shape. In this study LINC complexes were investigated with regard to their potential role in sperm head formation, in order to gain further insight into the processes occurring during spermiogenesis. To this end, the behavior and function of the testis-specific SUN4 protein was studied. The SUN-domain protein SUN4, which had received limited characterization prior to this work, was found to be exclusively expressed in haploid stages during germ cell development. In these cell stages, it specifically localized to the posterior NE at regions decorated by the manchette, a spermatid-specific structure which was previously shown to be involved in nuclear shaping. Mice deficient for SUN4 exhibited severely disorganized manchette residues and gravely misshapen sperm heads. These defects resulted in a globozoospermia-like phenotype and male mice infertility. Therefore, SUN4 was not only found to be mandatory for the correct assembly and anchorage of the manchette, but also for the correct localization of SUN3 and Nesprin1, as well as of other NE components. Interaction studies revealed that SUN4 had the potential to interact with SUN3, Nesprin1, and itself, and as such is likely to build functional LINC complexes that anchor the manchette and transfer cytoskeletal forces onto the nucleus. Taken together, the severe impact of SUN4 deficiency on the nucleocytoplasmic junction during sperm development provided direct evidence for a crucial role of SUN4 and other LINC complex components in mammalian sperm head formation and fertility.}, subject = {Maus}, language = {en} } @phdthesis{Bertho2016, author = {Bertho, Sylvain}, title = {Biochemical and molecular characterization of an original master sex determining gene in Salmonids}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139130}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Sexual development is a fundamental and versatile process that shapes animal morphology, physiology and behavior. The underlying developmental process is composed of the sex determination and the sex differentiation. Sex determination mechanisms are extremely labile among taxa. The initial triggers of the sex determination process are often genetics called sex determining genes. These genes are expressed in the bipotential gonad and tilt the balance to a developmental program allowing the differentiation of either a testis or an ovary. Fish represent a large and fascinating vertebrate group to study both sex determination and sex differentiation mechanisms. To date, among the known sex determining genes, three gene families namely sox, dmrt and TGF-β factors govern this developmental program. As exception to this rule, sdY "sexually dimorphic on the Y" does not belong to one of these families as it comes from the duplication / evolution of an ancestor gene related to immunity, i.e., the interferon related factor 9, irf9. sdY is the master sex determining gene in salmonids, a group of fishes that include species such as rainbow trout and Atlantic salmon. The present study was aimed to firstly characterize the features of SdY protein. Results indicate that SdY is predominantly localized in the cytoplasm tested in various fish and mammalian cell lines and confirmed by different methods. Predictive in silico analysis revealed that SdY is composed of a β-sandwich core surrounded by three α-helices as well specific characteristics conferring a putative protein-protein interaction site. Secondly, the study was aimed to understand how SdY could trigger testicular differentiation. SdY is a truncated divergent version of Irf9 that has a conserved protein-protein domain but lost the DNA interaction domain of its ancestor gene. It was then hypothesized that SdY could initiate testicular differentiation by protein-protein interactions. To evaluate this we first conducted a yeast-two-hybrid screen that revealed a high proportion of transcription factors including fox proteins. Using various biochemical and cellular methods we confirm an interaction between SdY and Foxl2, a major transcription factor involved in ovarian differentiation and identity maintenance. Interestingly, the interaction of SdY with Foxl2 leads to nuclear translocation of SdY from the cytoplasm. Furthermore, this SdY translocation mechanism was found to be specific to fish Foxl2 and to a lesser extend Foxl3 and not other Fox proteins or mammalian FoxL2. In addition, we found that this interaction allows the stabilization of SdY and prevents its degradation. Finally, to better decipher SdY action we used as a model a mutated version of SdY that was identified in XY females of Chinook salmon natural population. Results show that this mutation induces a local conformation defect obviously leading to a misfolded protein and a quick degradation. Moreover, the mutated version compromised the interaction with Foxl2 defining a minimal threshold to induce testicular differentiation. Altogether results from my thesis propose that SdY would trigger testicular differentiation in salmonids by preventing Foxl2 to promote ovarian differentiation. Further research should be now carried out on how this interaction of SdY and Foxl2 acts in-vivo.}, subject = {Lachsartige }, language = {en} } @phdthesis{Costea2016, author = {Costea, Paul Igor}, title = {Stratification and variation of the human gut microbiota}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139649}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The microbial communities that live inside the human gastrointestinal tract -the human gut microbiome- are important for host health and wellbeing. Characterizing this new "organ", made up of as many cells as the human body itself, has recently become possible through technological advances. Metagenomics, the high-throughput sequencing of DNA directly from microbial communities, enables us to take genomic snapshots of thousands of microbes living together in this complex ecosystem, without the need for isolating and growing them. Quantifying the composition of the human gut microbiome allows us to investigate its properties and connect it to host physiology and disease. The wealth of such connections was unexpected and is probably still underestimated. Due to the fact that most of our dietary as well as medicinal intake affects the microbiome and that the microbiome itself interacts with our immune system through a multitude of pathways, many mechanisms have been proposed to explain the observed correlations, though most have yet to be understood in depth. An obvious prerequisite to characterizing the microbiome and its interactions with the host is the accurate quantification of its composition, i.e. determining which microbes are present and in what numbers they occur. Historically, standard practices have existed for sample handling, DNA extraction and data analysis for many years. However, these were generally developed for single microbe cultures and it is not always feasible to implement them in large scale metagenomic studies. Partly because of this and partly because of the excitement that new technology brings about, the first metagenomic studies each took the liberty to define their own approach and protocols. From early meta-analysis of these studies it became clear that the differences in sample handling, as well as differences in computational approaches, made comparisons across studies very difficult. This restricts our ability to cross-validate findings of individual studies and to pool samples from larger cohorts. To address the pressing need for standardization, we undertook an extensive comparison of 21 different DNA extraction methods as well as a series of other sample manipulations that affect quantification. We developed a number of criteria for determining the measurement quality in the absence of a mock community and used these to propose best practices for sampling, DNA extraction and library preparation. If these were to be accepted as standards in the field, it would greatly improve comparability across studies, which would dramatically increase the power of our inferences and our ability to draw general conclusions about the microbiome. Most metagenomics studies involve comparisons between microbial communities, for example between fecal samples from cases and controls. A multitude of approaches have been proposed to calculate community dissimilarities (beta diversity) and they are often combined with various preprocessing techniques. Direct metagenomics quantification usually counts sequencing reads mapped to specific taxonomic units, which can be species, genera, etc. Due to technology-inherent differences in sampling depth, normalizing counts is necessary, for instance by dividing each count by the sum of all counts in a sample (i.e. total sum scaling), or by subsampling. To derive a single value for community (dis-)similarity, multiple distance measures have been proposed. Although it is theoretically difficult to benchmark these approaches, we developed a biologically motivated framework in which distance measures can be evaluated. This highlights the importance of data transformations and their impact on the measured distances. Building on our experience with accurate abundance estimation and data preprocessing techniques, we can now try and understand some of the basic properties of microbial communities. In 2011, it was proposed that the space of genus level variation of the human gut microbial community is structured into three basic types, termed enterotypes. These were described in a multi-country cohort, so as to be independent of geography, age and other host properties. Operationally defined through a clustering approach, they are "densely populated areas in a multidimensional space of community composition"(source) and were proposed as a general stratifier for the human population. Later studies that applied this concept to other datasets raised concerns about the optimum number of clusters and robustness of the clustering approach. This heralded a long standing debate about the existence of structure and the best ways to determine and capture it. Here, we reconsider the concept of enterotypes, in the context of the vastly increased amounts of available data. We propose a refined framework in which the different types should be thought of as weak attractors in compositional space and we try to implement an approach to determining which attractor a sample is closest to. To this end, we train a classifier on a reference dataset to assign membership to new samples. This way, enterotypes assignment is no longer dataset dependent and effects due to biased sampling are minimized. Using a model in which we assume the existence of three enterotypes characterized by the same driver genera, as originally postulated, we show the relevance of this stratification and propose it to be used in a clinical setting as a potential marker for disease development. Moreover, we believe that these attractors underline different rules of community assembly and we recommend they be accounted for when analyzing gut microbiome samples. While enterotypes describe structure in the community at genus level, metagenomic sequencing can in principle achieve single-nucleotide resolution, allowing us to identify single nucleotide polymorphisms (SNPs) and other genomic variants in the gut microbiome. Analysis methodology for this level of resolution has only recently been developed and little exploration has been done to date. Assessing SNPs in a large, multinational cohort, we discovered that the landscape of genomic variation seems highly structured even beyond species resolution, indicating that clearly distinguishable subspecies are prevalent among gut microbes. In several cases, these subspecies exhibit geo-stratification, with some subspecies only found in the Chinese population. Generally however, they present only minor dispersion limitations and are seen across most of our study populations. Within one individual, one subspecies is commonly found to dominate and only rarely are several subspecies observed to co-occur in the same ecosystem. Analysis of longitudinal data indicates that the dominant subspecies remains stable over periods of more than three years. When interrogating their functional properties we find many differences, with specific ones appearing relevant to the host. For example, we identify a subspecies of E. rectale that is lacking the flagellum operon and find its presence to be significantly associated with lower body mass index and lower insulin resistance of their hosts; it also correlates with higher microbial community diversity. These associations could not be seen at the species level (where multiple subspecies are convoluted), which illustrates the importance of this increased resolution for a more comprehensive understanding of microbial interactions within the microbiome and with the host. Taken together, our results provide a rigorous basis for performing comparative metagenomics of the human gut, encompassing recommendations for both experimental sample processing and computational analysis. We furthermore refine the concept of community stratification into enterotypes, develop a reference-based approach for enterotype assignment and provide compelling evidence for their relevance. Lastly, by harnessing the full resolution of metagenomics, we discover a highly structured genomic variation landscape below the microbial species level and identify common subspecies of the human gut microbiome. By developing these high-precision metagenomics analysis tools, we thus hope to contribute to a greatly improved understanding of the properties and dynamics of the human gut microbiome.}, subject = {Mensch}, language = {en} } @phdthesis{Eck2016, author = {Eck, Saskia}, title = {The impact of thermogenetic depolarizations of specific clock neurons on Drosophila melanogaster's circadian clock}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-137118}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The rotation of the earth around its own axis determines periodically changing environmental conditions, like alterations in light and temperature. For the purpose of adapting all organisms' behavior, physiology and metabolism to recurring changes, endogenous clocks have evolved, which allow the organisms to anticipate environmental changes. In chronobiology, the scientific field dealing with the investigation of the underlying mechanisms of the endogenous clock, the fruit fly Drosophila melanogaster serves as a beneficial model organism. The fruit fly's circadian clock exhibits a rather simple anatomical organization, but nevertheless constitutes homologies to the mammalian system. Thus also in this PhD-thesis the fruit fly was used to decipher general features of the circadian clock's interneuronal communication. Drosophila melanogaster's circadian clock consists of about 150 clock neurons, which are located in the central nervous system of the fly. These clock neurons can be subdivided regarding to their anatomical position in the brain into the dorsal neurons (DN1s, DN2s, DN3s), as well as into the lateral neurons (LPNs, LNds, s-LNvs, l-LNvs). Functionally these clock neuron clusters can be classified as Morning- and Evening oscillators (M- and E- oscillators), driving different parts of the fly's locomotor activity in light-dark conditions (LD). The Morning-oscillators are represented by the s-LNvs and are known to be the main pacemakers, driving the pace of the clock in constant conditions (constant darkness; DD). The group of Evening-oscillators consists of the LNds, the DN1s and the 5th s-LNv and is important for the proper timing of the evening activity in LD. All of these clock neurons are not functionally independent, but form complex neuronal connections, which are highly plastic in their response to different environmental stimuli (Zeitgebers), like light or temperature. Even though a lot is known about the function and the importance of some clock neuron clusters, the exact interplay between the neurons is not fully known yet. To investigate the mechanisms, which are involved in communication processes among different clock neurons, we depolarized specific clock cells in a temporally and cell-type restricted manner using dTrpA1, a thermosensitive cation channel, which allows the depolarization of neurons by application of temperature pulses (TP) above 29°C to the intact and freely moving fly. Using different clock specific GAL4-driver lines and applying TPs at different time points within the circadian cycle in DD enabled us with the help of phase shift experiments to draw conclusions on the properties of the endogenous clock. The obtained phase shifts in locomotor behavior elicited by specific clock neuronal activation were plotted as phase response curves (PRCs). The depolarization of all clock neurons shifted the phase of activity the strongest, especially in the delay zone of the PRC. The exclusive depolarization of the M oscillators together with the l-LNvs (PDF+ neurons: s-LNvs \& l-LNvs) caused shifts in the delay and in the advance zone as well, however the advances were severely enhanced in their temporal occurrence ranging into the subjective day. We concluded that light might have inhibitory effects on the PDF+ cells in that particular part of the PRC, as typical light PRCs do not exhibit that kind of distinctive advances. By completely excluding light in the PRC-experiments of this PhD-thesis, this photic inhibitory input to the PDF+ neurons is missing, probably causing the broadened advance zone. These findings suggest the existence of an inhibitory light-input pathway to the PDF+ cells from the photoreceptive organs (Hofbauer-Buchner eyelet, photoreceptor cells of compound eyes, ocelli) or from other clock neurons, which might inhibit phase advances during the subjective day. To get an impression of the molecular state of the clock in the delay and advance zone, staining experiments against Period (PER), one of the most important core clock components, and against the neuropeptide Pigment Dispersing Factor (PDF) were performed. The cycling of PER levels mirrored the behavioral phase shifts in experimental flies, whereas the controls were widely unaffected. As just those neurons, which had been depolarized, exhibited immediate shifted PER oscillations, this effect has to be rapidly regulated in a cell-autonomous manner. However, the molecular link between clock neuron depolarization and shifts in the molecular clock's cycling is still missing. This issue was addressed by CREB (cAMP responsive element binding protein) quantification in the large ventrolateral neurons (l-LNvs), as these neurons responded unexpectedly and strongest to the artificial depolarization exhibiting a huge increase in PER levels. It had been previously suggested that CREB is involved in circadian rhythms by binding to regulatory sequences of the period gene (Belvin et al., 1999), thus activating its transcription. We were able to show, that CREB levels in the l-LNvs are under circadian regulation, as they exhibit higher CREB levels at the end of the subjective night relative to the end of the subjective day. That effect was further reinforced by artificial depolarization, independently of the time point of depolarization. Furthermore the data indicate that rises in CREB levels are coinciding with the time point of increases of PER levels in the l-LNvs, suggesting CREB being the molecular link between the neuronal electrical state and the molecular clock. Taking together, the results indicate that a temporal depolarization using dTrpA1 is able to significantly phase shift the clock on the behavioral and protein level. An artificial depolarization at the beginning of the subjective night caused phase delays, whereas a depolarization at the end of the subjective night resulted in advances. The activation of all clock neurons caused a PRC that roughly resembled a light-PRC. However, the depolarization of the PDF+ neurons led to a PRC exhibiting a shape that did not resemble that of a light-mediated PRC, indicating the complex processing ability of excitatory and inhibitory input by the circadian clock. Even though this experimental approach is highly artificial, just the exclusion of light-inputs enabled us to draw novel conclusions on the network communication and its light input pathways.}, subject = {Chronobiologie}, language = {en} } @phdthesis{Koenig2016, author = {K{\"o}nig, Sebastian}, title = {Spatially selective visual attention in Drosophila melanogaster}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134452}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Finding the right behavior at the right time is one of the major tasks of brains. In a natural scenery there is often an abundance of stimuli present and the brain has to separate the relevant from the irrelevant ones. Selective visual attention (SVA) is a property of higher visual systems that achieves this separation, as it allows to '[…] focus on one source of sensory input to the exclusion of others' (Luck and Mangun, 1996). There are probably several forms of SVA depending upon the criteria used for the separation, such as salience, color, location in space, novelty, or motion. Many studies have investigated SVA in humans and non-human primates. However, complex functions like attention were initially not expected to be already implemented in the brains of simple organisms like Drosophila. After a first demonstration of selective attention in the fly (Wolf and Heisenberg, 1980), it took some time until other studies included attentional mechanisms in their argumentation to explain certain behaviors of Drosophila. However, their definition and characterization of attention differed and often was ambiguous. Here, one particular form, spatially selective visual attention in the fly Drosophila is investigated. It has been shown earlier that the fly spontaneously may restrict its behavioral responses in stationary flight to the visual stimuli on one side of the visual field. On the basis of experiments of Sareen et al., (2011) it has been conjectured that the fly has a focus of attention (FoA) and that the fly responds to the visual stimuli within this area of the visual field. Whether the FoA is the adequate concept for this spatial property of SVA in the fly needs to be further discussed and is a subject also of the present study. At this stage, the concept will be used in the description of the new results expanding the characterization of SVA. This study continued the investigation of SVA during tethered flight with variable but controlled visual input and an automated primary data evaluation. This standardized paradigm allowed for analysis of wild-type behavior as well as for a comparison of several mutant and pharmacologically manipulated strains to the wild-type. Some properties of human SVA like the occurrence of externally as well as internally caused shifts of attention were found in Drosophila and it could be shown, that SVA in the fly can be externally guided and has an attention span. Additionally, a neurotransmitter and proteins, which play a significant role in SVA were discovered. Based on this, the genetic tools available for Drosophila provided the means to a first examination of cells and circuits involved in SVA. Finally, the free walk behavior of flies that had been shown to have compromised SVA was characterized. The results suggested that the observed phenotypes of SVA were not behavior specific. Covert shifts of the FoA were investigated. The FoA can be externally guided by visual cues to one or the other side of the visual field and even after the cue has disappeared it remains there for <4s. An intriguing finding of this study is the fact, that the quality of the cue determines whether it is attractive or repellent. For example a cue can be changed from being repellent (negative) to being attractive (positive) by changing its oscillation amplitude from 4° to 2°. Testing the effectiveness of cues in the upper and lower visual field separately, revealed that the perception of a cue by the fly is not exclusively based on a sum of its specifications. Because positive cueing did not have an after-effect in each of the two half-fields alone, but did so if the cue was shown in both, the fly seems to evaluate the cue for each combination of parameters specifically. Whether this evaluation of the cue changed on a trial-to-trial basis or if the cue in some cases failed to shift the FoA can at this point not be determined. Looking at the responses of the fly to the displacement of a black vertical stripe showed that they can be categorized as no responses, syn-directional responses (following the direction of motion of the stripe) and anti-directional responses (in the opposite direction of the motion of the stripe). The yaw-torque patterns of the latter bared similarities with spontaneous body saccades and they most likely represented escape attempts of the fly. Syn-directional responses, however, were genuine object responses, distinguishable by a longer latency until they were elicited and a larger amplitude. These properties as well as the distribution of response polarities were not influenced by the presence or absence of a cue. When two stripes were displaced simultaneously in opposite directions the rate of no responses increased in comparison to the displacement of a single stripe. If one of the stripes was cued, both, the responses towards and away from the side of cue resembled the syn-directional responses. Significant progress was made with the elucidation of the neuronal underpinnings of SVA. Ablation of the mushroom bodies (MB) demonstrated their requirement for SVA. Furthermore, it was shown that dopamine signaling has to be balanced between too much and too little. Either inhibiting the synthesis of dopamine or its re-uptake at the synapse via the dDAT impaired the flies' susceptibility to cueing. Using the Gal4/UAS system, cell specific expression or knockdown of the dDAT was used to scrutinize the role of MB sub-compartments in SVA. The αβ-lobes turned out to be necessary and sufficient to maintain SVA. The Gal4-line c708a labels only a subset of Kenyon cells (KC) within the αβ-lobes, αβposterior. These cells stand out, because of (A) the mesh-like arrangement of their fibers within the lobes and (B) the fact that unlike the other KCs they bypass the calyx and thereby the main source of olfactory input to the MBs, forming connections only in the posterior accessory calyx (Tanaka et al., 2008). This structure receives no or only marginal olfactory input, suggesting for it a role in tasks other than olfaction. This study shows their requirement in a visual task by demonstrating that they are necessary to uphold SVA. Restoring dDAT function in these approximately only 90 cells was probably insufficient to lower the dopamine concentration at the relevant synapses and hence a rescue failed. Alternatively, the processes mediating SVA at the αβ-lobes might require an interplay between all of their KCs. In conclusion, the results provide an initial point for future research to fully understand the localization of and circuitry required for SVA in the brain. In the experiments described so far, attention has been externally guided. However, flies are also able to internally shift their FoA without any cues from the outside world. In a set of 60 consecutive simultaneous displacements of two stripes, they were more likely to produce a response with the same polarity as the preceding one than a random polarity selection predicted. This suggested a dwelling of the FoA on one side of the visual field. Assuming that each response was influenced by the previous one in a way that the probability to repeat the response polarity was increased by a certain factor (dwelling factor, df), a random selection of response type including a df was computed. Implementation of the df removed the difference between observed probability of polarity repetition and the one suggested by random selection. When the interval between displacements was iteratively increased to 5s, no significant df could be detected anymore for pauses longer than 4s. In conclusion, Drosophila has an attention span of approximately 4s. Flies with a mutation in the radish gene expressed no after-effect of cueing and had a shortened attention span of about 1s. The dDAT inhibitor methylphenidate is able to rescue the first, but does not affect the latter phenotype. Probably, radish is differently involved in the two mechanisms. This study showed, that endogenous (covert) shifts of spatially selective visual attention in the fly Drosophila can be internally and externally guided. The variables determining the quality of a cue turned out to be multifaceted and a more systematic approach is needed for a better understanding of what property or feature of the cue changes the way it is evaluated by the fly. A first step has been made to demonstrate that SVA is a fundamental process and compromising it can influence the characteristics of other behaviors like walking. The existence of an attention span, the dependence of SVA on dopamine as well as the susceptibility to pharmacological manipulations, which in humans are used to treat respective diseases, point towards striking similarities between SVA in humans and Drosophila.}, subject = {Taufliege}, 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} } @article{BemmBeckerLarischetal.2016, author = {Bemm, Felix and Becker, Dirk and Larisch, Christina and Kreuzer, Ines and Escalante-Perez, Maria and Schulze, Waltraud X. and Ankenbrand, Markus and Van de Weyer, Anna-Lena and Krol, Elzbieta and Al-Rasheid, Khaled A. and Mith{\"o}fer, Axel and Weber, Andreas P. and Schultz, J{\"o}rg and Hedrich, Rainer}, title = {Venus flytrap carnivorous lifestyle builds on herbivore defense strategies}, series = {Genome Research}, volume = {26}, journal = {Genome Research}, number = {6}, doi = {10.1101/gr.202200.115}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188799}, pages = {812-825}, year = {2016}, abstract = {Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.}, language = {en} } @article{BenoitAdelmanReinhardtetal.2016, author = {Benoit, Joshua B. and Adelman, Zach N. and Reinhardt, Klaus and Dolan, Amanda and Poelchau, Monica and Jennings, Emily C. and Szuter, Elise M. and Hagan, Richard W. and Gujar, Hemant and Shukla, Jayendra Nath and Zhu, Fang and Mohan, M. and Nelson, David R. and Rosendale, Andrew J. and Derst, Christian and Resnik, Valentina and Wernig, Sebastian and Menegazzi, Pamela and Wegener, Christian and Peschel, Nicolai and Hendershot, Jacob M. and Blenau, Wolfgang and Predel, Reinhard and Johnston, Paul R. and Ioannidis, Panagiotis and Waterhouse, Robert M. and Nauen, Ralf and Schorn, Corinna and Ott, Mark-Christoph and Maiwald, Frank and Johnston, J. Spencer and Gondhalekar, Ameya D. and Scharf, Michael E. and Raje, Kapil R. and Hottel, Benjamin A. and Armis{\´e}n, David and Crumi{\`e}re, Antonin Jean Johan and Refki, Peter Nagui and Santos, Maria Emilia and Sghaier, Essia and Viala, S{\`e}verine and Khila, Abderrahman and Ahn, Seung-Joon and Childers, Christopher and Lee, Chien-Yueh and Lin, Han and Hughes, Daniel S.T. and Duncan, Elizabeth J. and Murali, Shwetha C. and Qu, Jiaxin and Dugan, Shannon and Lee, Sandra L. and Chao, Hsu and Dinh, Huyen and Han, Yi and Doddapaneni, Harshavardhan and Worley, Kim C. and Muzny, Donna M. and Wheeler, David and Panfilio, Kristen A. and Jentzsch, Iris M. Vargas and Jentzsch, IMV and Vargo, Edward L. and Booth, Warren and Friedrich, Markus and Weirauch, Matthew T. and Anderson, Michelle A.E. and Jones, Jeffery W. and Mittapalli, Omprakash and Zhao, Chaoyang and Zhou, Jing-Jiang and Evans, Jay D. and Attardo, Geoffrey M. and Robertson, Hugh M. and Zdobnov, Evgeny M. and Ribeiro, Jose M.C. and Gibbs, Richard A. and Werren, John H. and Palli, Subba R. and Schal, Coby and Richards, Stephen}, title = {Unique features of a global human ectoparasite identified through sequencing of the bed bug genome}, series = {Nature Communications}, volume = {7}, journal = {Nature Communications}, number = {10165}, doi = {10.1038/ncomms10165}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166221}, year = {2016}, abstract = {The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.}, language = {en} } @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{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} } @article{DiaoMoussetHorsburghetal.2016, author = {Diao, Wenwen and Mousset, Mathilde and Horsburgh, Gavin J. and Vermeulen, Cornelis J. and Johannes, Frank and van de Zande, Louis and Ritchie, Michael G. and Schmitt, Thomas and Beukeboom, Leo W.}, title = {Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps}, series = {G3: Genes Genomes Genetics}, volume = {6}, journal = {G3: Genes Genomes Genetics}, number = {6}, doi = {10.1534/g3.116.029074}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165412}, pages = {1549-1562}, year = {2016}, abstract = {A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S)-5-hydroxy-4-decanolide (RS-HDL). Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL) analysis involving 475 recombinant hybrid males (F2), 2148 reciprocally backcrossed females (F3), and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP) markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.}, language = {en} } @article{daCruzRodriguezCasuriagaSantinaqueetal.2016, author = {da Cruz, Irene and Rodr{\´i}guez-Casuriaga, Rosana and Santi{\~n}aque, Frederico F. and Far{\´i}as, Joaquina and Curti, Gianni and Capoano, Carlos A. and Folle, Gustavo A. and Benavente, Ricardo and Sotelo-Silveira, Jos{\´e} Roberto and Geisinger, Adriana}, title = {Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage}, series = {BMC Genomics}, volume = {17}, journal = {BMC Genomics}, doi = {10.1186/s12864-016-2618-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164574}, pages = {294}, year = {2016}, abstract = {Background Spermatogenesis is a complex differentiation process that involves the successive and simultaneous execution of three different gene expression programs: mitotic proliferation of spermatogonia, meiosis, and spermiogenesis. Testicular cell heterogeneity has hindered its molecular analyses. Moreover, the characterization of short, poorly represented cell stages such as initial meiotic prophase ones (leptotene and zygotene) has remained elusive, despite their crucial importance for understanding the fundamentals of meiosis. Results We have developed a flow cytometry-based approach for obtaining highly pure stage-specific spermatogenic cell populations, including early meiotic prophase. Here we combined this methodology with next generation sequencing, which enabled the analysis of meiotic and postmeiotic gene expression signatures in mouse with unprecedented reliability. Interestingly, we found that a considerable number of genes involved in early as well as late meiotic processes are already on at early meiotic prophase, with a high proportion of them being expressed only for the short time lapse of lepto-zygotene stages. Besides, we observed a massive change in gene expression patterns during medium meiotic prophase (pachytene) when mostly genes related to spermiogenesis and sperm function are already turned on. This indicates that the transcriptional switch from meiosis to post-meiosis takes place very early, during meiotic prophase, thus disclosing a higher incidence of post-transcriptional regulation in spermatogenesis than previously reported. Moreover, we found that a good proportion of the differential gene expression in spermiogenesis corresponds to up-regulation of genes whose expression starts earlier, at pachytene stage; this includes transition protein-and protamine-coding genes, which have long been claimed to switch on during spermiogenesis. In addition, our results afford new insights concerning X chromosome meiotic inactivation and reactivation. Conclusions This work provides for the first time an overview of the time course for the massive onset and turning off of the meiotic and spermiogenic genetic programs. Importantly, our data represent a highly reliable information set about gene expression in pure testicular cell populations including early meiotic prophase, for further data mining towards the elucidation of the molecular bases of male reproduction in mammals.}, language = {en} } @article{ShenChalopinGarciaetal.2016, author = {Shen, Yingjia and Chalopin, Domitille and Garcia, Tzintzuni and Boswell, Mikki and Boswell, William and Shiryev, Sergey A. and Agarwala, Richa and Volff, Jean-Nicolas and Postlethwait, John H. and Schartl, Manfred and Minx, Patrick and Warren, Wesley C. and Walter, Ronald B.}, title = {X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species}, series = {BMC Genomics}, volume = {17}, journal = {BMC Genomics}, doi = {10.1186/s12864-015-2361-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164582}, pages = {37}, year = {2016}, abstract = {Background Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. Results We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 \% and 102 \% of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Conclusions Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.}, language = {en} } @article{HartelGloggerJonesetal.2016, author = {Hartel, Andreas J.W. and Glogger, Marius and Jones, Nicola G. and Abuillan, Wasim and Batram, Christopher and Hermann, Anne and Fenz, Susanne F. and Tanaka, Motomu and Engstler, Markus}, title = {N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold}, series = {Nature Communications}, volume = {7}, journal = {Nature Communications}, doi = {10.1038/ncomms12870}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171368}, year = {2016}, abstract = {The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.}, language = {en} } @article{PetersHempAppelhansetal.2016, author = {Peters, Marcell K. and Hemp, Andreas and Appelhans, Tim and Behler, Christina and Classen, Alice and Detsch, Florian and Ensslin, Andreas and Ferger, Stefan W. and Frederiksen, Sara B. and Gebert, Frederike and Haas, Michael and Helbig-Bonitz, Maria and Hemp, Claudia and Kindeketa, William J. and Mwangomo, Ephraim and Ngereza, Christine and Otte, Insa and R{\"o}der, Juliane and Rutten, Gemma and Costa, David Schellenberger and Tardanico, Joseph and Zancolli, Giulia and Deckert, J{\"u}rgen and Eardley, Connal D. and Peters, Ralph S. and R{\"o}del, Mark-Oliver and Schleuning, Matthias and Ssymank, Axel and Kakengi, Victor and Zhang, Jie and B{\"o}hning-Gaese, Katrin and Brandl, Roland and Kalko, Elisabeth K.V. and Kleyer, Michael and Nauss, Thomas and Tschapka, Marco and Fischer, Markus and Steffan-Dewenter, Ingolf}, title = {Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level}, series = {Nature Communications}, volume = {7}, journal = {Nature Communications}, doi = {10.1038/ncomms13736}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169374}, year = {2016}, abstract = {The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities.}, language = {en} } @article{GattoSchulzeNielsen2016, author = {Gatto, Francesco and Schulze, Almut and Nielsen, Jens}, title = {Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics}, series = {Cell Reports}, volume = {16}, journal = {Cell Reports}, number = {3}, doi = {10.1016/j.celrep.2016.06.038}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164814}, pages = {878-895}, year = {2016}, abstract = {Mutations are the basis of the clonal evolution of most cancers. Nevertheless, a systematic analysis of whether mutations are selected in cancer because they lead to the deregulation of specific biological processes independent of the type of cancer is still lacking. In this study, we correlated the genome and transcriptome of 1,082 tumors. We found that nine commonly mutated genes correlated with substantial changes in gene expression, which primarily converged on metabolism. Further network analyses circumscribed the convergence to a network of reactions, termed AraX, that involves the glutathione- and oxygen-mediated metabolism of arachidonic acid and xenobiotics. In an independent cohort of 4,462 samples, all nine mutated genes were consistently correlated with the deregulation of AraX. Among all of the metabolic pathways, AraX deregulation represented the strongest predictor of patient survival. These findings suggest that oncogenic mutations drive a selection process that converges on the deregulation of the AraX network.}, language = {en} } @article{SenthilanHelfrichFoerster2016, author = {Senthilan, Pingkalai R. and Helfrich-F{\"o}rster, Charlotte}, title = {Rhodopsin 7-The unusual Rhodopsin in Drosophila}, series = {PeerJ}, volume = {4}, journal = {PeerJ}, doi = {10.7717/peerj.2427}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177998}, year = {2016}, abstract = {Rhodopsins are the major photopigments in the fruit fly Drosophila melanogaster. Drosophila express six well-characterized Rhodopsins (Rh1-Rh6) with distinct absorption maxima and expression pattern. In 2000, when the Drosophila genome was published, a novel Rhodopsin gene was discovered: Rhodopsin 7 (Rh7). Rh7 is highly conserved among the Drosophila genus and is also found in other arthropods. Phylogenetic trees based on protein sequences suggest that the seven Drosophila Rhodopsins cluster in three different groups. While Rh1, Rh2 and Rh6 form a "vertebrate-melanopsin-type"-cluster, and Rh3, Rh4 and Rh5 form an "insect-type"-Rhodopsin cluster, Rh7 seem to form its own cluster. Although Rh7 has nearly all important features of a functional Rhodopsin, it differs from other Rhodopsins in its genomic and structural properties, suggesting it might have an overall different role than other known Rhodopsins.}, language = {en} } @article{FeldbauerSchlegelWeissbeckeretal.2016, author = {Feldbauer, Katrin and Schlegel, Jan and Weissbecker, Juliane and Sauer, Frank and Wood, Phillip G. and Bamberg, Ernst and Terpitz, Ulrich}, title = {Optochemokine Tandem for Light-Control of Intracellular Ca\(^{2+}\)}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {10}, doi = {10.1371/journal.pone.0165344}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178921}, year = {2016}, abstract = {An optochemokine tandem was developed to control the release of calcium from endosomes into the cytosol by light and to analyze the internalization kinetics of G-protein coupled receptors (GPCRs) by electrophysiology. A previously constructed rhodopsin tandem was re-engineered to combine the light-gated Ca\(^{2+}\)-permeable cation channel Channelrhodopsin-2(L132C), CatCh, with the chemokine receptor CXCR4 in a functional tandem protein tCXCR4/CatCh. The GPCR was used as a shuttle protein to displace CatCh from the plasma membrane into intracellular areas. As shown by patch-clamp measurements and confocal laser scanning microscopy, heterologously expressed tCXCR4/CatCh was internalized via the endocytic SDF1/CXCR4 signaling pathway. The kinetics of internalization could be followed electrophysiologically via the amplitude of the CatCh signal. The light-induced release of Ca\(^{2+}\) by tandem endosomes into the cytosol via CatCh was visualized using the Ca\(^{2+}\)-sensitive dyes rhod2 and rhod2-AM showing an increase of intracellular Ca\(^{2+}\) in response to light.}, 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} } @article{DePalmaAbrahamczykAizenetal.2016, author = {De Palma, Adriana and Abrahamczyk, Stefan and Aizen, Marcelo A. and Albrecht, Matthias and Basset, Yves and Bates, Adam and Blake, Robin J. and Boutin, C{\´e}line and Bugter, Rob and Connop, Stuart and Cruz-L{\´o}pez, Leopoldo and Cunningham, Saul A. and Darvill, Ben and Diek{\"o}tter, Tim and Dorn, Silvia and Downing, Nicola and Entling, Martin H. and Farwig, Nina and Felicioli, Antonio and Fonte, Steven J. and Fowler, Robert and Franzen, Markus Franz{\´e}n and Goulson, Dave and Grass, Ingo and Hanley, Mick E. and Hendrix, Stephen D. and Herrmann, Farina and Herzog, Felix and Holzschuh, Andrea and Jauker, Birgit and Kessler, Michael and Knight, M. E. and Kruess, Andreas and Lavelle, Patrick and Le F{\´e}on, Violette and Lentini, Pia and Malone, Louise A. and Marshall, Jon and Mart{\´i}nez Pach{\´o}n, Eliana and McFrederick, Quinn S. and Morales, Carolina L. and Mudri-Stojnic, Sonja and Nates-Parra, Guiomar and Nilsson, Sven G. and {\"O}ckinger, Erik and Osgathorpe, Lynne and Parra-H, Alejandro and Peres, Carlos A. and Persson, Anna S. and Petanidou, Theodora and Poveda, Katja and Power, Eileen F. and Quaranta, Marino and Quintero, Carolina and Rader, Romina and Richards, Miriam H. and Roulston, T'ai and Rousseau, Laurent and Sadler, Jonathan P. and Samneg{\aa}rd, Ulrika and Schellhorn, Nancy A. and Sch{\"u}epp, Christof and Schweiger, Oliver and Smith-Pardo, Allan H. and Steffan-Dewenter, Ingolf and Stout, Jane C. and Tonietto, Rebecca K. and Tscharntke, Teja and Tylianakis, Jason M. and Verboven, Hans A. F. and Vergara, Carlos H. and Verhulst, Jort and Westphal, Catrin and Yoon, Hyung Joo and Purvis, Andy}, title = {Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, doi = {10.1038/srep31153}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167642}, pages = {31153}, year = {2016}, abstract = {Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.}, 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} } @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{KramerPiperEstevezetal.2016, author = {Kramer, Susanne and Piper, Sophie and Estevez, Antonio and Carrington, Mark}, title = {Polycistronic trypanosome mRNAs are a target for the exosome}, series = {Molecular and Biochemical Parasitology}, volume = {205}, journal = {Molecular and Biochemical Parasitology}, number = {1-2}, doi = {10.1016/j.molbiopara.2016.02.009}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191350}, pages = {1-5}, year = {2016}, abstract = {Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control.}, language = {en} } @article{MederKoenigOzretićetal.2016, author = {Meder, Lydia and K{\"o}nig, Katharina and Ozretić, Luka and Schultheis, Anne M. and Ueckeroth, Frank and Ade, Carsten P. and Albus, Kerstin and Boehm, Diana and Rommerscheidt-Fuss, Ursula and Florin, Alexandra and Buhl, Theresa and Hartmann, Wolfgang and Wolf, J{\"u}rgen and Merkelbach-Bruse, Sabine and Eilers, Martin and Perner, Sven and Heukamp, Lukas C. and Buettner, Reinhard}, title = {NOTCH, ASCL1, p53 and RB alterations define an alternative pathway driving neuroendocrine and small cell lung carcinomas}, series = {International Journal of Cancer}, volume = {138}, journal = {International Journal of Cancer}, number = {4}, doi = {10.1002/ijc.29835}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190853}, pages = {927-938}, year = {2016}, abstract = {Small cell lung cancers (SCLCs) and extrapulmonary small cell cancers (SCCs) are very aggressive tumors arising de novo as primary small cell cancer with characteristic genetic lesions in RB1 and TP53. Based on murine models, neuroendocrine stem cells of the terminal bronchioli have been postulated as the cellular origin of primary SCLC. However, both in lung and many other organs, combined small cell/non-small cell tumors and secondary transitions from non-small cell carcinomas upon cancer therapy to neuroendocrine and small cell tumors occur. We define features of "small cell-ness" based on neuroendocrine markers, characteristic RB1 and TP53 mutations and small cell morphology. Furthermore, here we identify a pathway driving the pathogenesis of secondary SCLC involving inactivating NOTCH mutations, activation of the NOTCH target ASCL1 and canonical WNT-signaling in the context of mutual bi-allelic RB1 and TP53 lesions. Additionaly, we explored ASCL1 dependent RB inactivation by phosphorylation, which is reversible by CDK5 inhibition. We experimentally verify the NOTCH-ASCL1-RB-p53 signaling axis in vitro and validate its activation by genetic alterations in vivo. We analyzed clinical tumor samples including SCLC, SCC and pulmonary large cell neuroendocrine carcinomas and adenocarcinomas using amplicon-based Next Generation Sequencing, immunohistochemistry and fluorescence in situ hybridization. In conclusion, we identified a novel pathway underlying rare secondary SCLC which may drive small cell carcinomas in organs other than lung, as well.}, language = {en} } @article{SinghVermaAkhoonetal.2016, author = {Singh, Krishna P. and Verma, Neeraj and Akhoon, Bashir A . and Bhatt, Vishal and Gupta, Shishir K. and Gupta, Shailendra K. and Smita, Suchi}, title = {Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains}, series = {3 Biotech}, volume = {6}, journal = {3 Biotech}, doi = {10.1007/s13205-015-0352-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191056}, pages = {10}, year = {2016}, abstract = {Human papilloma virus (HPV) is the primary etiological agent responsible for cervical cancer in women. Although in total 16 high-risk HPV strains have been identified so far. Currently available commercial vaccines are designed by targeting mainly HPV16 and HPV18 viral strains as these are the most common strains associated with cervical cancer. Because of the high level of antigenic specificity of HPV capsid antigens, the currently available vaccines are not suitable to provide cross-protection from all other high-risk HPV strains. Due to increasing reports of cervical cancer cases from other HPV high-risk strains other than HPV16 and 18, it is crucial to design vaccine that generate reasonable CD8+ T-cell responses for possibly all the high-risk strains. With this aim, we have developed a computational workflow to identify conserved cross-clade CD8+ T-cell HPV vaccine candidates by considering E1, E2, E6 and E7 proteins from all the high-risk HPV strains. We have identified a set of 14 immunogenic conserved peptide fragments that are supposed to provide protection against infection from any of the high-risk HPV strains across globe.}, language = {en} } @article{VieraElMerahbiNieswandtetal.2016, author = {Viera, Jonathan Trujillo and El-Merahbi, Rabih and Nieswandt, Bernhard and Stegner, David and Sumara, Grzegorz}, title = {Phospholipases D1 and D2 Suppress Appetite and Protect against Overweight}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {6}, doi = {10.1371/journal.pone.0157607}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-179729}, year = {2016}, abstract = {Obesity is a major risk factor predisposing to the development of peripheral insulin resistance and type 2 diabetes (T2D). Elevated food intake and/or decreased energy expenditure promotes body weight gain and acquisition of adipose tissue. Number of studies implicated phospholipase D (PLD) enzymes and their product, phosphatidic acid (PA), in regulation of signaling cascades controlling energy intake, energy dissipation and metabolic homeostasis. However, the impact of PLD enzymes on regulation of metabolism has not been directly determined so far. In this study we utilized mice deficient for two major PLD isoforms, PLD1 and PLD2, to assess the impact of these enzymes on regulation of metabolic homeostasis. We showed that mice lacking PLD1 or PLD2 consume more food than corresponding control animals. Moreover, mice deficient for PLD2, but not PLD1, present reduced energy expenditure. In addition, deletion of either of the PLD enzymes resulted in development of elevated body weight and increased adipose tissue content in aged animals. Consistent with the fact that elevated content of adipose tissue predisposes to the development of hyperlipidemia and insulin resistance, characteristic for the pre-diabetic state, we observed that Pld1\(^{-/-}\) and Pld2\(^{-/-}\) mice present elevated free fatty acids (FFA) levels and are insulin as well as glucose intolerant. In conclusion, our data suggest that deficiency of PLD1 or PLD2 activity promotes development of overweight and diabetes.}, 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{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{BiscottiGerdolCanapaetal.2016, author = {Biscotti, Maria Assunta and Gerdol, Marco and Canapa, Adriana and Forconi, Mariko and Olmo, Ettore and Pallavicini, Alberto and Barucca, Marco and Schartl, Manfred}, title = {The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, number = {21571}, doi = {10.1038/srep21571}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167753}, year = {2016}, abstract = {Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a "living fossil" status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.}, language = {en} } @article{KuenstnerHoffmannFraseretal.2016, author = {K{\"u}nstner, Axel and Hoffmann, Margarete and Fraser, Bonnie A. and Kottler, Verena A. and Sharma, Eshita and Weigel, Detlef and Dreyer, Christine}, title = {The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {12}, doi = {10.1371/journal.pone.0169087}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166755}, pages = {e0169087}, year = {2016}, abstract = {For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95\% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.}, 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{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{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{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{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{DreschersSauppHornefetal.2016, author = {Dreschers, Stephan and Saupp, Peter and Hornef, Mathias and Prehn, Andrea and Platen, Christopher and Morschh{\"a}user, Joachim and Orlikowsky, Thorsten W.}, title = {Reduced PICD in Monocytes Mounts Altered Neonate Immune Response to Candida albicans}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {11}, doi = {10.1371/journal.pone.0166648}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166778}, pages = {e0166648}, year = {2016}, abstract = {Background Invasive fungal infections with Candida albicans (C. albicans) occur frequently in extremely low birthweight (ELBW) infants and are associated with poor outcome. Phagocytosis of C.albicans initializes apoptosis in monocytes (phagocytosis induced cell death, PICD). PICD is reduced in neonatal cord blood monocytes (CBMO). Hypothesis Phagocytosis of C. albicans causes PICD which differs between neonatal monocytes (CBMO) and adult peripheral blood monocytes (PBMO) due to lower stimulation of TLR-mediated immune responses. Methods The ability to phagocytose C. albicans, expression of TLRs, the induction of apoptosis (assessment of sub-G1 and nick-strand breaks) were analyzed by FACS. TLR signalling was induced by agonists such as lipopolysaccharide (LPS), Pam3Cys, FSL-1 and Zymosan and blocked (neutralizing TLR2 antibodies and MYD88 inhibitor). Results Phagocytic indices of PBMO and CBMO were similar. Following stimulation with agonists and C. albicans induced up-regulation of TLR2 and consecutive phosphorylation of MAP kinase P38 and expression of TNF-α, which were stronger on PBMO compared to CBMO (p < 0.005). Downstream, TLR2 signalling initiated caspase-3-dependent PICD which was found reduced in CBMO (p < 0.05 vs PBMO). Conclusion Our data suggest direct involvement of TLR2-signalling in C. albicans-induced PICD in monocytes and an alteration of this pathway in CBMO.}, 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{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{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{WeisschuhMayerStrometal.2016, author = {Weisschuh, Nicole and Mayer, Anja K. and Strom, Tim M. and Kohl, Susanne and Gl{\"o}ckle, Nicola and Schubach, Max and Andreasson, Sten and Bernd, Antje and Birch, David G. and Hamel, Christian P. and Heckenlively, John R. and Jacobson, Samuel G. and Kamme, Christina and Kellner, Ulrich and Kunstmann, Erdmute and Maffei, Pietro and Reiff, Charlotte M. and Rohrschneider, Klaus and Rosenberg, Thomas and Rudolph, G{\"u}nther and V{\´a}mos, Rita and Vars{\´a}nyi, Bal{\´a}zs and Weleber, Richard G. and Wissinger, Bernd}, title = {Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {1}, doi = {10.1371/journal.pone.0145951}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167398}, pages = {e0145951}, year = {2016}, abstract = {Retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different nonsyndromic and syndromic forms of RD can be attributed to mutations in more than 200 genes. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. We screened a large cohort of patients comprising 89 independent cases and families with various subforms of RD applying different NGS platforms. While mutation screening in 50 cases was performed using a RD gene capture panel, 47 cases were analyzed using whole exome sequencing. One family was analyzed using whole genome sequencing. A detection rate of 61\% was achieved including mutations in 34 known and two novel RD genes. A total of 69 distinct mutations were identified, including 39 novel mutations. Notably, genetic findings in several families were not consistent with the initial clinical diagnosis. Clinical reassessment resulted in refinement of the clinical diagnosis in some of these families and confirmed the broad clinical spectrum associated with mutations in RD genes.}, language = {en} } @article{HeurichZeisKuechenhoffetal.2016, author = {Heurich, Marco and Zeis, Klara and K{\"u}chenhoff, Helmut and M{\"u}ller, J{\"o}rg and Belotti, Elisa and Bufka, Luděk and Woelfing, Benno}, title = {Selective Predation of a Stalking Predator on Ungulate Prey}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal.pone.0158449}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166827}, pages = {e0158449}, year = {2016}, abstract = {Prey selection is a key factor shaping animal populations and evolutionary dynamics. An optimal forager should target prey that offers the highest benefits in terms of energy content at the lowest costs. Predators are therefore expected to select for prey of optimal size. Stalking predators do not pursue their prey long, which may lead to a more random choice of prey individuals. Due to difficulties in assessing the composition of available prey populations, data on prey selection of stalking carnivores are still scarce. We show how the stalking predator Eurasian lynx (Lynx lynx) selects prey individuals based on species identity, age, sex and individual behaviour. To address the difficulties in assessing prey population structure, we confirm inferred selection patterns by using two independent data sets: (1) data of 387 documented kills of radio-collared lynx were compared to the prey population structure retrieved from systematic camera trapping using Manly's standardized selection ratio alpha and (2) data on 120 radio-collared roe deer were analysed using a Cox proportional hazards model. Among the larger red deer prey, lynx selected against adult males—the largest and potentially most dangerous prey individuals. In roe deer lynx preyed selectively on males and did not select for a specific age class. Activity during high risk periods reduced the risk of falling victim to a lynx attack. Our results suggest that the stalking predator lynx actively selects for size, while prey behaviour induces selection by encounter and stalking success rates.}, 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{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{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{AhmedZeeshanDandekar2016, author = {Ahmed, Zeeshan and Zeeshan, Saman and Dandekar, Thomas}, title = {Mining biomedical images towards valuable information retrieval in biomedical and life sciences}, series = {Database - The Journal of Biological Databases and Curation}, volume = {2016}, journal = {Database - The Journal of Biological Databases and Curation}, doi = {10.1093/database/baw118}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162697}, pages = {baw118}, year = {2016}, abstract = {Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries.}, 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{JahnMarkertRyuetal.2016, author = {Jahn, Martin T. and Markert, Sebastian M. and Ryu, Taewoo and Ravasi, Timothy and Stigloher, Christian and Hentschel, Ute and Moitinho-Silva, Lucas}, title = {Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, number = {35860}, doi = {10.1038/srep35860}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167513}, year = {2016}, abstract = {Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.}, language = {en} } @article{YadavSelvarajBenderetal.2016, author = {Yadav, Preeti and Selvaraj, Bhuvaneish T. and Bender, Florian L. P. and Behringer, Marcus and Moradi, Mehri and Sivadasan, Rajeeve and Dombert, Benjamin and Blum, Robert and Asan, Esther and Sauer, Markus and Julien, Jean-Pierre and Sendtner, Michael}, title = {Neurofilament depletion improves microtubule dynamics via modulation of Stat3/stathmin signaling}, series = {Acta Neuropathologica}, volume = {132}, journal = {Acta Neuropathologica}, number = {1}, doi = {10.1007/s00401-016-1564-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188234}, pages = {93-110}, year = {2016}, abstract = {In neurons, microtubules form a dense array within axons, and the stability and function of this microtubule network is modulated by neurofilaments. Accumulation of neurofilaments has been observed in several forms of neurodegenerative diseases, but the mechanisms how elevated neurofilament levels destabilize axons are unknown so far. Here, we show that increased neurofilament expression in motor nerves of pmn mutant mice, a model of motoneuron disease, causes disturbed microtubule dynamics. The disease is caused by a point mutation in the tubulin-specific chaperone E (Tbce) gene, leading to an exchange of the most C-terminal amino acid tryptophan to glycine. As a consequence, the TBCE protein becomes instable which then results in destabilization of axonal microtubules and defects in axonal transport, in particular in motoneurons. Depletion of neurofilament increases the number and regrowth of microtubules in pmn mutant motoneurons and restores axon elongation. This effect is mediated by interaction of neurofilament with the stathmin complex. Accumulating neurofilaments associate with stathmin in axons of pmn mutant motoneurons. Depletion of neurofilament by Nefl knockout increases Stat3-stathmin interaction and stabilizes the microtubules in pmn mutant motoneurons. Consequently, counteracting enhanced neurofilament expression improves axonal maintenance and prolongs survival of pmn mutant mice. We propose that this mechanism could also be relevant for other neurodegenerative diseases in which neurofilament accumulation and loss of microtubules are prominent features.}, language = {en} } @article{KaluzaWallaceKelleretal.2017, author = {Kaluza, Benjamin F. and Wallace, Helen and Keller, Alexander and Heard, Tim A. and Jeffers, Bradley and Drescher, Nora and Bl{\"u}thgen, Nico and Leonhardt, Sara D.}, title = {Generalist social bees maximize diversity intake in plant species-rich and resource-abundant environments}, series = {Ecosphere}, volume = {8}, journal = {Ecosphere}, number = {3}, doi = {10.1002/ecs2.1758}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171155}, pages = {e01758}, year = {2017}, abstract = {Numerous studies revealed a positive relationship between biodiversity and ecosystem functioning, suggesting that biodiverse environments may not only enhance ecosystem processes, but also benefit individual ecosystem members by, for example, providing a higher diversity of resources. Whether and how the number of available resources affects resource collection and subsequently consumers (e.g., through impacting functions associated with resources) have, however, been little investigated, although a better understanding of this relationship may help explain why the abundance and richness of many animal species typically decline with decreasing plant (resource) diversity. Using a social bee species as model (Tetragonula carbonaria), we investigated how plant species richness—recorded for study sites located in different habitats—and associated resource abundance affected the diversity and functionality (here defined as nutritional content and antimicrobial activity) of resources (i.e., pollen, nectar, and resin) collected by a generalist herbivorous consumer. The diversity of both pollen and resin collected strongly increased with increasing plant/tree species richness, while resource abundance was only positively correlated with resin diversity. These findings suggest that bees maximize resource diversity intake in (resource) diverse habitats. Collecting more diverse resources did, however, not increase their functionality, which appeared to be primarily driven by the surrounding (plant) source community in our study. In generalist herbivores, maximizing resource diversity intake may therefore primarily secure collection of sufficient amounts of resources across the entire foraging season, but it also ensures that the allocated resources meet all functional needs. Decreasing available resource diversity may thus impact consumers primarily by reduced resource abundance, but also by reduced resource functionality, particularly when resources of high functionality (e.g., from specific plant species) become scarce.}, language = {en} } @article{DegenHovestadtMitesseretal.2017, author = {Degen, Tobias and Hovestadt, Thomas and Mitesser, Oliver and H{\"o}lker, Franz}, title = {Altered sex-specific mortality and female mating success: ecological effects and evolutionary responses}, series = {Ecosphere}, volume = {8}, journal = {Ecosphere}, number = {5}, doi = {10.1002/ecs2.1820}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170953}, pages = {e01820}, year = {2017}, abstract = {Theory predicts that males and females should often join the mating pool at different times (sexual dimorphism in timing of emergence [SDT]) as the degree of SDT affects female mating success. We utilize an analytical model to explore (1) how important SDT is for female mating success, (2) how mating success might change if either sex's mortality (abruptly) increases, and (3) to what degree evolutionary responses in SDT may be able to mitigate the consequences of such mortality increase. Increasing male pre-mating mortality has a non-linear effect on the fraction of females mated: The effect is initially weak, but at some critical level a further increase in male mortality has a stronger effect than a similar increase in female mortality. Such a change is expected to impose selection for reduced SDT. Increasing mortality during the mating season has always a stronger effect on female mating success if the mortality affects the sex that emerges first. This bias results from the fact that enhancing mortality of the earlier emerging sex reduces female-male encounter rates. However, an evolutionary response in SDT may effectively mitigate such consequences. Further, if considered independently for females and males, the predicted evolutionary response in SDT could be quite dissimilar. The difference between female and male evolutionary response in SDT leads to marked differences in the fraction of fertilized females under certain conditions. Our model may provide general guidelines for improving harvesting of populations, conservation management of rare species under altered environmental conditions, or maintaining long-term efficiency of pest-control measures.}, language = {en} } @article{ZieglerWeissSchmittetal.2017, author = {Ziegler, Sabrina and Weiss, Esther and Schmitt, Anna-Lena and Schlegel, Jan and Burgert, Anne and Terpitz, Ulrich and Sauer, Markus and Moretta, Lorenzo and Sivori, Simona and Leonhardt, Ines and Kurzai, Oliver and Einsele, Hermann and Loeffler, Juergen}, title = {CD56 Is a Pathogen Recognition Receptor on Human Natural Killer Cells}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, number = {6138}, doi = {10.1038/s41598-017-06238-4}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170637}, year = {2017}, abstract = {Aspergillus (A.) fumigatus is an opportunistic fungal mold inducing invasive aspergillosis (IA) in immunocompromised patients. Although antifungal activity of human natural killer (NK) cells was shown in previous studies, the underlying cellular mechanisms and pathogen recognition receptors (PRRs) are still unknown. Using flow cytometry we were able to show that the fluorescence positivity of the surface receptor CD56 significantly decreased upon fungal contact. To visualize the interaction site of NK cells and A. fumigatus we used SEM, CLSM and dSTORM techniques, which clearly demonstrated that NK cells directly interact with A. fumigatus via CD56 and that CD56 is re-organized and accumulated at this interaction site time-dependently. The inhibition of the cytoskeleton showed that the receptor re-organization was an active process dependent on actin re-arrangements. Furthermore, we could show that CD56 plays a role in the fungus mediated NK cell activation, since blocking of CD56 surface receptor reduced fungal mediated NK cell activation and reduced cytokine secretion. These results confirmed the direct interaction of NK cells and A. fumigatus, leading to the conclusion that CD56 is a pathogen recognition receptor. These findings give new insights into the functional role of CD56 in the pathogen recognition during the innate immune response.}, language = {en} } @article{KollmannsbergerKerschnitzkiReppetal.2017, author = {Kollmannsberger, Philip and Kerschnitzki, Michael and Repp, Felix and Wagermaier, Wolfgang and Weinkamer, Richard and Fratzl, Peter}, title = {The small world of osteocytes: connectomics of the lacuno-canalicular network in bone}, series = {New Journal of Physics}, volume = {19}, journal = {New Journal of Physics}, number = {073019}, doi = {10.1088/1367-2630/aa764b}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170662}, year = {2017}, abstract = {Osteocytes and their cell processes reside in a large, interconnected network of voids pervading the mineralized bone matrix of most vertebrates. This osteocyte lacuno-canalicular network (OLCN) is believed to play important roles in mechanosensing, mineral homeostasis, and for the mechanical properties of bone. While the extracellular matrix structure of bone is extensively studied on ultrastructural and macroscopic scales, there is a lack of quantitative knowledge on how the cellular network is organized. Using a recently introduced imaging and quantification approach, we analyze the OLCN in different bone types from mouse and sheep that exhibit different degrees of structural organization not only of the cell network but also of the fibrous matrix deposited by the cells. We define a number of robust, quantitative measures that are derived from the theory of complex networks. These measures enable us to gain insights into how efficient the network is organized with regard to intercellular transport and communication. Our analysis shows that the cell network in regularly organized, slow-growing bone tissue from sheep is less connected, but more efficiently organized compared to irregular and fast-growing bone tissue from mice. On the level of statistical topological properties (edges per node, edge length and degree distribution), both network types are indistinguishable, highlighting that despite pronounced differences at the tissue level, the topological architecture of the osteocyte canalicular network at the subcellular level may be independent of species and bone type. Our results suggest a universal mechanism underlying the self-organization of individual cells into a large, interconnected network during bone formation and mineralization.}, language = {en} } @article{MemmelSisarioZoelleretal.2017, author = {Memmel, Simon and Sisario, Dmitri and Z{\"o}ller, Caren and Fiedler, Vanessa and Katzer, Astrid and Heiden, Robin and Becker, Nicholas and Eing, Lorenz and Ferreira, F{\´a}bio L.R. and Zimmermann, Heiko and Sauer, Markus and Flentje, Michael and Sukhorukov, Vladimir L. and Djuzenova, Cholpon S.}, title = {Migration pattern, actin cytoskeleton organization and response to PI3K-, mTOR-, and Hsp90-inhibition of glioblastoma cells with different invasive capacities}, series = {Oncotarget}, volume = {8}, journal = {Oncotarget}, number = {28}, doi = {10.18632/oncotarget.16847}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170719}, pages = {45298-45310}, year = {2017}, abstract = {High invasiveness and resistance to chemo- and radiotherapy of glioblastoma multiforme (GBM) make it the most lethal brain tumor. Therefore, new treatment strategies for preventing migration and invasion of GBM cells are needed. Using two different migration assays, Western blotting, conventional and super-resolution (dSTORM) fluorescence microscopy we examine the effects of the dual PI3K/mTOR-inhibitor PI-103 alone and in combination with the Hsp90 inhibitor NVP-AUY922 and/or irradiation on the migration, expression of marker proteins, focal adhesions and F-actin cytoskeleton in two GBM cell lines (DK-MG and SNB19) markedly differing in their invasive capacity. Both lines were found to be strikingly different in morphology and migration behavior. The less invasive DK-MG cells maintained a polarized morphology and migrated in a directionally persistent manner, whereas the highly invasive SNB19 cells showed a multipolar morphology and migrated randomly. Interestingly, a single dose of 2 Gy accelerated wound closure in both cell lines without affecting their migration measured by single-cell tracking. PI-103 inhibited migration of DK-MG (p53 wt, PTEN wt) but not of SNB19 (p53 mut, PTEN mut) cells probably due to aberrant reactivation of the PI3K pathway in SNB19 cells treated with PI-103. In contrast, NVP-AUY922 exerted strong anti-migratory effects in both cell lines. Inhibition of cell migration was associated with massive morphological changes and reorganization of the actin cytoskeleton. Our results showed a cell line-specific response to PI3K/mTOR inhibition in terms of GBM cell motility. We conclude that anti-migratory agents warrant further preclinical investigation as potential therapeutics for treatment of GBM.}, language = {en} } @phdthesis{Borst2017, author = {Borst, Andreas}, title = {Apoptosis \& senescence: cell fate determination in inhibitor-treated melanoma cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-155085}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Neoplasms of the skin represent the most frequent tumors worldwide; fortunately, most of them are benign or semi-malignant and well treatable. However, the two most aggressive and deadly forms of malignant skin-neoplasms are melanoma and Merkel cell carcinoma (MCC), being responsible for more than 90\% of skin-cancer related deaths. The last decade has yielded enormous progress in melanoma therapy with the advent of targeted therapies, like BRAF or MEK inhibitors, and immune-stimulating therapies, using checkpoint antibodies targeting CTLA- 4, PD-1 or PD-L1. Very recent studies suggest that also MCC patients benefit from a treatment with checkpoint antibodies. Nevertheless, in an advanced metastatic stage, a cure for both of these aggressive malignancies is still hard to achieve: while only a subset of patients experience durable benefit from the immune-based therapies, the widely applicable targeted therapies struggle with development of resistances that inevitably occur in most patients, and finally lead to their death. The four articles included in this thesis addressed current questions concerning therapy and carcinogenesis of melanoma and MCC. Moreover, they are discussed in the light of the up-to-date research regarding targeted and immune-based therapies. In article I we demonstrated that besides apoptosis, MAPK pathway inhibition in BRAF-mutated melanoma cells also induces senescence, a permanent cell cycle arrest. These cells may provide a source for relapse, as even permanently arrested cancer cells can contribute to a pro-tumorigenic milieu. To identify molecular factors determining the differential response, we established M14 melanoma cell line derived single cell clones that either undergo cell death or arrest when treated with BRAF/MEK inhibitors. Using these single cell clones, we demonstrated in article IV that downregulation of the pro-apoptotic BH3-only protein BIK via epigenetic silencing is involved in apoptosis deficiency, which can be overcome by HDAC inhibitors. These observations provide a possible explanation for the lack of a complete and durable response to MAPK inhibitor treatment in melanoma patients, and suggest the application of HDAC inhibitors as a complimentary therapy to MAPK pathway inhibition. Concerning MCC, we scrutinized the interactions between the Merkel cell polyomavirus' (MCV) T antigens (TA) and the tumor suppressors p53 and Rb in article II and III, respectively. In article III, we demonstrated that the cell cycle master regulator Rb is the crucial target of MCV large T (LT), while it - in contrast to other polyomavirus LTs - exhibits much lower affinity to the related proteins p107 and p130. Knockdown of MCV LT led to proliferation arrest in MCC cells, which can be rescued by knockdown of Rb, but not by knockdown of p107 and p130. Contrary to Rb, restriction of p53 in MCC seems to be independent of the MCV TAs, as we demonstrated in article II. In conclusion, the presented thesis has revealed new molecular details, regarding the response of melanoma cells towards an important treatment modality and the mechanisms of viral carcinogenesis in MCC.}, subject = {Melanom}, language = {en} } @phdthesis{Hagen2017, author = {Hagen, Franziska}, title = {Sphingolipids in gonococcal infection}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-153852}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea, has the potential to spread in the human host and cause a severe complication called disseminated gonococcal infection (DGI). The expression of the major outer membrane porin PorBIA is a characteristic of most gonococci associated with DGI. PorBIA binds to the scavenger receptor expressed on endothelial cells (SREC-I), which mediates the so-called low phosphate-dependent invasion (LPDI). This uptake mechanism enables N. gonorrhoeae to rapidly invade epithelial and endothelial cells in a phosphate-sensitive manner. We recently demonstrated that the neutral sphingomyelinase, which catalyses the hydrolysis of sphingomyelin to ceramide and phosphorylcholine, is required for the LPDI of gonococci in non-phagocytic cells. Neutral sphingomyelinase 2 (NSM2) plays a key role in the early PorBIA signaling by recruiting the PI3 kinase to caveolin. The following activation of the PI3 kinase-dependent downstream signaling leads to the engulfment of the bacteria. As a part of this work, I could confirm the involvement of the NSM2. The role of the enzyme was further elucidated by the generation of antibodies directed against NSM2 and the construction of an epithelium-based NSM2 knockout cell line using CRISPR/Cas9. The knockout of the NSM2 strongly inhibits the LPDI. The invasion could be, however, restored by the complementation of the knockout using an NSM2-GFP construct. However, the results could not be reproduced. In this work, I could show the involvement of further members of the sphingolipid pathway in the PorBIA-mediated invasion. Lipidome analysis revealed an increase of the bioactive molecules ceramide and sphingosine due to gonococcal infection. Both molecules do not only affect the host cell, but seem to influence the bacteria as well: while ceramide seems to be incorporated by the gonococci, sphingosine is toxic for the bacteria. Furthermore, the sphingosine kinase 2 (SPHK2) plays an important role in invasion, since the inhibition and knockdown of the enzyme revealed a negative effect on gonococcal invasion. To elucidate the role of the sphingosine kinases in invasion in more detail, an activity assay was established in this study. Additionally, the impact of the sphingosine-1-phosphate lyase (S1PL) on invasion was investigated. Inhibitor studies and infection experiments conducted with a CRISPR/Cas9 HeLa S1PL knockout cell line revealed a role of the enzyme not only in the PorBIA-mediated invasion, but also in the Opa50/HSPG-mediated gonococcal invasion. The signaling experiments allowed the categorization of the SPHK and S1PL activation in the context of infection. Like the NSM2, both enzymes play a role in the early PorBIA signaling events leading to the uptake of the bacteria. All those findings indicate an important role of sphingolipids in the invasion and survival of N. gonorrhoeae. In the last part of this work, the role of the NSM2 in the inhibition of apoptosis in neutrophils due to gonococcal infection was investigated. It could be demonstrated that the delayed onset of apoptosis is independent of neisserial porin and Opa proteins. Furthermore, the influence of neisserial peptidoglycan on PMN apoptosis was analysed using mutant strains, but no connection could be determined. Since the NSM2 is the most prominent sphingomyelinase in PMNs, fulfils manifold cell physiological functions and has already been connected to apoptosis, the impact of the enzyme on apoptosis inhibition due to gonococcal infection was investigated using inhibitors, with no positive results.}, subject = {gonococcal}, language = {en} } @phdthesis{Reis2017, author = {Reis, Helena}, title = {Characterization of telomere protein complexes in Trypanosoma brucei}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151323}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {African trypanosomiasis is a disease endemic to sub-Saharan Africa. It affects humans as well as wild and domestic animals. The human form of the disease is known as sleeping sickness and the animal form as nagana, which are usually fatal if left untreated. The cause of African trypanosomiasis is the unicellular parasite Trypanosoma brucei. During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host the parasite multiplies as bloodstream form (BSF) extracellularly in the bloodstream or the lymphatic system. Survival of BSF parasites relies on immune evasion by antigenic variation of surface proteins because its extracellular lifestyle leads to direct exposure to immune responses. At any given time each BSF cell expresses a single type of variant surface glycoprotein (VSG) on its surface from a large repertoire. The active VSG is transcribed from one of 15 specialized subtelomeric domains, termed bloodstream expression sites (BESs). The remaining 14 BESs are silenced. This monoallelic expression and periodic switching of the expressed VSG enables to escape the immune response and to establish a persistent infection in the mammalian host. During developmental differentiation from BSF to the insect vector-resident procyclic form (PCF), the active BES is transcriptionally silenced to stop VSG transcription. Thus, all 15 BESs are inactive in the PCF cells as surface protein expression is developmentally regulated. Previous reports have shown that the telomere complex components TbTRF, TbRAP1 and TbTIF2 are involved in VSG transcriptional regulation. However, the precise nature of their contribution remains unclear. In addition, no information is available about the role of telomeres in the initiation and regulation of developmental BES silencing. To gain insights into the regulatory mechanisms of telomeres on VSG transcription and developmental repression it is therefore essential to identify the complete composition of the trypanosome telomere complex. To this end, we used two complementary biochemical approaches and quantitative label-free interactomics to determine the composition of telomere protein complexes in T. brucei. Firstly, using a telomeric pull-down assay we found 17 potential telomere-binding proteins including the known telomere-binding proteins TbTRF and TbTIF2. Secondly, by performing a co-immunoprecipitation experiment to elucidate TbTRF interactions we co-purified five proteins. All of these five proteins were also enriched with telomeric DNA in the pull-down assay. To validate these data, I characterized one of the proteins found in both experiments (TelBP1). In BSF cells, TelBP1 co-localizes with TbTRF and interacts with already described telomere-binding proteins such as TbTRF, TbTIF2 and TbRAP1 indicating that TelBP1 is a novel component of the telomere complex in trypanosomes. Interestingly, protein interaction studies in PCF cells suggested a different telomere complex composition compared to BSF cells. In contrast to known members of the telomere complex, TelBP1 is dispensable for cell viability indicating that its function might be uncoupled from the known telomere-binding proteins. Overexpression of TelBP1 had also no effect on cell viability, but led to the discovery of two additional shorter isoforms of TelBP1. However, their source and function remained elusive. Although TelBP1 is not essential for cell viability, western blot analysis revealed a 4-fold upregulation of TelBP1 in the BSF stage compared to the PCF stage supporting the concept of a dynamic telomere complex composition. We observed that TelBP1 influences the kinetics of transcriptional BES silencing during developmental transition from BSF to PCF. Deletion of TelBP1 caused faster BES silencing compared to wild-type parasites. Taken together, TelBP1 function illustrates that developmental BES silencing is a fine-tuned process, which involves stage-specific changes in telomere complex formation.}, subject = {Trypanosoma brucei}, language = {en} } @phdthesis{Bruehlmann2017, author = {Br{\"u}hlmann, David}, title = {Tailoring Recombinant Protein Quality by Rational Media Design}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147345}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Nowadays, more than half of the biotherapeutics are produced in mammalian cell lines as a result of correct protein folding and assembly as well as their faculty to bring about a variety of post-translational modifications. The widespread progression of biosimilars has moved the focus in mammalian cell-culture process development. Thereby, the modulation of quality attributes of recombinant therapeutic proteins has increasingly gained importance from early process development stages. Protein quality directly shapes the clinical efficacy and safety in vivo, and therefore, the control of the complex post-translational modifications, such as glycosylation (e.g. high mannose, fucosylation, galactosylation and sialylation), charge variants, aggregates and low-molecular-weight species formation, is pivotal for efficient receptor binding and for triggering the desired immune responses in patients. In the frame of biosimilar development, product quality modulation methods using the potential of the host cell line are particularly sought after to match the quality profile of the targeted reference medicinal product (RMP) as closely as possible. The environment the cell is dwelling in directly influences its metabolism and the resulting quality profile of the expressed protein. Thereby the cell culture medium plays a central role in upstream manufacturing. In this work, concentration adjustment of selected media components and supplementation with a variety of compounds was performed to alter various metabolic pathways, enzyme activities and in some cases the gene expression levels of Chinese Hamster Ovary (CHO) cells in culture. The supplementation of cell culture medium with the trisaccharide raffinose in fed-batch cultures entailed an increase of the abundance of high mannose glycans in two different CHO cell lines. Raffinose especially favored mannose 5 glycans. At the same time, it impaired cell culture performance, induced changes on the intracellular nucleotide levels and even varied the expression levels of glycosylation-related genes. Supplementation with a number of galactosyltransferase inhibiting compounds, in particular fluorinated galactose analogs (alpha- and beta-2F-peracetyl-galactose), consistently decreased the production of galactosylated monoclonal antibodies (mAb). By means of targeted addition during the culture rather than at the beginning, the inhibition was further increased, while limiting detrimental effects on both growth and productivity. High-throughput screening in 96-deepwell plates showed that spermine and L-ornithine also reduced the level of galactosylation. On the other hand, exploratory screening of a variety of potentially disulfide-bridge-reducing agents highlighted that the inherent low-molecular-species level of the proprietary platform cell culture process was likely due to favored reduction. This hypothesis was reinforced by the observation that supplementation of cysteine and N-acetylcysteine promoted fragmentation. Additionally, fragmentation decreased with higher protein expression. At that point, aiming to improve the efficiency in process development, a rational experimental design method was developed to identify and to define the optimal concentration range of quality modulating compounds by calling on a combination of high throughput fed-batch testing and multivariate data analysis. Seventeen medium supplements were tested in five parallel 96-deepwell plate experiments. The selection process of promising modulators for the follow-up experiment in shake tubes consisted in a three-step procedure, including principal component analysis, quantitative evaluation of their performance with respect to the specifications for biosimilarity and selection following a hierarchical order of decisions using a decision tree. The method resulted in a substantial improvement of the targeted glycosylation profile in only two experimental rounds. Subsequent development stages, namely validation and transfer to industrial-scale facilities require tight control of product quality. Accordingly, further mechanistic understanding of the underlying processes was acquired by non-targeted metabolomic profiling of a CHO cell line expressing a mAb cultured in four distinct process formats. Univariate analysis of intra- and extracellular metabolite and temporal glycosylation profiles provided insights in various pathways. The numerous of parameters were the main driver to carry out principal component analysis, and then, using the methodology of partial-least-square (PLS) projection on latent structures, a multivariate model was built to correlate the extracellular data with the distinct glycosylation profiles. The PLS observation model proved to be reliable and showed its great benefit for glycan pattern control in routine manufacturing, especially at large scale. Rather than relying on post-production interpretation of glycosylation results, glycosylation can be predicted in real-time based on the extracellular metabolite levels in the bioreactor. Finally, for the bioactivity assessment of the glycan differences between the biosimilar and the reference medicinal product (RMP), the health agencies may ask for in the drug registration process, extended ranges of glycan variants need to be generated so that the in vitro assays pick up the changes. The developed glycosylation modulator library enabled the generation of extreme glycosylation variants, including high mannose, afucosylated, galactosylated as well as sialic acid species of both a mAb and an antibody fusion molecule with three N-glycosylation sites. Moreover, to create increased variety, enzymatic glycoengineering was explored for galactosylation and sialylation. The glyco variants induced significant responses in the respective in vitro biological activity assays. The data of this work highlight the immense potential of cell culture medium optimization to adjust product quality. Medium and feed supplementation of a variety of compounds resulted in reproducible and important changes of the product quality profile of both mAbs and a fusion antibody. In addition to the intermediate modulation ranges that largely met the requirements for new-biological-entity and biosimilar development, medium supplementation even enabled quick and straightforward generation of extreme glycan variants suitable for biological activity testing.}, subject = {Zellkultur}, language = {en} } @phdthesis{Reimer2017, author = {Reimer, Anastasija}, title = {Search for novel antimicrobials against \(Neisseria\) \(gonorrhoeae\) and \(Chlamydia\) \(trachomatis\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143168}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {The obligate human pathogen Neisseria gonorrhoeae is responsible for the widespread sexually transmitted disease gonorrhoea, which in rare cases also leads to the development of disseminated gonococcal infection (DGI). DGI is mediated by PorBIA-expressing bacteria that invade host cells under low phosphate condition by interaction with the scavenger receptor-1 (SREC-I) expressed on the surface of endothelial cells. The interaction of PorBIA and SREC-I was analysed using different in vitro approaches, including surface plasmon resonance experiments that revealed a direct phosphate-independent high affinity interaction of SREC-I to PorBIA. However, the same binding affinity was also found for the other allele PorBIB, which indicates unspecific binding and suggests that the applied methods were unsuitable for this interaction analysis. Since N. gonorrhoeae was recently classified as a "super-bug" due to a rising number of antibiotic-resistant strains, this study aimed to discover inhibitors against the PorBIA-mediated invasion of N. gonorrhoeae. Additionally, inhibitors were searched against the human pathogen Chlamydia trachomatis, which causes sexually transmitted infections as well as infections of the upper inner eyelid. 68 compounds, including plant-derived small molecules, extracts or pure compounds of marine sponges or sponge-associated bacteria and pipecolic acid derivatives, were screened using an automated microscopy based approach. No active substances against N. gonorrhoeae could be identified, while seven highly antichlamydial compounds were detected. The pipecolic acid derivatives were synthesized as potential inhibitors of the virulence-associated "macrophage infectivity potentiator" (MIP), which exhibits a peptidyl prolyl cis-trans isomerase (PPIase) enzyme activity. This study investigated the role of C. trachomatis and N. gonorrhoeae MIP during infection. The two inhibitors PipN3 and PipN4 decreased the PPIase activity of recombinant chlamydial and neisserial MIP in a dose-dependent manner. Both compounds affected the chlamydial growth and development in epithelial cells. Furthermore, this work demonstrated the contribution of MIP to a prolonged survival of N. gonorrhoeae in the presence of neutrophils, which was significantly reduced in the presence of PipN3 and PipN4. SF2446A2 was one of the compounds that had a severe effect on the growth and development of C. trachomatis. The analysis of the mode of action of SF2446A2 revealed an inhibitory effect of the compound on the mitochondrial respiration and mitochondrial ATP production of the host cell. However, the chlamydial development was independent of proper functional mitochondria, which excluded the connection of the antichlamydial properties of SF2446A2 with its inhibition of the respiratory chain. Only the depletion of cellular ATP by blocking glycolysis and mitochondrial respiratory chain inhibited the chlamydial growth. A direct effect of SF2446A2 on C. trachomatis was assumed, since the growth of the bacteria N. gonorrhoeae and Staphylococcus aureus was also affected by the compound. In summary, this study identified the severe antichlamydial activity of plant-derived naphthoquinones and the compounds derived from marine sponges or sponge-associated bacteria SF2446A2, ageloline A and gelliusterol E. Furthermore, the work points out the importance of the MIP proteins during infection and presents pipecolic acid derivatives as novel antimicrobials against N. gonorrhoeae and C. trachomatis.}, subject = {Neisseria gonorrhoeae}, language = {en} } @phdthesis{Hofmann2017, author = {Hofmann, Stefan}, title = {Hybridisierungsbasierte Multiplex-Detektion von microRNA mit CMOS-Technologie f{\"u}r die Anwendung in der Point-of-Care-Diagnostik}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150949}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {MicroRNAs sind kurze, nicht-kodierende Ribonukleins{\"a}uren, die eine wichtige Rolle bei der Genregulation spielen. Sie sind an vielen physiologischen Prozessen beteiligt und werden als vielversprechende Kandidaten f{\"u}r eine neue Generation von Biomarkern gehandelt. Die Quantifizierung von miRNAs aus Blut oder anderen K{\"o}rperfl{\"u}ssigkeiten verspricht eine fr{\"u}he Diagnose verschiedener Krankheitsbilder. Dazu z{\"a}hlen neben zahlreichen Krebsformen unter anderem auch Autoimmun- oder Herz-Kreislauferkrankungen. Um diese Biomarker schnell, sensitiv und spezifisch detektieren zu k{\"o}nnen, werden geeignete Detektionssysteme ben{\"o}tigt. Dabei liegt ein besonderer Fokus auf der Entwicklung von Point-of-Care-Systemen, die eine automatisierte Durchf{\"u}hrung mit einfacher Handhabung verlangen. Mikrochips k{\"o}nnen als leistungsf{\"a}hige technische Hilfsmittel f{\"u}r eine robuste und miniaturisierte Signalerfassung an biochemischen Grenzfl{\"a}chen dienen. Auf der Grundlage eines CMOS-Chips mit einem Sensorarray aus interdigitalen Gold-Elektroden sollte in dieser Arbeit eine quantitative und multiplexf{\"a}hige miRNA-Detektionsmethode mit elektrochemischer Signaltransduktion entworfen und untersucht werden. Weitere wichtige Zielfaktoren waren eine einfache und schnelle Durchf{\"u}hrbarkeit, eine hohe Spezifit{\"a}t und eine gute Sensitivit{\"a}t bei gleichzeitigem Verzicht auf Amplifikation und Vormarkierung des Ausgangsmaterials. Es wurden verschiedene Methoden entworfen, {\"u}berpr{\"u}ft, untersucht, optimiert und weiterentwickelt. Das beste Ergebnis wurde letztlich mit einem als Sandwich-Ligations-Methode bezeichneten Verfahren erzielt. Dabei wird zun{\"a}chst ein aus zwei doppelstr{\"a}ngigen Assay-Komponenten und der Ziel-miRNA bestehender dreiteiliger Hybridisierungskomplex gebildet, der eine beidseitige spezifische Ligation der miRNA mit einem auf der Sensoroberfl{\"a}che immobilisierten F{\"a}ngerstrang und einem enzymmarkierten Reporterstrang vermittelt. Durch einen anschließenden Waschschritt werden alle {\"u}bersch{\"u}ssigen Markierungen vom Detektionsbereich entfernt, so dass bei der Detektion nur Reporterenzyme ausgelesen werden, die {\"u}ber die Ziel-miRNA kovalent mit dem immobilisierten Strang verbunden sind. Dieses Signal ist daher proportional zur Ausgangskonzentration der gesuchten miRNA. Die Methode wurde mit Hilfe von synthetischen miRNAs etabliert und optimiert. Sie erreichte eine analytische Sensitivit{\"a}t von unter 1 pM Ziel-Nukleins{\"a}ure bei einer Gesamt-Versuchsdauer von nur 30 Minuten. Konzentrationsreihen demonstrierten einen linearen dynamischen Messbereich zwischen 1 pM und 1 nM, der eine verl{\"a}ssliche Quantifizierung der detektierten miRNAs in diesem Bereich erm{\"o}glicht. Die sehr gute Spezfifit{\"a}t des Assays zeigte sich bei der Untersuchung des Einflusses verschiedener IsomiRs auf das Messergebnis sowie im Rahmen von Experimenten mit miRNAs der let-7-Familie. Dabei konnten Ziel-Nukleins{\"a}uren mit Einzelbasenunterschieden klar differenziert werden. Die Multiplexf{\"a}higkeit der vorgestellten Methode wurde durch die gleichzeitige Quantifizierung von bis zu acht miRNAs auf einem CMOS-Chip demonstriert, zuz{\"u}glich Kontrollen. Die Validierung der Detektionsmethode erfolgte mit Gesamt-RNA-Extrakten aus Vollblutproben. Dazu wurde ein kardiales Panel aus acht miRNAs, die auf Basis von Studien zu zirkulierenden miRNAs bei Herzerkrankungen ausgew{\"a}hlt wurden, festgelegt. Mit Hilfe der entsprechenden optimierten Detektionskomponenten wurden aus Spenderblut gewonnene endogene miRNAs analysiert. Dabei zeigte sich f{\"u}r f{\"u}nf der acht Kandidaten sowohl eine solide Korrelation zwischen eingesetzter Gesamt-RNA-Menge und Messsignal, als auch eine gute Reproduzierbarkeit der Ergebnisse. Die Konzentrationen der {\"u}brigen drei miRNAs lagen nah am unteren Detektionslimit und lieferten daher keine verl{\"a}sslichen Daten. Mit Hilfe sogenannter branched DNA zur Signalamplifikation k{\"o}nnte bei Bedarf die Sensitivit{\"a}t des Assays noch verbessert werden, was durch weitere Experimente dieser Arbeit demonstriert wurde. Ein Vergleichsexperiment zwischen der Sandwich-Ligations-Methode und qRT-PCR zeigte nur eine schwache Korrelation der Messergebnisse. Dies ist jedoch konsistent mit anderen Studien zur Vergleichbarkeit unterschiedlicher Detektionsmethoden. Abschließend wurden die miRNAs des kardialen Panels in Gesamt-RNA-Extrakten aus Vollblut von Herzinfarktpatienten und Kontrollen mit der entwickelten Detektionsmethode analysiert und die Ergebnisse verglichen. Dabei konnten Abweichungen in den Konzentrationen von miR-15a und miR-425 aufgedeckt werden. Eine entsprechende diagnostische Untersuchung mit der hier vorgelegten und validierten Detektionsmethode k{\"o}nnte eine Alternative oder Erg{\"a}nzung zu aktuell eingesetzten proteinbasierten Tests bieten.}, subject = {miRNS}, language = {de} } @phdthesis{Fuchs2017, author = {Fuchs, Benjamin Felix}, title = {Effects of timing and herbivory on a grass-endophyte association and its trophic interactions}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-141465}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {I.) Plant associated microorganisms can affect the plant`s interaction with herbivores and higher trophic levels. For instance, endophytic fungi infecting aerial plant parts of grass species produce bioactive alkaloids that can negatively affect species from higher trophic levels, indicating a defensive mutualism between the grass and the endophyte. However, beneficial insects can also be negatively affected by the endophyte, which might question the mutualistic effect of endophytic fungi. On the other hand, grass-endophytes are affected by environmental conditions and species interactions. Grazing can increase endophyte frequencies in natural habitats. Furthermore, endophyte mediated effects on herbivores are most pronounced during warm summers following rainy springs. In this study, we investigated whether endophyte derived alkaloids cascade up a food chain (chapter II) and whether their concentrations depend on plant age and season (chapter III). Further we analysed, whether altered herbivore phenology affects the endophytic fungus (chapter IV) and whether endophyte derived alkaloid production is induced by different herbivore species (chapter V). II.) In our first experimental study we analysed whether grass-endophyte derived alkaloids decreased the performance of two ladybird species feeding on aphids exclusively reared on endophyte infected grass (6 weeks young grass). Further, we screened species from three trophic levels (grass, herbivores and aphid predators) for their alkaloid content using two year old infected grass as diet for herbivores. We established an UPLC-MS method to detect and quantify the amount of the endophyte derived alkaloids peramine and lolitrem B extracted from the organic plant and insect material. Performance parameters of ladybirds revealed little differences between ladybirds fed on aphids reared on endophyte infected and non-infected grass, which probably resulted from low alkaloid concentrations in the young (6-weeks old) endophyte infected grass used in this part of the study. Alkaloid quantification of the two year old endophyte infected grass, herbivores and aphid predators revealed similar concentrations between grass and aphids, while aphid predators contained approximately half of that amount which still exceeded the bioactive threshold. We conclude that alkaloids produced by grass-endophytes cascade up the food chain and are responsible for fitness disadvantages of higher trophic levels. III.) In the second study we investigated the impact of plant age and seasonal timing on grass-endophyte growth and alkaloid production. Plants were sown in April of 2013 and sampled monthly over 30 consecutive months. Endophyte growth was quantified with real-time PCR (qPCR) and alkaloid concentrations with UPLC-MS. We showed that alkaloid concentrations and fungal growth followed a seasonal rhythmicity and that alkaloid concentrations increased with plant age. Alkaloid concentrations peak during summer, when also herbivore abundances are high. Consequently, we conclude that plant age and season contribute to the toxicity of endophytes on grass herbivores IV.) In the third study we simulated earlier spring arrival of aphids by enhancing aphid abundance on endophyte infected and endophyte-free grass in spring and analysed responses across three trophic levels. Enhanced aphid abundance in spring caused higher aphid abundances during the study period. Predators stayed unaffected by increased herbivore abundances; however they did level aphid numbers within two weeks after arrival on the plants, independent of aphid abundance. Grass-endophyte showed a time delayed growth, two weeks after aphid abundance peak and after predators already controlled aphid infestations on the plants. We conclude that phenology shifts of herbivorous insects can affect multi-trophic interactions leading to desynchronizations between phenologies of interacting species and mismatches in food-webs. V.) In the fourth study we analysed whether herbivores induce endophyte growth and alkaloid production and whether different types of herbivores induce specific alkaloid production. We applied three different herbivore treatments on endophyte infected grass over 18 weeks. Locust herbivory increased the insect deterring alkaloid peramine and clipping of plants (simulation of grazing livestock) increased the vertebrate toxic alkaloid lolitrem B. Aphid herbivory did not affect endophyte derived alkaloid concentrations. Endophyte responses to herbivory were species specific which indicates a primarily plant protecting role of alkaloid synthesis in endophyte infected plants and a close chemical crosstalk between interacting species. VI.) In summary, we showed that endophyte derived alkaloids affect higher trophic levels and that alkaloid concentrations in the plant depend on prevalent herbivore species, plant age and seasonal timing. Our results indicate a close chemical crosstalk between the host plant and the endophytic fungus which is susceptible to environmental changes altering the endophyte`s alkaloid production in plants. We gained insights into the grass-endophyte symbiosis in ecological contexts and conclude that several factors determine the herbivore toxic potential of endophytic fungi and thereby their plant mutualistic or parasitic character. Future studies should investigate the mechanisms behind the herbivore induced alkaloid concentration increase, shown in this thesis, especially whether plant signals mediate the endophyte response. Furthermore it would be interesting to study the induction of indirect endophyte mediated defence and how it affects multi-trophic level interactions.}, language = {en} } @article{WolterHanselmannPattschulletal.2017, author = {Wolter, Patrick and Hanselmann, Steffen and Pattschull, Grit and Schruf, Eva and Gaubatz, Stefan}, title = {Central spindle proteins and mitotic kinesins are direct transcriptional targets of MuvB, B-MYB and FOXM1 in breast cancer cell lines and are potential targets for therapy}, series = {Oncotarget}, volume = {8}, journal = {Oncotarget}, number = {7}, doi = {10.18632/oncotarget.14466}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171851}, pages = {11160-11172}, year = {2017}, abstract = {The MuvB multiprotein complex, together with B-MYB and FOXM1 (MMB-FOXM1), plays an essential role in cell cycle progression by regulating the transcription of genes required for mitosis and cytokinesis. In many tumors, B-MYB and FOXM1 are overexpressed as part of the proliferation signature. However, the transcriptional targets that are important for oncogenesis have not been identified. Given that mitotic kinesins are highly expressed in cancer cells and that selected kinesins have been reported as target genes of MMB-FOXM1, we sought to determine which mitotic kinesins are directly regulated by MMB-FOXM1. We demonstrate that six mitotic kinesins and two microtubule-associated non-motor proteins (MAPs) CEP55 and PRC1 are direct transcriptional targets of MuvB, B-MYB and FOXM1 in breast cancer cells. Suppression of KIF23 and PRC1 strongly suppressed proliferation of MDA-MB-231 cells. The set of MMB-FOXM1 regulated kinesins genes and 4 additional kinesins which we referred to as the mitotic kinesin signature (MKS) is linked to poor outcome in breast cancer patients. Thus, mitotic kinesins could be used as prognostic biomarker and could be potential therapeutic targets for the treatment of breast cancer.}, language = {en} } @article{SanderXuEilersetal.2017, author = {Sander, Bodo and Xu, Wenshan and Eilers, Martin and Popov, Nikita and Lorenz, Sonja}, title = {A conformational switch regulates the ubiquitin ligase HUWE1}, series = {eLife}, volume = {6}, journal = {eLife}, doi = {10.7554/eLife.21036}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171862}, year = {2017}, abstract = {The human ubiquitin ligase HUWE1 has key roles in tumorigenesis, yet it is unkown how its activity is regulated. We present the crystal structure of a C-terminal part of HUWE1, including the catalytic domain, and reveal an asymmetric auto-inhibited dimer. We show that HUWE1 dimerizes in solution and self-associates in cells, and that both occurs through the crystallographic dimer interface. We demonstrate that HUWE1 is inhibited in cells and that it can be activated by disruption of the dimer interface. We identify a conserved segment in HUWE1 that counteracts dimer formation by associating with the dimerization region intramolecularly. Our studies reveal, intriguingly, that the tumor suppressor p14ARF binds to this segment and may thus shift the conformational equilibrium of HUWE1 toward the inactive state. We propose a model, in which the activity of HUWE1 underlies conformational control in response to physiological cues—a mechanism that may be exploited for cancer therapy.}, language = {en} } @article{LukešGlatzovaKvičalovaetal.2017, author = {Lukeš, Tom{\´a}š and Glatzov{\´a}, Daniela and Kv{\´i}čalov{\´a}, Zuzana and Levet, Florian and Benda, Aleš and Letschert, Sebastian and Sauer, Markus and Brdička, Tom{\´a}š and Lasser, Theo and Cebecauer, Marek}, title = {Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging}, series = {Nature Communications}, volume = {8}, journal = {Nature Communications}, doi = {10.1038/s41467-017-01857-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172993}, year = {2017}, abstract = {Quantitative approaches for characterizing molecular organization of cell membrane molecules under physiological and pathological conditions profit from recently developed super-resolution imaging techniques. Current tools employ statistical algorithms to determine clusters of molecules based on single-molecule localization microscopy (SMLM) data. These approaches are limited by the ability of SMLM techniques to identify and localize molecules in densely populated areas and experimental conditions of sample preparation and image acquisition. We have developed a robust, model-free, quantitative clustering analysis to determine the distribution of membrane molecules that excels in densely labeled areas and is tolerant to various experimental conditions, i.e. multiple-blinking or high blinking rates. The method is based on a TIRF microscope followed by a super-resolution optical fluctuation imaging (SOFI) analysis. The effectiveness and robustness of the method is validated using simulated and experimental data investigating nanoscale distribution of CD4 glycoprotein mutants in the plasma membrane of T cells.}, language = {en} } @phdthesis{Scholz2017, author = {Scholz, Nicole}, title = {Genetic analyses of sensory and motoneuron physiology in Drosophila melanogaster}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123249}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {During my PhD I studied two principal biological aspects employing Drosophila melanogaster. Therefore, this study is divided into Part I and II. Part I: Bruchpilot and Complexin interact to regulate synaptic vesicle tethering to the active zone cytomatrix At the presynaptic active zone (AZ) synaptic vesicles (SVs) are often physically linked to an electron-dense cytomatrix - a process referred to as "SV tethering". This process serves to concentrate SVs in close proximity to their release sites before contacting the SNARE complex for subsequent fusion (Hallermann and Silver, 2013). In Drosophila, the AZ protein Bruchpilot (BRP) is part of the proteinous cytomatrix at which SVs accumulate (Kittel et al., 2006b; Wagh et al., 2006; Fouquet et al., 2009). Intriguingly, truncation of only 1\% of the C-terminal region of BRP results in a severe defect in SV tethering to this AZ scaffold (hence named brpnude; Hallermann et al., 2010b). Consistent with these findings, cell-specific overexpression of a C-terminal BRP fragment, named mBRPC-tip (corresponds to 1\% absent in brpnude; m = mobile) phenocopied the brpnude mutant in behavioral and functional experiments. These data indicate that mBRPC-tip suffices to saturate putative SV binding sites, which induced a functional tethering deficit at motoneuronal AZs. However, the molecular identity of the BRP complement to tether SVs to the presynaptic AZ scaffold remains unknown. Moreover, within larval motoneurons membrane-attached C-terminal portions of BRP were sufficient to tether SVs to sites outside of the AZ. Based on this finding a genetic screen was designed to identify BRP interactors in vivo. This screen identified Complexin (CPX), which is known to inhibit spontaneous SV fusion and to enhance stimulus evoked SV release (Huntwork and Littleton, 2007; Cho et al., 2010; Martin et al., 2011). However, so far CPX has not been associated with a function upstream of priming/docking and release of SVs. This work provides morphological and functional evidence, which suggests that CPX promotes recruitment of SVs to the AZ and thereby curtails synaptic short-term depression. Together, the presented findings indicate a functional interaction between BRP and CPX at Drosophila AZs. Part II: The Adhesion-GPCR Latrophilin/CIRL shapes mechanosensation The calcium independent receptor of α-latrotoxin (CIRL), also named Latrophilin, represents a prototypic Adhesion class G-protein coupled-receptor (aGPCR). Initially, Latrophilin was identified based on its capacity to bind the α-component of latrotoxin (α-LTX; Davletov et al., 1996; Krasnoperov et al., 1996), which triggers massive exocytotic activity from neurons of the peripheral nervous system (Scheer et al., 1984; Umbach et al., 1998; Orlova et al., 2000). As a result Latrophilin is considered to play a role in synaptic transmission. Later on, Latrophilins have been associated with other biological processes including tissue polarity (Langenhan et al., 2009), fertility (Pr{\"o}mel et al., 2012) and synaptogenesis (Silva et al., 2011). However, thus far its subcellular localization and the identity of endogenous ligands, two aspects crucial for the comprehension of Latrophilin's in vivo function, remain enigmatic. Drosophila contains only one latrophilin homolog, named dCirl, whose function has not been investigated thus far. This study demonstrates abundant dCirl expression throughout the nervous system of Drosophila larvae. dCirlKO animals are viable and display no defects in development and neuronal differentiation. However, dCirl appears to influence the dimension of the postsynaptic sub-synaptic reticulum (SSR), which was accompanied by an increase in the postsynaptic Discs-large abundance (DLG). In contrast, morphological and functional properties of presynaptic motoneurons were not compromised by the removal of dCirl. Instead, dCirl is required for the perception of mechanical challenges (acoustic-, tactile- and proprioceptive stimuli) through specialized mechanosensory devices, chordotonal organs (Eberl, 1999). The data indicate that dCirl modulates the sensitivity of chordotonal neurons towards mechanical stimulation and thereby adjusts their input-output relation. Genetic interaction analyses suggest that adaption of the molecular mechanotransduction machinery by dCirl may underlie this process. Together, these results uncover an unexpected function of Latrophilin/dCIRL in mechanosensation and imply general modulatory roles of aGPCR in mechanoception.}, subject = {Drosophila}, language = {en} } @phdthesis{Tsoneva2017, author = {Tsoneva, Desislava}, title = {Humanized mouse model: a system to study the interactions of human immune system with vaccinia virus-infected human tumors in mice}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-118983}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Ein vielversprechender neuer Ansatz zur Behandlung von Krebs beim Menschen ist die Verwendung von onkolytischen Viren, die einen Tumor-spezifischen Tropismus aufweisen. Einer der Top-Kandidaten in diesem Bereich ist das onkolytische Vaccinia Virus (VACV), das bereits vielversprechende Ergebnisse in Tierversuchen und in klinischen Studien gezeigt hat. Aber die von den in vivo in tierischen Modellen erhaltenen Resultate k{\"o}nnten ungenaue Informationen wegen der anatomischen und physiologischen Unterschiede zwischen den Spezies liefern. Andererseits sind Studien in Menschen aufgrund ethischer Erw{\"a}gungen und potenzieller Toxizit{\"a}t nur limitiert m{\"o}glich. Die zahlreichen Einschr{\"a}nkungen und Risiken, die mit den Humanstudien verbunden sind, k{\"o}nnten mit der Verwendung eines humanisierten Mausmodells vermieden werden. Die LIVP-1.1.1, GLV-2b372, GLV-1h68, GLV-1h375, GLV-1h376 and GLV-1h377 VACV St{\"a}mmen wurden von der Genelux Corporation zur Verf{\"u}gung gestellt. GLV-2b372 wurde durch Einf{\"u}gen der TurboFP635 Expressionskassette in den J2R Genlocus des parentalen LIVP-1.1.1-Stammes konstruiert. GLV-1h375, -1h376 and -1h377 kodiert das Gen f{\"u}r den menschlichen CTLA4-blockierenden Einzelketten-Antik{\"o}rper (CTLA4 scAb). Befunde aus Replikations- and Zytotoxizit{\"a}tsstudien zeigten, dass alle sechs Viren Tumorzellen infizieren, sich in ihnen replizieren und sie in Zellkultur schließlich ebenso dosis- und zeitabh{\"a}ngig effizient abt{\"o}ten konnten. CTLA4 scAb und β-Glucuronidase (GusA) Expression sowie Virus Titer in GLV-1h376-infizierten A549-Zellen wurde anhand von ELISA-, β-Glucuronidase- and Standard Plaque-Assays bestimmt. Hierbei zeigte sich eine ausgezeichnete Korrelation mit Korrelationskoeffizienten R2>0.9806. Der durch das GLV-1h376 kodierte CTLA4 scAb wurde erfolgreich aus {\"U}berst{\"a}nden von infizierten CV-1-Zellen gereinigt. CTLA4 scAb hat eine hohe in-vitro-Affinit{\"a}t zu seinem menschlichen CTLA4-Zielmolek{\"u}l sowie abwesende Kreuzreaktivit{\"a}t gegen{\"u}ber murine CTLA4 gezeigt. CTLA4 scAb Funktionalit{\"a}t wurde in Jurkat-Zellen best{\"a}tigt. LIVP-1.1.1, GLV-2b372, GLV-1h68 und GLV-1h376 wurden auch in nicht-tumor{\"o}sen und/oder tumortragenden humanisierten M{\"a}usen getestet. Zun{\"a}chst wurde gezeigt, dass die Injektion von menschlichen CD34+ Stammzellen in die Leber von vorkonditionierten neugeborenen NSG M{\"a}usen zu einer erfolgreichen systemische Rekonstitution mit menschlichen Immunzellen gef{\"u}hrt hat. CD19+-B-Zellen, CD4+- und CD8+-CD3+-T-Zellen, NKp46+CD56- und NKp46+CD56+-NK-Zellen sowie CD33+-myeloischen Zellen wurden detektiert. Die Mehrheit der nachgewisenen humanen h{\"a}matopoetischen Zellen im M{\"a}useblut in den ersten Wochen nach der Humanisierung waren CD19+-B-Zellen, und nur ein kleiner Teil waren CD3+-T-Zellen. Mit der Zeit wurde eine signifikante Ver{\"a}nderung in CD19+/CD3+-Verh{\"a}ltnis beobachtet, die parallel zur Abnahme der B-Zellen und einem Anstieg der T-Zellen kam. Die Implantation von A549-Zellen unter die Haut dieser M{\"a}use f{\"u}hrte zu einem progressiven Tumorwachstum. Bildgebende Verfahren zur Detektion von Virus-vermittelter TurboFP635- und GFP-Expression, Standard Plaque Assays sowie immunohistochemische Analysen best{\"a}tigten die erfolgreiche Invasion der Viren in die subkutanen Tumoren. Die humane CD45+-Zellpopulation in Tumoren wurde haupts{\"a}chlich durch NKp46+CD56bright-NK-Zellen und einen hohen Anteil von aktivierten CD4+- und zytotoxische CD8+-T-Zellen dargestellt. Es wurden jedoch keine signifikanten Unterschiede zwischen den Kontroll- und LIVP-1.1.1-infizierten Tumoren beobachtet, was darauf hindeutete, dass die Rekrutierung von NK- und aktivierten T-Zellen, mehr Tumorgewebe-spezifisch als Virus-abh{\"a}ngig waren. Die GLV-1h376-vermittelten CTLA4 scAb-Expression in den infizierten Tumoren war ebenfalls nicht in der Lage, die Aktivierung von Tumor-infiltrierenden T-Zellen im Vergleich zur Kontrolle und GLV-1h68-behandelten M{\"a}usen, signifikant zu erh{\"o}hen. ELISA-, β-Glucuronidase- and Standard Plaque-Assays zeigten eine eindeutige Korrelation mit den Korrelationskoeffizienten R2>0,9454 zwischen CTLA4 scAb- und GusA-Konzentrationen und Virus Titer in Tumorproben von GLV-1h376-behandelten M{\"a}usen. T-Zellen, die aus der Milz dieser Tumor-tragenden M{\"a}use isoliert wurden, waren funktionell und konnten erfolgreich mit Beads aktiviert werden. Mehr CD25+ und IFN-ɣ+ T-Zellen wurden in der GLV-1h376-Gruppe gefunden, wahrscheinlich aufgrund der CTLA4-Blockade durch die Virus-vermittelte CTLA4 scAb-Expression in den M{\"a}usen. Außerdem wurde eine h{\"o}here Konzentration von IL-2 in dem Kultur{\"u}berstand von diesen Splenozyten im Vergleich zu Kontrollproben nachgewiesen. Im Gegensatz zu der Aktivierung mit Beads konnten T-Zellen von allen drei Maus-Gruppen nicht durch A549 Tumorzellen ex vivo aktiviert werden. Unser Mausmodell hat den besonderen Vorteil, dass sich Tumoren unter der Haut der humanisierten M{\"a}use entwickeln, was eine genaue {\"U}berwachung des Tumorwachstums und Auswertung der onkolytischen Virotherapie erm{\"o}glicht.}, subject = {Vaccinia virus}, language = {en} } @phdthesis{Ritter2017, author = {Ritter, Cathrin}, title = {Scientific basics for new immunotherapeutic approaches towards Merkel cell carcinoma}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124162}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer that has been associated with the Merkel cell polyomavirus (MCPyV). Indeed, MCC is one of the cancers with the best-established viral carcinogenesis. Despite persistence of the virus in MCC cells and the subsequent expression of viral antigens, the majority of MCC tumors are able to escape the surveillance of the immune system. Therefore the aim of the here presented thesis was to scrutinize immune escape mechanisms operative in MCC. A better understanding of their underlying molecular processes should allow to improve immunotherapeutic treatment strategies for MCC patients. The manuscripts included in this thesis characterize three novel immune evasion strategies of MCC. I) the epigenetic silencing of the NKG2D ligands MICA and MICB via histone H3 hypoacetylation II) reduced HLA class I surface expression via epigenetic silencing of the antigen processing machinery (APM) III) the activation of the PI3K-AKT pathway in a mutation independent manner as potential immune escape strategy MCC tumors and MCC cell lines were analyzed for their expression of MICA/B, HLA and components of the antigen processing machinery as well as for the activation of the PI3K-AKT pathway in situ and in vitro. These analysis reviled MICA and MICB, as well as HLA class I were not expressed or at least markedly reduced in ~80\% of MCCs in situ. The PI3K-AKT pathway, that had only recently been demonstrated to play a significant role in tumor immune escape, was activated in almost 90\% of MCCs in situ. To determine the underlying molecular mechanisms of these aberrations well characterized MCC cell lines were further analyzed in vitro. The fact that the PI3K-AKT pathway activation was due to oncogenic mutations in the PIK3CA or AKT1 gene in only 10\% of MCCs, suggested an epigenetic regulation of this pathway in MCC. In line with this MICA/B as well as components of the APM were indeed silenced epigenetically via histone hypoacetylation in their respective promoter region. Notably MICA/B and HLA class I expression on the cell surface of MCC cells could be restored after treatment with HDAC inhibitors in combination with the Sp1 inhibitor Mithramycin A in all analyzed MCC cell lines in vitro and in a xenotransplantation mouse model in vivo. Moreover inhibition of HDACs increased immune recognition of MCC cell lines in a MICA/B and HLA class I dependent manner. Several studies have accumulated evidence that immunotherapy is a promising treatment option for MCC patients due to the exquisite immunogenicity of this malignancy. However, current immunotherapeutic interventions towards solid tumors like MCC have to account for the plentitude of tumor immune escape strategies, in order to increase response rates. The immune escape mechanisms of MCC described in this thesis can be reverted by HDAC inhibition, thus providing the rationale to combine 'epigenetic priming' with currently tested immunotherapeutic regimens.}, subject = {Merkel-Zellkarzinom}, language = {en} } @phdthesis{ContarAdolfi2017, author = {Contar Adolfi, Mateus}, title = {Sex determination and meiosis in medaka: The role of retinoic acid}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136335}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Sex determination (SD) is a complex and diverse developmental process that leads to the decision whether the bipotential gonad anlage will become a testis or an ovary. This mechanism is regulated by gene cascades, networks and/or chromosomal systems, and can be influenced by fluctuations of extrinsic factors like temperature, exposure to hormones and pollution. Within vertebrates, the group of fish show the widest variety of sex determination mechanism. This whole diversity of processes and mechanisms converges to the formation of two different gametes, the eggs and the sperm, the first bigger and static, and the second smaller and motile. Meiosis is crucial for the formation of both types of gametes, and the timing of meiosis entry is one of the first recognizable differences between male and female in vertebrates. The germ cells go into meiosis first in female than in male, and in mammals, this event has been shown to be regulated by retinoic acid (RA). This small polar molecule induces in the germ cells the expression of the pre-meiotic marker Stra8 (stimulated by retinoic acid gene 8), which is necessary for meiosis initiation. Interestingly, genome analyzes have shown that the majority of fish (including medaka) lack the stra8 gene, adding a question mark to the role of RA in meiosis induction in this group. Since a role of RA in entry of meiosis and sexual development of fish is still far from being understood, I investigated in medaka (Oryzias latipes) a possible signaling function of RA during the SD period in embryos and in reproductively active gonads of adults. I generated a transgenic medaka line that reports responsiveness to RA in vivo. With this tool, I compared RA responsiveness with the expression of the main gene involved in the synthesis of RA. My results show that there is a de-correlation between the action of RA with its source. In adults, expression of the RA metabolizing enzymes show sexually dimorphic RA levels, with aldh1a2 levels being higher in testis, and cyp26a1 stronger in female gonad. In ovary, the responsiveness is restricted to the early meiotic oocytes. In testis, RA is acting directly in the pre-meiotic cells, but also in Sertoli and Leydig cells. Treatment experiments on testis organ culture showed that RA pathway activation leads to a decrease in meiosis markers expression levels. During the development, RA responsiveness in the germ cells was observed in both sexes much earlier than the first female meiosis entry. Treatments with RA-synthesis inhibitor show a decrease in meiosis markers expression levels only after the sex differentiation period in female. Expression analyzes of embryos treated with exogenous RA showed induction of dmrt1a at the gonad levels and an increase of amh levels. Both genes are not only involved in male formation, but also in the regulation of germ cell proliferation and differentiation. RA is important in meiosis induction and gametogenesis in adult medaka. However, there is no evidence for a similar role of RA in initiating the first meiosis in female germ cells at the SD stage. Moreover, contrary to common expectation, RA seems to induce sex related genes that are involved indirectly in meiosis inhibition. In this thesis, I showed for the first time that RA can be involved in both induction and inhibition of meiosis entry, depending on the sex and the developmental stage in a stra8-independent model organism.}, subject = {Japank{\"a}rpfling}, language = {en} } @phdthesis{Danner2017, author = {Danner, Nadja}, title = {Honey bee foraging in agricultural landscapes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139322}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {1. Today honey bee colonies face a wide range of challenges in modern agricultural landscapes which entails the need for a comprehensive investigation of honey bees in a landscape context and the assessment of environmental risks. Within this dissertation the pollen foraging of honey bee colonies is studied in different agricultural landscapes to gain insight into the use of pollen resources and the influence of landscape structure across the season. General suggestions for landscape management to support honey bees and other pollinators are derived. 2. Decoding of waggle dances and a subsequent spatial foraging analysis are used as methods in Chapters 4 and 5 to study honey bee colonies in agricultural landscapes. The recently developed metabarcoding of mixed pollen samples was applied for the first time in honey bee foraging ecology and allowed for a detailed analysis of pollen, that was trapped from honey bees in front hive entrances (Chapter 6). 3. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach to light microscopy, which still is a tedious and error-prone task. In this study we assessed mixed pollen probes through next-generation sequencing and developed a bioinformatic workflow to analyse these high-throughput data with a newly created reference database. To evaluate the feasibility, we compared results from classical identification based on light microscopy from the same samples with our sequencing results. Abundance estimations from sequencing data were significantly correlated with counted abundances through light microscopy. Next-generation sequencing thus presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialized palynological expert knowledge. 4. During maize flowering, four observation hives were placed in and rotated between 11 landscapes covering a gradient in maize acreage. A higher foraging frequency on maize fields compared to other landuse types showed that maize is an intensively used pollen resource for honey bee colonies. Mean foraging distances were significantly shorter for maize pollen than for other pollen origins, indicating that effort is put into collecting a diverse pollen diet. The percentage of maize pollen foragers did not increase with maize acreage in the landscape and was not reduced by grassland area as an alternative pollen resource. Our findings allow estimating the distance-related exposure risk of honey bee colonies to pollen from surrounding maize fields treated with systemic insecticides. 5. It is unknown how an increasing area of mass-flowering crops like oilseed rape (OSR) or a decrease of semi-natural habitats (SNH) change the temporal and spatial availability of pollen resources for honey bee colonies, and thus foraging distances and frequency in different habitat types. Sixteen observation hives were placed in and rotated between 16 agricultural landscapes with independent gradients of OSR and SNH area within 2 km to analyze foraging distances and frequencies. SNH and OSR reduced foraging distance at different spatial scales and depending on season, with possible benefits for the performance of honey bee colonies. Frequency of pollen foragers per habitat type was equally high for SNH, grassland and OSR fields, but lower for other crops and forest. In landscapes with a small proportion of SNH a significantly higher density of pollen foragers on SNH was observed, indicating the limitation of pollen resources in simple agricultural landscapes and the importance of SNH. 6. Quantity and diversity of collected pollen can influence the growth and health of honey bee colonies, but little is known about the influence of landscape structure on pollen diet. In a field experiment we rotated 16 honey bee colonies across 16 agricultural landscapes (see also Chapter 5), used traps to get samples of collected pollen and observed the intra-colonial dance communication to gain information about foraging distances. Neither the amount of collected pollen nor pollen diversity were related to landscape diversity. The revealed increase of foraging distances with decreasing landscape diversity suggests that honey bees compensate for a lower landscape diversity by increasing their pollen foraging range in order to maintain pollen amount and diversity. 7. Our results show the importance of diverse pollen resources for honey bee colonies in agricultural landscapes. Beside the risk of exposure to pesticides honey bees face the risk of nutritional deficiency with implications for their health. By modifying landscape composition and therefore availability of resources we are able to contribute to the wellbeing of honey bees. Agri-environmental schemes aiming to support pollinators should focus on possible spatial and temporal gaps in pollen availability and diversity in agricultural landscapes.}, subject = {Apis mellifera}, language = {en} } @phdthesis{Zimnol2017, author = {Zimnol, Anna}, title = {Relevance of angiotensin II type 1a receptor and NADPH oxidase for the formation of angiotensin II-mediated DNA damage}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-137469}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Das Renin-Angiotensin-Aldosteron-System (RAAS) reguliert den Blutdruck sowie den Elektrolyt- und Wasserhaushalt. Das aktive Peptid, Angiotensin II (AngII), f{\"u}hrt dabei zur Vasokonstriktion und in h{\"o}heren Konzentrationen zu Bluthochdruck. Hypertensive Patienten haben ein erh{\"o}htes Risiko an Krebs zu erkranken, vor allem an Nierenkrebs. Wir konnten bereits in vivo zeigen, dass AngII in der Lage ist, den Blutdruck zu steigern und dosisabh{\"a}ngig zu DNA-Sch{\"a}den {\"u}ber den Angiotensin II Typ 1-Rezeptor (AT1R) f{\"u}hrt. Ein stimuliertes RAAS kann ferner {\"u}ber die Aktivierung der NADPH-Oxidase, einer Hauptquelle der Generierung reaktiver Sauerstoffspezies (ROS) in der Zelle, zu oxidativem Stress f{\"u}hren. Zielsetzung dieser Arbeit war es zum einen, mit Hilfe von AT1a-Rezeptor-defizienten M{\"a}usen in vivo zu pr{\"u}fen, ob die Bildung von ROS, sowie die Bildung von DNA-Sch{\"a}den in der Niere und im Herzen unabh{\"a}ngig von einem erh{\"o}hten Blutdruck auftreten. Zum anderen sollte, ebenfalls in vivo, untersucht werden, ob eine oder beide von zwei untersuchten Isoformen der NADPH-Oxidase (Nox) f{\"u}r die Ausl{\"o}sung oxidativen Stresses in der Niere verantwortlich ist. Zun{\"a}chst wurden f{\"u}r den Versuch zur {\"U}berpr{\"u}fung der Abh{\"a}ngigkeit AngII-induzierter DNA-Sch{\"a}den vom Blutdruck m{\"a}nnliche C57BL/6-M{\"a}use und AT1a-Knockout (KO)-M{\"a}use mit osmotischen Minipumpen ausgestattet, die AngII in einer Konzentrationen von 600 ng/kg min {\"u}ber einen Zeitraum von 28 Tagen abgaben. Zus{\"a}tzlich wurde eine Gruppe von AngII-behandelten Wildtyp (WT)-M{\"a}usen mit dem AT1-Rezeptor-Blocker Candesartan (Cand) behandelt. W{\"a}hrend des Versuchszeitraumes fanden regelm{\"a}ßige, nicht-invasive Blutdruckmessungen an den wachen M{\"a}usen statt. In WT-M{\"a}usen induzierte AngII Bluthochdruck, verursachte erh{\"o}hte Albumin-Level im Urin und f{\"u}hrte zur Bildung von ROS in Niere und im Herzen. Außerdem traten in dieser Gruppe DNA-Sch{\"a}den in Form von Einzel- und Doppelstrangbr{\"u}chen auf. All diese Reaktionen auf AngII konnten jedoch durch gleichzeitige Behandlung mit Cand verhindert werden. AT1a-KO-M{\"a}use hatten, verglichen mit WT-Kontrollm{\"a}usen, einen signifikant niedrigeren Blutdruck und normale Albumin-Level im Urin. In AT1a-KO-M{\"a}usen, die mit AngII behandelt wurden, konnte kein Anstieg des systolischen Blutdrucks sowie kein Einfluss auf die Nierenfunktion gefunden werden. Jedoch f{\"u}hrte AngII in dieser Gruppe zu einer Steigerung von ROS in der Niere und im Herzen. Zus{\"a}tzlich wurden genomische Sch{\"a}den, vor allem in Form von Doppelstrangbr{\"u}chen signifikant in dieser Gruppe induziert. Auch wenn AT1a-KO-Tiere, unabh{\"a}ngig von einer AngII-Infusion, keine eingeschr{\"a}nkte Nierenfunktion zeigten, so wiesen sie erhebliche histopathologische Sch{\"a}den im Hinblick auf die Glomeruli und das Tubulussystem auf. Diese Art von Sch{\"a}den deuten auf eine besondere Bedeutung des AT1aR im Hinblick auf die embryonale Entwicklung der Niere hin. Zusammenfassend beweisen die Ergebnisse dieses Experiments eindeutig, dass eine AngII-induzierte ROS-Produktion und die Induktion von DNA-Sch{\"a}den unabh{\"a}ngig von einem erh{\"o}hten Blutdruck auftreten. Da in der AngII-behandelten AT1a-KO-Gruppe eine signifikant h{\"o}here Expression des AT1b-Rezeptors zu finden war und die Blockade von beiden Rezeptorsubtypen mit Cand zu einer Verhinderung der sch{\"a}dlichen Effekte durch AngII f{\"u}hrte, scheint der AT1bR im Falle einer AT1aR-Defizienz f{\"u}r die Entstehung der Sch{\"a}den zust{\"a}ndig zu sein. Ziel des zweiten Experimentes war es, den Beitrag der Nox2 und Nox4 zum oxidativen DNA-Schaden in vivo zu untersuchen. Hierf{\"u}r wurden m{\"a}nnliche C57BL/6-M{\"a}use und Nox2- oder Nox4-defiziente M{\"a}use mit osmotischen Minipumpen ausgestattet, die AngII in einer Konzentration von 600 ng/kg min {\"u}ber einen Zeitraum von 28 Tagen abgaben. Im WT-Stamm und in beiden Nox-defizienten St{\"a}mmen induzierte AngII Bluthochdruck, verursachte erh{\"o}hte Albumin-Level im Urin und f{\"u}hrte zur Bildung von ROS in der Niere. Außerdem waren in allen AngII-behandelten Gruppen genomische Sch{\"a}den, vor allem in Form von Doppelstrangbr{\"u}chen, erh{\"o}ht. Auch in Abwesenheit von AngII wiesen Nox2- und Nox4-defiziente M{\"a}use mehr Doppelstrangbr{\"u}che im Vergleich zu WT-Kontrollm{\"a}usen auf. Interessanterweise kompensieren allerdings weder Nox2 noch Nox4 das Fehlen der jeweils anderen Isoform auf RNA-Basis. Aufgrund dieser Ergebnisse schließen wir, dass bislang keine Isoform alleine f{\"u}r die Generierung von oxidativen DNA-Sch{\"a}den in der Niere verantwortlich gemacht werden kann und dass eine Beteiligung einer weiteren Nox-Isoform sehr wahrscheinlich ist. M{\"o}glicherweise k{\"o}nnten aber auch andere ROS-generierende Enzyme, wie Xanthinoxidase oder Stickoxidsynthase involviert sein. Da genomische Sch{\"a}den in Nieren von Nox2- und Nox4-defizienten M{\"a}usen in Abwesenheit von AngII gegen{\"u}ber den Sch{\"a}den in WT-Kontrollm{\"a}usen erh{\"o}ht waren, k{\"o}nnten die beiden Isoformen auch eine sch{\"u}tzende Funktion im Bereich von Nierenkrankheiten {\"u}bernehmen. Da dies aber bislang nur f{\"u}r Nox4 beschrieben ist, ist es wahrscheinlicher, dass das Fehlen von einer der beiden Isoformen eher einen Einfluss auf die Embryonalentwicklung hat. Um dies jedoch abschließend zu kl{\"a}ren w{\"a}re es sinnvoll mit induzierbaren Knockout-Modellen zu arbeiten, bei denen m{\"o}gliche entwicklungsbedingte Effekte minimiert werden k{\"o}nnen.}, subject = {Angiotensin II}, language = {de} } @phdthesis{Kunz2017, author = {Kunz, Meik}, title = {Systembiologische Analysen von Interaktionen: Zytokinine (Pflanzenpathogene), 3D-Zellkulturen (Krebstherapie) und Drugtargets}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134911}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Der Einsatz von computergest{\"u}tzten Analysen hat sich zu einem festen Bestandteil der biowissenschaftlichen Forschung etabliert. Im Rahmen dieser vorliegenden Arbeit wurden systembiologische Untersuchungen auf verschiedene biologische Themengebiete und Organismen angewendet. In diesem Zusammenhang liefert die Arbeit einen innovativen und interdisziplin{\"a}ren methodischen Ansatz. Die grundlegende Frage lautet: Wie verstehe und beschreibe ich Signalwege und wie kann ich sie beeinflussen? Der Ansatz verkn{\"u}pft verschiedene biologische Datens{\"a}tze und Datenebenen miteinander, beginnend vom Genom und Interaktionskontext {\"u}ber semiquantitative Simulationen hin zu neuen Interventionen und Experimenten, welche therapeutisch und biotechnologisch genutzt werden k{\"o}nnen. Die Analysen k{\"o}nnen auf diese Weise - zu einem besseren Verst{\"a}ndnis experimenteller Daten und biologischer Fragestellungen beitragen und erm{\"o}glichen ein systematisches Verst{\"a}ndnis der zugrunde liegenden Signalwege und Netzwerkeffekte (z.B. in Pflanzen). - Dar{\"u}ber hinaus erm{\"o}glichen sie die Identifizierung wichtiger funktioneller Hubproteine und die Entwicklung neuer therapeutischer Strategien f{\"u}r weitere experimentelle Testungen (z.B. Tumormodelle), - stellen zudem einen hilfreichen Schritt auf dem Weg zur personalisierten Medizin (z.B. lncRNAs und Tumormodelle) und Medikamentenentwicklung (z.B. Datenbank DrumPID) dar. (i) Als Grundlage wurde hierzu eine integrierte systembiologische Methode entwickelt, welche experimentelle Daten (z.B. Transkriptomdaten) hinsichtlich ihrer biologischen Funktionen untersucht und die Identifizierung relevanter funktioneller Cluster und Hubproteine erm{\"o}glicht. In einem ersten Teil wurden Analysen zum pflanzlichen Immunsystem durchgef{\"u}hrt. Mithilfe der entwickelten Methode wurden Genexpressionsdatens{\"a}tze von A. thaliana, die mit dem Pathogen Pst DC3000 infiziert wurden, untersucht, um den Einfluss verschiedener Virulenzfaktoren auf das Interaktom der Wirtspflanze zu untersuchen und neue Modulatoren einer CK-vermittelten Immunabwehr zu finden. In diesem Zusammenhang konnte gezeigt werden, dass die von Pst DC3000 sekretierten Abwehrstoffe wichtige pflanzliche Hormonsignalwege f{\"u}r die Immunabwehr in A. thaliana beeinflussen. Die Ergebnisse zeigen zudem, dass sich der Einfluss auf das Netzwerkverhalten der Effektorproteine und COR-Phytotoxine von dem der PAMPs unterscheidet, sich jedoch auch eine Regulierung gemeinsamer Signalwege und eine {\"U}berlappung der beiden Phasen der Immunantwort (PTI und ETI) in A. thaliana finden lassen. Die komplexe Immunantwort auf eine Infektion spiegelt sich zudem in einer h{\"o}heren Anzahl an funktionellen Clustern und Hubproteinen in Pst DC3000 gegen{\"u}ber den beiden untersuchten Mutanten wider, wobei sich f{\"u}r Pst DC3000 insbesondere ein stark vernetztes immunrelevantes Cluster um den JA-Signalweg zeigt. Weiterhin wurden anhand der entwickelten Methode wichtige Hubproteine f{\"u}r die Immunabwehr identifiziert. Als bedeutende Vertreter sind AHK2 und AAR14 zu nennen, welche Teil des Zweikomponentensystems der Signal{\"u}bertragung von CK sind und hierbei wichtige Modulatoren f{\"u}r eine CK-vermittelte Immunabwehr darstellen. (ii) Im zweiten Teil der Arbeit schließen sich Untersuchungen an einem in vitro-Experiment einer 2D- und 3D-Zellkultur einer HSP90-Behandlung in einem Lungentumormodell an. In diesem Zusammenhang wurden mithilfe der entwickelten Methode Unterschiede zwischen den beiden Zellkultursystemen gefunden, die das unterschiedliche Behandlungsansprechen erkl{\"a}ren, und f{\"u}r die beiden KRAS-mutierten Zelllinien A549 und H441 des 3D-Testsystems neue prognostische und therapeutische Kandidaten identifiziert. Hierbei haben die durchgef{\"u}hrten Analysen zwei funktionelle Cluster von Protein-Interaktionen um p53 und die STAT-Familie gefunden, welche eine Verbindung zu HSP90 haben und die entsprechenden Behandlungsunterschiede nach einer HSP90-Inhibierung zwischen den beiden Zellkultursystemen erkl{\"a}ren k{\"o}nnen. Unter Ber{\"u}cksichtigung des zelllinien-spezifischen Mutationshintergrunds wurde eine prognostische Markersignatur und daraus abgeleitet HIF1A f{\"u}r die H441-Zelllinie und AMPK f{\"u}r die A549-Zelllinie als neue therapeutische Targets gefunden, wobei die anschließend durchgef{\"u}hrten in silico-Simulationen einen potentiellen therapeutischen Effekt aufzeigen konnten. Weiterhin wurden wichtige experimentelle Readout-Parameter in ein in silico-Lungentumormodell integriert, wobei unter Einbeziehung des Mutationshintergrunds f{\"u}r die verwendeten Zelllinien die HSP90-Behandlung des 3D-Testsystems computergest{\"u}tzt abgebildet werden konnte. Im weiteren Verlauf wurden im in silico-Lungentumormodell Resistenzmechanismen nach einer Gefitinib-Behandlung mit bekanntem Mutationsstatus f{\"u}r die Zelllinien HCC827 und A549 untersucht und daraus folgend neue Therapieans{\"a}tze abgeleitet, die von potentieller klinischer Bedeutung sein k{\"o}nnen. Die durchgef{\"u}hrten in silico-Simulationen f{\"u}r HCC827 konnten hierbei zeigen, dass eine EGFR- und c-MET-Koaktivierung zu einer Gefitinib-Resistenz f{\"u}hren kann, wohingegen bei den A549 eine Komutation von KRAS und IGF-1R zu einem geringen Behandlungsansprechen beitr{\"a}gt. Die Simulationen lassen zudem erkennen, dass eine direkte Inhibierung der an der Resistenzentwicklung beteiligten Rezeptoren c-MET und IGF-1R in beiden F{\"a}llen nicht die bestm{\"o}gliche Therapiestrategie darstellt. In beiden Zelllinien konnte gezeigt werden, dass eine kombinierte Inhibierung von PI3K und MEK den bestm{\"o}glichen therapeutischen Effekt liefert, was demnach einen vielversprechenden Therapieansatz bei Gefitinib-resistenten Lungentumorpatienten darstellt. In einem weiteren Schritt wurde das therapeutische Potential der miRNA-21 im in silico-Modell f{\"u}r die HCC827-Zelllinie untersucht. Die durchgef{\"u}hrten Simulationen zeigen, dass eine miRNA-21-{\"U}berexpression zu einer Resistenzentwickung nach Gefitinib-Behandlung beitragen kann, wobei eine Inhibierung der miRNA-21 diesen Effekt umkehren kann. Die Ergebnisse lassen zudem erkennen, dass eine PTEN-Aktivierung als potentieller Marker einer erfolgreichen therapeutischen Inhibierung der miRNA-21 fungieren kann, wohingegen eine reduzierte miRNA-21-Expression als m{\"o}glicher Marker f{\"u}r eine erfolgreiche Gefitinib-Behandlung dienen kann. (iii) Im dritten Teil der Arbeit wurden systematisch RNA- und Protein-Interaktionen untersucht. Hierzu wurden integrierte systembiologische Analysen an neu identifizierten und funktionell bislang unbekannten lncRNAs durchgef{\"u}hrt. Die Analysen f{\"u}r die infolge einer Herzhypertrophie hochregulierte lncRNA Chast haben umfassend gezeigt, dass diese Proteine und Transkriptionsfaktoren regulieren und binden kann, welche die Signal{\"u}bertragung und Genexpression regulieren, aber auch eine Verbindung zum kardiovaskul{\"a}ren System und stressinduzierter Herzhypertrophie besitzt. Anhand der Ergebnisse l{\"a}sst sich schlussfolgern, dass Chast direkt und indirekt (a) Proteine binden und die Translation beeinflussen kann, zudem eine Chromatin-modifizierende Funktion besitzt und so die Transkription, z.B. f{\"u}r herz- und stress-assoziierte Gene, reguliert, und/oder (b) in einem negativen Feedbackloop seine eigene Transkription reguliert. Obwohl lncRNAs meist eine geringe Konservierung aufweisen, konnten die durchgef{\"u}hrten Analysen f{\"u}r Chast eine Sequenz-Struktur-Konservierung in S{\"a}ugetieren aufzeigen. Weiterhin haben die Untersuchungen an zwei hypoxie-induzierten lncRNAs in Endothelzellen gezeigt, dass die lncRNA MIR503HG eine hohe Sequenz-Struktur-Konservierung in S{\"a}ugetieren besitzt, wohingegen die LINC00323-003 eine geringe Konservierung aufzeigt. Dies untermauert die Tatsache, dass lncRNAs h{\"a}ufig eine geringe Konservierung aufweisen, was Untersuchungen in Modellorganismen hinsichtlich einer therapeutischen Nutzung schwierig machen. Da sich zahlreiche Untersuchungen auf Interaktionen und Signalwege konzentriert haben, wurde abschließend eine Datenbank entwickelt, welche Analysen von Protein-Interaktionen und Signalwegen nachhaltig voranbringt. Die entwickelte DrumPID-Datenbank stellt insbesondere die Interaktion zwischen einem Medikament und seinem Target in den Fokus und erm{\"o}glicht Analysen einzelner Interaktionen und beteiligter Signalwege, bietet zus{\"a}tzlich aber auch verschiedene Links zu anderen Datenbanken f{\"u}r individuelle weiterf{\"u}hrende Analysen. DrumPID erm{\"o}glicht ein geeignetes Medikament u. a. f{\"u}r ein vorgegebenes Zielprotein zu finden und dessen Wirkmechanismus und Interaktionskontext zu untersuchen, was zu einem besseren experimentellen Verst{\"a}ndnis beitragen kann. Zudem erlaubt DrumPID eine potentielle chemische Leitstruktur f{\"u}r ein Zielprotein zu entwickeln, was z.B. spezifisch ein parasitisches Protein inhibiert, ohne dabei einen toxischen Effekt im Menschen zu haben. Zahlreiche weitere Pharmakabeispiele belegen, dass DrumPID f{\"u}r den t{\"a}glichen wissenschaftlichen Gebrauch auf dem Gebiet der Analyse von Protein-Pharmaka-Interaktionen und der Medikamentenentwicklung geeignet ist. Die beschriebenen Ergebnisse der Promotionsarbeit wurden in f{\"u}nf Originalarbeiten, zwei {\"U}bersichtsartikeln und einem Buchteil, u. a. in Science Translational Medicine, ver{\"o}ffentlicht, sechs dieser Publikationen erfolgten im Rahmen von Erstautorschaften.}, subject = {Systembiologie}, language = {de} } @article{WegertVokuhZiegleretal.2017, author = {Wegert, Jenny and Vokuh, Christian and Ziegler, Barbara and Ernestus, Karen and Leuschner, Ivo and Furtw{\"a}ngler, Rhoikos and Graf, Norbert and Gessler, Manfred}, title = {TP53 alterations in Wilms tumour represent progression events with strong intratumour heterogeneity that are closely linked but not limited to anaplasia}, series = {The Journal of Pathology: Clinical Research}, volume = {3}, journal = {The Journal of Pathology: Clinical Research}, doi = {10.1002/cjp2.77}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158302}, pages = {234-248}, year = {2017}, abstract = {TP53 mutations have been associated with anaplasia in Wilms tumour, which conveys a high risk for relapse and fatal outcome. Nevertheless, TP53 alterations have been reported in no more than 60\% of anaplastic tumours, and recent data have suggested their presence in tumours that do not fulfil the criteria for anaplasia, questioning the clinical utility of TP53 analysis. Therefore, we characterized the TP53 status in 84 fatal cases of Wilms tumour, irrespective of histological subtype. We identified TP53 alterations in at least 90\% of fatal cases of anaplastic Wilms tumour, and even more when diffuse anaplasia was present, indicating a very strong if not absolute coupling between anaplasia and deregulation of p53 function. Unfortunately, TP53 mutations do not provide additional predictive value in anaplastic tumours since the same mutation rate was found in a cohort of non-fatal anaplastic tumours. When classified according to tumour stage, patients with stage I diffuse anaplastic tumours still had a high chance of survival (87\%), but this rate dropped to 26\% for stages II-IV. Thus, volume of anaplasia or possible spread may turn out to be critical parameters. Importantly, among non-anaplastic fatal tumours, 26\% had TP53 alterations, indicating that TP53 screening may identify additional cases at risk. Several of these non-anaplastic tumours fulfilled some criteria for anaplasia, for example nuclear unrest, suggesting that such partial phenotypes should be under special scrutiny to enhance detection of high-risk tumours via TP53 screening. A major drawback is that these alterations are secondary changes that occur only later in tumour development, leading to striking intratumour heterogeneity that requires multiple biopsies and analysis guided by histological criteria. In conclusion, we found a very close correlation between histological signs of anaplasia and TP53 alterations. The latter may precede development of anaplasia and thereby provide diagnostic value pointing towards aggressive disease.}, language = {en} } @article{KaltdorfSchulzeHelmprobstetal.2017, author = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian}, title = {Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms}, series = {PLoS Computational Biology}, volume = {13}, journal = {PLoS Computational Biology}, number = {1}, doi = {10.1371/journal.pcbi.1005317}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172112}, year = {2017}, abstract = {Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.}, language = {en} } @article{LiuChenGaoetal.2017, author = {Liu, Han and Chen, Chunhai and Gao, Zexia and Min, Jiumeng and Gu, Yongming and Jian, Jianbo and Jiang, Xiewu and Cai, Huimin and Ebersberger, Ingo and Xu, Meng and Zhang, Xinhui and Chen, Jianwei and Luo, Wei and Chen, Boxiang and Chen, Junhui and Liu, Hong and Li, Jiang and Lai, Ruifang and Bai, Mingzhou and Wei, Jin and Yi, Shaokui and Wang, Huanling and Cao, Xiaojuan and Zhou, Xiaoyun and Zhao, Yuhua and Wei, Kaijian and Yang, Ruibin and Liu, Bingnan and Zhao, Shancen and Fang, Xiaodong and Schartl, Manfred and Qian, Xueqiao and Wang, Weimin}, title = {The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet}, series = {GigaScience}, volume = {6}, journal = {GigaScience}, number = {7}, doi = {10.1093/gigascience/gix039}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170844}, year = {2017}, abstract = {The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses, we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores. As a valuable resource for the improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation.}, language = {en} } @article{SeherLaglerStuehmeretal.2017, author = {Seher, Axel and Lagler, Charlotte and St{\"u}hmer, Thorsten and M{\"u}ller-Richter, Urs Dietmar Achim and K{\"u}bler, Alexander Christian and Sebald, Walter and M{\"u}ller, Thomas Dieter and Nickel, Joachim}, title = {Utilizing BMP-2 muteins for treatment of multiple myeloma}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {5}, doi = {10.1371/journal.pone.0174884}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158144}, pages = {e0174884}, year = {2017}, abstract = {Multiple myeloma (MM) represents a haematological cancer characterized by the pathological hyper proliferation of antibody-producing B-lymphocytes. Patients typically suffer from kidney malfunction and skeletal disorders. In the context of MM, the transforming growth factor β (TGFβ) member Activin A was recently identified as a promoter of both accompanying symptoms. Because studies have shown that bone morphogenetic protein (BMP)-2-mediated activities are counteracted by Activin A, we analysed whether BMP2, which also binds to the Activin A receptors ActRII and ActRIIB but activates the alternative SMAD-1/5/8 pathway, can be used to antagonize Activin A activities, such as in the context of MM. Therefore three BMP2 derivatives were generated with modified binding activities for the type II (ActRIIB) and/or type I receptor (BMPRIA) showing either increased or decreased BMP2 activity. In the context of MM these BMP2 muteins show two functionalities since they act as a) an anti-proliferative/apoptotic agent against neoplastic B-cells, b) as a bone-formation promoting growth factor. The molecular basis of both activities was shown in two different cellular models to clearly rely on the properties of the investigated BMP2 muteins to compete for the binding of Activin A to the Activin type II receptors. The experimental outcome suggests new therapeutic strategies using BMP2 variants in the treatment of MM-related pathologies.}, language = {en} } @article{KleinHesslingMuhammadKleinetal.2017, author = {Klein-Hessling, Stefan and Muhammad, Khalid and Klein, Matthias and Pusch, Tobias and Rudolf, Ronald and Fl{\"o}ter, Jessica and Qureischi, Musga and Beilhack, Andreas and Vaeth, Martin and Kummerow, Carsten and Backes, Christian and Schoppmeyer, Rouven and Hahn, Ulrike and Hoth, Markus and Bopp, Tobias and Berberich-Siebelt, Friederike and Patra, Amiya and Avots, Andris and M{\"u}ller, Nora and Schulze, Almut and Serfling, Edgar}, title = {NFATc1 controls the cytotoxicity of CD8\(^{+}\) T cells}, series = {Nature Communications}, volume = {8}, journal = {Nature Communications}, number = {511}, doi = {10.1038/s41467-017-00612-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170353}, year = {2017}, abstract = {Cytotoxic T lymphocytes are effector CD8\(^{+}\) T cells that eradicate infected and malignant cells. Here we show that the transcription factor NFATc1 controls the cytotoxicity of mouse cytotoxic T lymphocytes. Activation of Nfatc1\(^{-/-}\) cytotoxic T lymphocytes showed a defective cytoskeleton organization and recruitment of cytosolic organelles to immunological synapses. These cells have reduced cytotoxicity against tumor cells, and mice with NFATc1-deficient T cells are defective in controlling Listeria infection. Transcriptome analysis shows diminished RNA levels of numerous genes in Nfatc1\(^{-/-}\) CD8\(^{+}\) T cells, including Tbx21, Gzmb and genes encoding cytokines and chemokines, and genes controlling glycolysis. Nfatc1\(^{-/-}\), but not Nfatc2\(^{-/-}\) CD8\(^{+}\) T cells have an impaired metabolic switch to glycolysis, which can be restored by IL-2. Genome-wide ChIP-seq shows that NFATc1 binds many genes that control cytotoxic T lymphocyte activity. Together these data indicate that NFATc1 is an important regulator of cytotoxic T lymphocyte effector functions.}, language = {en} } @article{CosteaCoelhoSunagawaetal.2017, author = {Costea, Paul I. and Coelho, Louis Pedro and Sunagawa, Shinichi and Munch, Robin and Huerta-Cepas, Jaime and Forslund, Kristoffer and Hildebrand, Falk and Kushugulova, Almagul and Zeller, Georg and Bork, Peer}, title = {Subspecies in the global human gut microbiome}, series = {Molecular Systems Biology}, volume = {13}, journal = {Molecular Systems Biology}, number = {12}, doi = {10.15252/msb.20177589}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172674}, year = {2017}, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72\% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, language = {en} } @article{MendeLetunicHuertaCepasetal.2017, author = {Mende, Daniel R. and Letunic, Ivica and Huerta-Cepas, Jaime and Li, Simone S. and Forslund, Kristoffer and Sunagawa, Shinichi and Bork, Peer}, title = {proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {D1}, doi = {10.1093/nar/gkw989}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171987}, pages = {D529-D534}, year = {2017}, abstract = {The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de.}, language = {en} } @article{WuPonsGoudetetal.2017, author = {Wu, Yu and Pons, Val{\´e}rie and Goudet, Am{\´e}lie and Panigai, Laetitia and Fischer, Annette and Herweg, Jo-Ana and Kali, Sabrina and Davey, Robert A. and Laporte, J{\´e}r{\^o}me and Bouclier, C{\´e}line and Yousfi, Rahima and Aubenque, C{\´e}line and Merer, Goulven and Gobbo, Emilie and Lopez, Roman and Gillet, Cynthia and Cojean, Sandrine and Popoff, Michel R. and Clayette, Pascal and Le Grand, Roger and Boulogne, Claire and Tordo, No{\"e}l and Lemichez, Emmanuel and Loiseau, Philippe M. and Rudel, Thomas and Sauvaire, Didier and Cintrat, Jean-Christophe and Gillet, Daniel and Barbier, Julien}, title = {ABMA, a small molecule that inhibits intracellular toxins and pathogens by interfering with late endosomal compartments}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, doi = {10.1038/s41598-017-15466-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173170}, year = {2017}, abstract = {Intracellular pathogenic microorganisms and toxins exploit host cell mechanisms to enter, exert their deleterious effects as well as hijack host nutrition for their development. A potential approach to treat multiple pathogen infections and that should not induce drug resistance is the use of small molecules that target host components. We identifed the compound 1-adamantyl (5-bromo-2-methoxybenzyl) amine (ABMA) from a cell-based high throughput screening for its capacity to protect human cells and mice against ricin toxin without toxicity. This compound efciently protects cells against various toxins and pathogens including viruses, intracellular bacteria and parasite. ABMA provokes Rab7-positive late endosomal compartment accumulation in mammalian cells without affecting other organelles (early endosomes, lysosomes, the Golgi apparatus, the endoplasmic reticulum or the nucleus). As the mechanism of action of ABMA is restricted to host-endosomal compartments, it reduces cell infection by pathogens that depend on this pathway to invade cells. ABMA may represent a novel class of broad-spectrum compounds with therapeutic potential against diverse severe infectious diseases.}, language = {en} } @article{KasaragodMidekessaSridharetal.2017, author = {Kasaragod, Prasad and Midekessa, Getnet B. and Sridhar, Shruthi and Schmitz, Werner and Kiema, Tiila-Riikka and Hiltunen, Jukka K. and Wierenga, Rik K.}, title = {Structural enzymology comparisons of multifunctional enzyme, type-1 (MFE1): the flexibility of its dehydrogenase part}, series = {FEBS Open Bio}, volume = {7}, journal = {FEBS Open Bio}, number = {12}, doi = {10.1002/2211-5463.12337}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172732}, pages = {1830-1842}, year = {2017}, abstract = {Multifunctional enzyme, type-1 (MFE1) is a monomeric enzyme with a 2E-enoyl-CoA hydratase and a 3S-hydroxyacyl-CoA dehydrogenase (HAD) active site. Enzyme kinetic data of rat peroxisomal MFE1 show that the catalytic efficiencies for converting the short-chain substrate 2E-butenoyl-CoA into acetoacetyl-CoA are much lower when compared with those of the homologous monofunctional enzymes. The mode of binding of acetoacetyl-CoA (to the hydratase active site) and the very similar mode of binding of NAD\(^+\) and NADH (to the HAD part) are described and compared with those of their monofunctional counterparts. Structural comparisons suggest that the conformational flexibility of the HAD and hydratase parts of MFE1 are correlated. The possible importance of the conformational flexibility of MFE1 for its biocatalytic properties is discussed.}, language = {en} } @article{TemmeFriebeSchmidtetal.2017, author = {Temme, Sebastian and Friebe, Daniela and Schmidt, Timo and Poschmann, Gereon and Hesse, Julia and Steckel, Bodo and St{\"u}hler, Kai and Kunz, Meik and Dandekar, Thomas and Ding, Zhaoping and Akhyari, Payam and Lichtenberg, Artur and Schrader, J{\"u}rgen}, title = {Genetic profiling and surface proteome analysis of human atrial stromal cells and rat ventricular epicardium-derived cells reveals novel insights into their cardiogenic potential}, series = {Stem Cell Research}, volume = {25}, journal = {Stem Cell Research}, doi = {10.1016/j.scr.2017.11.006}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172716}, pages = {183-190}, year = {2017}, abstract = {Epicardium-derived cells (EPDC) and atrial stromal cells (ASC) display cardio-regenerative potential, but the molecular details are still unexplored. Signals which induce activation, migration and differentiation of these cells are largely unknown. Here we have isolated rat ventricular EPDC and rat/human ASC and performed genetic and proteomic profiling. EPDC and ASC expressed epicardial/mesenchymal markers (WT-1, Tbx18, CD73,CD90, CD44, CD105), cardiac markers (Gata4, Tbx5, troponin T) and also contained phosphocreatine. We used cell surface biotinylation to isolate plasma membrane proteins of rEPDC and hASC, Nano-liquid chromatography with subsequent mass spectrometry and bioinformatics analysis identified 396 rat and 239 human plasma membrane proteins with 149 overlapping proteins. Functional GO-term analysis revealed several significantly enriched categories related to extracellular matrix (ECM), cell migration/differentiation, immunology or angiogenesis. We identified receptors for ephrin and growth factors (IGF, PDGF, EGF, anthrax toxin) known to be involved in cardiac repair and regeneration. Functional category enrichment identified clusters around integrins, PI3K/Akt-signaling and various cardiomyopathies. Our study indicates that EPDC and ASC have a similar molecular phenotype related to cardiac healing/regeneration. The cell surface proteome repository will help to further unravel the molecular details of their cardio-regenerative potential and their role in cardiac diseases.}, language = {en} } @article{FereroRiveroWaeldchenetal.2017, author = {Ferero, Andrea and Rivero, Olga and W{\"a}ldchen, Sina and Ku, Hsing-Ping and Kiser, Dominik P. and G{\"a}rtner, Yvonne and Pennington, Laura S. and Waider, Jonas and Gaspar, Patricia and Jansch, Charline and Edenhofer, Frank and Resink, Th{\´e}r{\`e}se J. and Blum, Robert and Sauer, Markus and Lesch, Klaus-Peter}, title = {Cadherin-13 Deficiency Increases Dorsal Raphe 5-HT Neuron Density and Prefrontal Cortex Innervation in the Mouse Brain}, series = {Frontiers in Cellular Neuroscience}, volume = {11}, journal = {Frontiers in Cellular Neuroscience}, number = {307}, doi = {10.3389/fncel.2017.00307}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170313}, year = {2017}, abstract = {Background: During early prenatal stages of brain development, serotonin (5-HT)-specific neurons migrate through somal translocation to form the raphe nuclei and subsequently begin to project to their target regions. The rostral cluster of cells, comprising the median and dorsal raphe (DR), innervates anterior regions of the brain, including the prefrontal cortex. Differential analysis of the mouse 5-HT system transcriptome identified enrichment of cell adhesion molecules in 5-HT neurons of the DR. One of these molecules, cadherin-13 (Cdh13) has been shown to play a role in cell migration, axon pathfinding, and synaptogenesis. This study aimed to investigate the contribution of Cdh13 to the development of the murine brain 5-HT system. Methods: For detection of Cdh13 and components of the 5-HT system at different embryonic developmental stages of the mouse brain, we employed immunofluorescence protocols and imaging techniques, including epifluorescence, confocal and structured illumination microscopy. The consequence of CDH13 loss-of-function mutations on brain 5-HT system development was explored in a mouse model of Cdh13 deficiency. Results: Our data show that in murine embryonic brain Cdh13 is strongly expressed on 5-HT specific neurons of the DR and in radial glial cells (RGCs), which are critically involved in regulation of neuronal migration. We observed that 5-HT neurons are intertwined with these RGCs, suggesting that these neurons undergo RGC-guided migration. Cdh13 is present at points of intersection between these two cell types. Compared to wildtype controls, Cdh13-deficient mice display increased cell densities in the DR at embryonic stages E13.5, E17.5, and adulthood, and higher serotonergic innervation of the prefrontal cortex at E17.5. Conclusion: Our findings provide evidence for a role of CDH13 in the development of the serotonergic system in early embryonic stages. Specifically, we indicate that Cdh13 deficiency affects the cell density of the developing DR and the posterior innervation of the prefrontal cortex (PFC), and therefore might be involved in the migration, axonal outgrowth and terminal target finding of DR 5-HT neurons. Dysregulation of CDH13 expression may thus contribute to alterations in this system of neurotransmission, impacting cognitive function, which is frequently impaired in neurodevelopmental disorders including attention-deficit/hyperactivity and autism spectrum disorders.}, language = {en} } @article{AmpattuHagmannLiangetal.2017, author = {Ampattu, Biju Joseph and Hagmann, Laura and Liang, Chunguang and Dittrich, Marcus and Schl{\"u}ter, Andreas and Blom, Jochen and Krol, Elizaveta and Goesmann, Alexander and Becker, Anke and Dandekar, Thomas and M{\"u}ller, Tobias and Schoen, Christoph}, title = {Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence}, series = {BMC Genomics}, volume = {18}, journal = {BMC Genomics}, number = {282}, doi = {10.1186/s12864-017-3616-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157534}, year = {2017}, abstract = {Background: Commensal bacteria like Neisseria meningitidis sometimes cause serious disease. However, genomic comparison of hyperinvasive and apathogenic lineages did not reveal unambiguous hints towards indispensable virulence factors. Here, in a systems biological approach we compared gene expression of the invasive strain MC58 and the carriage strain α522 under different ex vivo conditions mimicking commensal and virulence compartments to assess the strain-specific impact of gene regulation on meningococcal virulence. Results: Despite indistinguishable ex vivo phenotypes, both strains differed in the expression of over 500 genes under infection mimicking conditions. These differences comprised in particular metabolic and information processing genes as well as genes known to be involved in host-damage such as the nitrite reductase and numerous LOS biosynthesis genes. A model based analysis of the transcriptomic differences in human blood suggested ensuing metabolic flux differences in energy, glutamine and cysteine metabolic pathways along with differences in the activation of the stringent response in both strains. In support of the computational findings, experimental analyses revealed differences in cysteine and glutamine auxotrophy in both strains as well as a strain and condition dependent essentiality of the (p)ppGpp synthetase gene relA and of a short non-coding AT-rich repeat element in its promoter region. Conclusions: Our data suggest that meningococcal virulence is linked to transcriptional buffering of cryptic genetic variation in metabolic genes including global stress responses. They further highlight the role of regulatory elements for bacterial virulence and the limitations of model strain approaches when studying such genetically diverse species as N. meningitidis.}, language = {en} } @article{KlughammerDittrichBlometal.2017, author = {Klughammer, Johanna and Dittrich, Marcus and Blom, Jochen and Mitesser, Vera and Vogel, Ulrich and Frosch, Matthias and Goesmann, Alexander and M{\"u}ller, Tobias and Schoen, Christoph}, title = {Comparative genome sequencing reveals within-host genetic changes in Neisseria meningitidis during invasive disease}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {1}, doi = {10.1371/journal.pone.0169892}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159547}, pages = {e0169892}, year = {2017}, abstract = {Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation. In line with the hypothesis that phase variation evolved as an adaptation to colonize diverse hosts, computational comparisons of all 27 to date completely sequenced and annotated meningococcal genomes retrieved from public databases showed that contingency genes are indeed enriched for genes involved in host interactions. To assess within-host genetic changes in meningococci, we further used ultra-deep whole-genome sequencing of throat-blood strain pairs isolated from four patients suffering from invasive meningococcal disease. We detected up to three mutations per strain pair, affecting predominantly contingency genes involved in type IV pilus biogenesis. However, there was not a single (set) of mutation(s) that could invariably be found in all four pairs of strains. Phenotypic assays further showed that these genetic changes were generally not associated with increased serum resistance, higher fitness in human blood ex vivo or differences in the interaction with human epithelial and endothelial cells in vitro. In conclusion, we hypothesize that virulence of meningococci results from accidental emergence of invasive variants during carriage and without within host evolution of invasive phenotypes during disease progression in vivo.}, language = {en} } @phdthesis{Faist2017, author = {Faist, Hanna}, title = {Bedeutung und Charakterisierung der bakteriellen Flora in Vitis vinifera mit und ohne Wurzelhalsgallen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154359}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Am Rebstock werden in der Natur von Agrobacterium vitis, dem Ausl{\"o}ser Wurzelhalsgallenerkrankung, charakteristische Wurzelhalsgallentumore induziert. Virulente Vertreter der Gattung der Agrobacteria schleusen bakterielle DNA in das pflanzliche Genom ein, wodurch die Pflanze Tumore produziert. Die Wurzelhalsgallenerkrankung wird seit einem Jahrhundert als ein Beispiel der Pflanzen-Pathogen-Interaktion untersucht. Die Rolle der bakteriellen Flora im Zusammenhang mit der Wurzelhalsgallenerkrankung beim Rebstock wurde bisher kaum betrachtet. Um dieser Frage nachzugehen, habe ich die endophytische mikrobielle Zusammensetzung von Rebst{\"o}cken mit und ohne Wurzelhalsgalle analysiert. Es werden Proben von drei Zeitpunkten einer Wachstumsperiode (Fr{\"u}hling, Sommer und Herbst) und von den Organen der Rebst{\"o}cke (Wurzeln, Pfropfstelle und einj{\"a}hrige Triebe) sowie dem Boden in einer Weinanlage bei Himmelstadt in Unterfranken genommen. Die Bakterienflora dieser Umweltproben wird mit kultivierungsabh{\"a}ngigen (Isolierung von Bakterien) und kultivierungsunabh{\"a}ngigen (Hochdurchsatzsequenzierungen) Methoden untersucht. Zudem werden i) die Virulenz der verschiedenen Agrobacterium-Isolate in Tumorassays bestimmt, ii) synthetische Bakteriengemeinschaften von in vitro kultivierten Weinpfl{\"a}nzchen mit Wurzelhalsgallen analysiert, iii) die Genome von einem virulenten und einem nicht-virulenten Agrobacteria-Isolat aus der Wurzelhalsgalle verglichen, iv) erste Interaktionsstudien auf festen N{\"a}hrmedien durchgef{\"u}hrt und v) virulente Agrobacteria mittels bildgebender Fluoreszenz-Lebenszeit-Mikroskopie (FLIM) in Wurzelhalsgallen lokalisiert. Die Rebst{\"o}cke dieser Studie haben eine organspezifische Bakterienflora, die innerhalb einer Wachstumsperiode variiert. Nur die Bakterienflora der Pfropfstelle (mit oder ohne Wurzelhalsgalle) aber nicht die des Bodens, der Wurzeln, und der einj{\"a}hrigen Triebe unterscheidet sich strukturell zwischen gesunden und erkrankten Rebst{\"o}cken. Mikroskopisch konnten virulente Agrobacteria punktuell in Interzellularen, sklerenchymatischen Geweben und assoziiert mit Leitgef{\"a}ßen nachgewiesen werden. Dadurch ist ausreichend Lebensraum vorhanden, der zus{\"a}tzlich von tumorspezifischen Bakterien besiedelt werden kann. Im Gegensatz zur gesunden Pfropfstelle ist in der Wurzelhalsgalle eine saisonal stabile Kernmikroflora, bestehend aus Vertreter von A. vitis, Pseudomonas, Enterobacteriaceae, Agrobacterium tumefaciens, Gammaproteobacteria und Burkholderiales, vorhanden. Diese Bakterien werden {\"u}berwiegend aus dem Boden rekrutiert und profitieren von der N{\"a}hrstoffsituation in der Wurzelhalsgalle. Wurzelhalsgallen enthalten Opine, die nur von der transformierten Pflanzenzelle produziert werden. Interessanterweise hat in dieser Arbeit ein Agrobacterium-Isolat Gene, die zum Opinkatabolismus beitragen und ein Pseudomonas-Isolat kann Opine als einzige Kohlenstoffquelle nutzen. Trotzdem sind beide Isolate weder virulent noch verdr{\"a}ngen sie die virulenten A. vitis, die ebenso Opine nutzen, aus der Wurzelhalsgalle. In synthetischen Bakteriengemeinschaften an in vitro kultivierten Weinpfl{\"a}nzchen konnte gezeigt werden, dass diese und weitere tumorspezifischen Bakterien, neben A. vitis, nicht essentiell zur Entstehung der Wurzelhalsgalle n{\"o}tig sind aber unterschiedliche Funktionen in der Wurzelhalsgalle {\"u}bernehmen. Ein Serratia-Isolat hemmt das Wachstum von A. vitis auf festen N{\"a}hrmedium, andere f{\"o}rdern oder hemmen das Wachstum der Wurzelhalsgalle. Nach Studien in der Literatur erh{\"o}hen weitere Bakterien die Resistenz des Rebstocks gegen{\"u}ber biotischem und abiotischem Stress. Zusammengefasst identifizierten und isolierte ich in dieser Studie unter 150 unterschiedlichen Bakterien in der Wurzelhalsgalle jene Bakterien, die neben A. vitis von der neuen {\"o}kologischen Nische profitieren und somit wahrscheinlich Opportunisten mit unterschiedlichen Funktionen sind. In Folge von multiplen Interaktionen in der Wurzelhalsgalle entsteht ein {\"o}kologisches Gleichgewicht zwischen den opportunistischen Bakterien, der Wurzelhalsgalle und dem Rebstock, das den Fortbestand des Rebstocks mit Wurzelhalsgalle erm{\"o}glicht.}, subject = {Wurzelhalsgalle}, language = {de} } @article{MitjansBegemannJuetal.2017, author = {Mitjans, M. and Begemann, M. and Ju, A. and Dere, E. and W{\"u}stefeld, L. and Hofer, S. and Hassouna, I. and Balkenhol, J. and Oliveira, B. and Van der Auwera, S. and Tammer, R. and Hammerschmidt, K. and V{\"o}lzke, H. and Homuth, G. and Cecconi, F. and Chowdhury, K. and Grabe, H. and Frahm, J. and Boretius, S. and Dandekar, T. and Ehrenreich, H.}, title = {Sexual dimorphism of \(AMBRA1\)-related autistic features in human and mouse}, series = {Translational Psychiatry}, volume = {2017}, journal = {Translational Psychiatry}, number = {7}, doi = {10.1038/tp.2017.213}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173782}, year = {2017}, abstract = {\(Ambra1\) is linked to autophagy and neurodevelopment. Heterozygous \(Ambra1\) deficiency induces autism-like behavior in a sexually dimorphic manner. Extraordinarily, autistic features are seen in female mice only, combined with stronger Ambra1 protein reduction in brain compared to males. However, significance of \(AMBRA1\) for autistic phenotypes in humans and, apart from behavior, for other autism-typical features, namely early brain enlargement or increased seizure propensity, has remained unexplored. Here we show in two independent human samples that a single normal \(AMBRA1\) genotype, the intronic SNP rs3802890-AA, is associated with autistic features in women, who also display lower \(AMBRA1\) mRNA expression in peripheral blood mononuclear cells relative to female GG carriers. Located within a non-coding RNA, likely relevant for mRNA and protein interaction, rs3802890 (A versus G allele) may affect its stability through modification of folding, as predicted by \(in\) \(silico\) analysis. Searching for further autism-relevant characteristics in \(Ambra1^{+/-}\) mice, we observe reduced interest of female but not male mutants regarding pheromone signals of the respective other gender in the social intellicage set-up. Moreover, altered pentylentetrazol-induced seizure propensity, an \(in\) \(vivo\) readout of neuronal excitation-inhibition dysbalance, becomes obvious exclusively in female mutants. Magnetic resonance imaging reveals mild prepubertal brain enlargement in both genders, uncoupling enhanced brain dimensions from the primarily female expression of all other autistic phenotypes investigated here. These data support a role of \(AMBRA1/Ambra1\) partial loss-of-function genotypes for female autistic traits. Moreover, they suggest \(Ambra1\) heterozygous mice as a novel multifaceted and construct-valid genetic mouse model for female autism.}, language = {en} } @article{BeerJoschinskiSastreetal.2017, author = {Beer, Katharina and Joschinski, Jens and Sastre, Alazne Arrazola and Krauss, Jochen and Helfrich-F{\"o}rster, Charlotte}, title = {A damping circadian clock drives weak oscillations in metabolism and locomotor activity of aphids (Acyrthosiphon pisum)}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, number = {14906}, doi = {10.1038/s41598-017-15014-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170020}, year = {2017}, abstract = {Timing seasonal events, like reproduction or diapause, is crucial for the survival of many species. Global change causes phenologies worldwide to shift, which requires a mechanistic explanation of seasonal time measurement. Day length (photoperiod) is a reliable indicator of winter arrival, but it remains unclear how exactly species measure day length. A reference for time of day could be provided by a circadian clock, by an hourglass clock, or, as some newer models suggest, by a damped circadian clock. However, damping of clock outputs has so far been rarely observed. To study putative clock outputs of Acyrthosiphon pisum aphids, we raised individual nymphs on coloured artificial diet, and measured rhythms in metabolic activity in light-dark illumination cycles of 16:08 hours (LD) and constant conditions (DD). In addition, we kept individuals in a novel monitoring setup and measured locomotor activity. We found that A. pisum is day-active in LD, potentially with a bimodal distribution. In constant darkness rhythmicity of locomotor behaviour persisted in some individuals, but patterns were mostly complex with several predominant periods. Metabolic activity, on the other hand, damped quickly. A damped circadian clock, potentially driven by multiple oscillator populations, is the most likely explanation of our results.}, language = {en} } @article{ArenasRoces2017, author = {Arenas, Andr{\´e}s and Roces, Flavio}, title = {Avoidance of plants unsuitable for the symbiotic fungus in leaf-cutting ants: Learning can take place entirely at the colony dump}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {3}, doi = {10.1371/journal.pone.0171388}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157559}, pages = {e0171388}, year = {2017}, abstract = {Plants initially accepted by foraging leaf-cutting ants are later avoided if they prove unsuitable for their symbiotic fungus. Plant avoidance is mediated by the waste produced in the fungus garden soon after the incorporation of the unsuitable leaves, as foragers can learn plant odors and cues from the damaged fungus that are both present in the recently produced waste particles. We asked whether avoidance learning of plants unsuitable for the symbiotic fungus can take place entirely at the colony dump. In order to investigate whether cues available in the waste chamber induce plant avoidance in na{\"i}ve subcolonies, we exchanged the waste produced by subcolonies fed either fungicide-treated privet leaves or untreated leaves and measured the acceptance of untreated privet leaves before and after the exchange of waste. Second, we evaluated whether foragers could perceive the avoidance cues directly at the dump by quantifying the visits of labeled foragers to the waste chamber. Finally, we asked whether foragers learn to specifically avoid untreated leaves of a plant after a confinement over 3 hours in the dump of subcolonies that were previously fed fungicide-treated leaves of that species. After the exchange of the waste chambers, workers from subcolonies that had access to waste from fungicide-treated privet leaves learned to avoid that plant. One-third of the labeled foragers visited the dump. Furthermore, na{\"i}ve foragers learned to avoid a specific, previously unsuitable plant if exposed solely to cues of the dump during confinement. We suggest that cues at the dump enable foragers to predict the unsuitable effects of plants even if they had never been experienced in the fungus garden.}, language = {en} } @article{KadochovaFrouzRoces2017, author = {Kadochov{\´a}, Štěp{\´a}nka and Frouz, Jan and Roces, Flavio}, title = {Sun basking in red wood ants Formica polyctena (Hymenoptera, Formicidae): Individual behaviour and temperature-dependent respiration rates}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {1}, doi = {10.1371/journal.pone.0170570}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171936}, year = {2017}, abstract = {In early spring, red wood ants Formica polyctena are often observed clustering on the nest surface in large numbers basking in the sun. It has been hypothesized that sun-basking behaviour may contribute to nest heating because of both heat carriage into the nest by sunbasking workers, and catabolic heat production from the mobilization of the workers' lipid reserves. We investigated sun-basking behaviour in laboratory colonies of F. polyctena exposed to an artificial heat source. Observations on identified individuals revealed that not all ants bask in the sun. Sun-basking and non-sun-basking workers did not differ in body size nor in respiration rates. The number of sun-basking ants and the number of their visits to the hot spot depended on the temperature of both the air and the hot spot. To investigate whether sun basking leads to a physiological activation linked with increased lipolysis, we measured respiration rates of individual workers as a function of temperature, and compared respiration rates of sun-basking workers before and two days after they were allowed to expose themselves to a heat source over 10 days, at self-determined intervals. As expected for ectothermic animals, respiration rates increased with increasing temperatures in the range 5 to 35˚C. However, the respiration rates of sun-basking workers measured two days after a long-term exposure to the heat source were similar to those before sun basking, providing no evidence for a sustained increase of the basal metabolic rates after prolonged sun basking. Based on our measurements, we argue that self-heating of the nest mound in early spring has therefore to rely on alternative heat sources, and speculate that physical transport of heat in the ant bodies may have a significant effect.}, language = {en} } @article{SteinCoulibalyStenchlyetal.2017, author = {Stein, Katharina and Coulibaly, Drissa and Stenchly, Kathrin and Goetze, Dethardt and Porembski, Stefan and Lindner, Andr{\´e} and Konat{\´e}, Souleymane and Linsenmair, Eduard K.}, title = {Bee pollination increases yield quantity and quality of cash crops in Burkina Faso, West Africa}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, number = {17691}, doi = {10.1038/s41598-017-17970-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169914}, year = {2017}, abstract = {Mutualistic biotic interactions as among flowering plants and their animal pollinators are a key component of biodiversity. Pollination, especially by insects, is a key element in ecosystem functioning, and hence constitutes an ecosystem service of global importance. Not only sexual reproduction of plants is ensured, but also yields are stabilized and genetic variability of crops is maintained, counteracting inbreeding depression and facilitating system resilience. While experiencing rapid environmental change, there is an increased demand for food and income security, especially in sub-Saharan communities, which are highly dependent on small scale agriculture. By combining exclusion experiments, pollinator surveys and field manipulations, this study for the first time quantifies the contribution of bee pollinators to smallholders' production of the major cash crops, cotton and sesame, in Burkina Faso. Pollination by honeybees and wild bees significantly increased yield quantity and quality on average up to 62\%, while exclusion of pollinators caused an average yield gap of 37\% in cotton and 59\% in sesame. Self-pollination revealed inbreeding depression effects on fruit set and low germination rates in the F1-generation. Our results highlight potential negative consequences of any pollinator decline, provoking risks to agriculture and compromising crop yields in sub-Saharan West Africa.}, language = {en} } @phdthesis{Kuen2017, author = {Kuen, Janina}, title = {Influence of 3D tumor cell/fibroblast co-culture on monocyte differentiation and tumor progression in pancreatic cancer}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156226}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Pancreatic cancer (PC) remains one of the most challenging solid tumors to treat with a high unmet medical need as patients poorly respond to standard-of-care-therapies. Prominent desmoplastic reaction involving cancer-associated fibroblasts (CAFs) and the immune cells in the tumor microenvironment (TME) and their cross-talk play a significant role in tumor immune escape and progression. To identify the key cellular mechanisms induce an immunosuppressive tumor microenvironment, we established 3D co-culture model with pancreatic cancer cells, CAFs, monocyte as well as T cells. Using this model, we analysed the influence of tumor cells and fibroblasts on monocytes and their immune suppressive phenotype. Phenotypic characterization of the monocytes after 3D co-culture with tumor/fibroblast spheroids was performed by analysing the expression of defined cell surface markers and soluble factors. Functionality of these monocytes and their ability to influence T cell phenotype and proliferation was investigated. 3D co-culture of monocytes with pancreatic cancer cells and fibroblasts induced the production of immunosuppressive cytokines which are known to promote polarization of M2 like macrophages and myeloid derived suppressive cells (MDSCs). These co-culture spheroid polarized monocyte derived macrophages (MDMs) were poorly differentiated and had an M2 phenotype. The immunosuppressive function of these co-culture spheroids polarized MDMs was demonstrated by their ability to inhibit autologous CD4+ and CD8+ T cell activation and proliferation in vitro, which we could partially reverse by 3D co-culture spheroid treatment with therapeutic molecules that are able to re-activate spheroid polarized MDMs or block immune suppressive factors such as Arginase-I. In conclusion, we generated a physiologically relevant 3D co-culture model, which can be used as a promising tool to study complex cell-cell interactions between different cell types within the tumor microenvironment and to support drug screening and development. In future, research focused on better understanding of resistance mechanisms to existing cancer immunotherapies will help to develop new therapeutic strategies in order to combat cancer.}, subject = {monocyte}, language = {en} } @article{ScheinerEntlerBarronetal.2017, author = {Scheiner, Ricarda and Entler, Brian V. and Barron, Andrew B. and Scholl, Christina and Thamm, Markus}, title = {The Effects of Fat Body Tyramine Level on Gustatory Responsiveness of Honeybees (Apis mellifera) Differ between Behavioral Castes}, series = {Frontiers in Systems Neuroscience}, volume = {11}, journal = {Frontiers in Systems Neuroscience}, number = {55}, doi = {10.3389/fnsys.2017.00055}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157874}, year = {2017}, abstract = {Division of labor is a hallmark of social insects. In the honeybee (Apis mellifera) each sterile female worker performs a series of social tasks. The most drastic changes in behavior occur when a nurse bee, who takes care of the brood and the queen in the hive, transitions to foraging behavior. Foragers provision the colony with pollen, nectar or water. Nurse bees and foragers differ in numerous behaviors, including responsiveness to gustatory stimuli. Differences in gustatory responsiveness, in turn, might be involved in regulating division of labor through differential sensory response thresholds. Biogenic amines are important modulators of behavior. Tyramine and octopamine have been shown to increase gustatory responsiveness in honeybees when injected into the thorax, thereby possibly triggering social organization. So far, most of the experiments investigating the role of amines on gustatory responsiveness have focused on the brain. The potential role of the fat body in regulating sensory responsiveness and division of labor has large been neglected. We here investigated the role of the fat body in modulating gustatory responsiveness through tyramine signaling in different social roles of honeybees. We quantified levels of tyramine, tyramine receptor gene expression and the effect of elevating fat body tyramine titers on gustatory responsiveness in both nurse bees and foragers. Our data suggest that elevating the tyramine titer in the fat body pharmacologically increases gustatory responsiveness in foragers, but not in nurse bees. This differential effect of tyramine on gustatory responsiveness correlates with a higher natural gustatory responsiveness of foragers, with a higher tyramine receptor (Amtar1) mRNA expression in fat bodies of foragers and with lower baseline tyramine titers in fat bodies of foragers compared to those of nurse bees. We suggest that differential tyramine signaling in the fat body has an important role in the plasticity of division of labor through changing gustatory responsiveness.}, language = {en} } @article{LamazeOeztuerkColakFischeretal.2017, author = {Lamaze, Angelique and {\"O}zt{\"u}rk-{\c{C}}olak, Arzu and Fischer, Robin and Peschel, Nicolai and Koh, Kyunghee and Jepson, James E. C.}, title = {Regulation of sleep plasticity by a thermo-sensitive circuit in Drosophila}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, doi = {10.1038/srep40304}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-181146}, pages = {12}, year = {2017}, abstract = {Sleep is a highly conserved and essential behaviour in many species, including the fruit fly Drosophila melanogaster. In the wild, sensory signalling encoding environmental information must be integrated with sleep drive to ensure that sleep is not initiated during detrimental conditions. However, the molecular and circuit mechanisms by which sleep timing is modulated by the environment are unclear. Here we introduce a novel behavioural paradigm to study this issue. We show that in male fruit flies, onset of the daytime siesta is delayed by ambient temperatures above 29°C. We term this effect Prolonged Morning Wakefulness (PMW). We show that signalling through the TrpA1 thermo-sensor is required for PMW, and that TrpA1 specifically impacts siesta onset, but not night sleep onset, in response to elevated temperatures. We identify two critical TrpA1-expressing circuits and show that both contact DN1p clock neurons, the output of which is also required for PMW. Finally, we identify the circadian blue-light photoreceptor CRYPTOCHROME as a molecular regulator of PMW, and propose a model in which the Drosophila nervous system integrates information encoding temperature, light, and time to dynamically control when sleep is initiated. Our results provide a platform to investigate how environmental inputs co-ordinately regulate sleep plasticity.}, language = {en} } @article{RuppertFranzSaratisetal.2017, author = {Ruppert, Manuela and Franz, Mirjam and Saratis, Anastasios and Escarcena, Laura Velo and Hendrich, Oliver and Gooi, Li Ming and Schwenkert, Isabell and Klebes, Ansgar and Scholz, Henrike}, title = {Hangover links nuclear RNA signaling to cAMP regulation via the phosphodiesterase 4d ortholog dunce}, series = {Cell Reports}, volume = {18}, journal = {Cell Reports}, number = {2}, doi = {10.1016/j.celrep.2016.12.048}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171950}, pages = {533-544}, year = {2017}, abstract = {The hangover gene defines a cellular stress pathway that is required for rapid ethanol tolerance in Drosophila melanogaster. To understand how cellular stress changes neuronal function, we analyzed Hangover function on a cellular and neuronal level. We provide evidence that Hangover acts as a nuclear RNA binding protein and we identified the phosphodiesterase 4d ortholog dunce as a target RNA. We generated a transcript-specific dunce mutant that is impaired not only in ethanol tolerance but also in the cellular stress response. At the neuronal level, Dunce and Hangover are required in the same neuron pair to regulate experience-dependent motor output. Within these neurons, two cyclic AMP (cAMP)-dependent mechanisms balance the degree of tolerance. The balance is achieved by feedback regulation of Hangover and dunce transcript levels. This study provides insight into how nuclear Hangover/RNA signaling is linked to the cytoplasmic regulation of cAMP levels and results in neuronal adaptation and behavioral changes.}, language = {en} } @article{EwaldBartlDandekaretal.2017, author = {Ewald, Jan and Bartl, Martin and Dandekar, Thomas and Kaleta, Christoph}, title = {Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism}, series = {PLOS Computational Biology}, volume = {13}, journal = {PLOS Computational Biology}, number = {2}, doi = {10.1371/journal.pcbi.1005371}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-180870}, pages = {19}, year = {2017}, abstract = {A precise and rapid adjustment of fluxes through metabolic pathways is crucial for organisms to prevail in changing environmental conditions. Based on this reasoning, many guiding principles that govern the evolution of metabolic networks and their regulation have been uncovered. To this end, methods from dynamic optimization are ideally suited since they allow to uncover optimality principles behind the regulation of metabolic networks. We used dynamic optimization to investigate the influence of toxic intermediates in connection with the efficiency of enzymes on the regulation of a linear metabolic pathway. Our results predict that transcriptional regulation favors the control of highly efficient enzymes with less toxic upstream intermediates to reduce accumulation of toxic downstream intermediates. We show that the derived optimality principles hold by the analysis of the interplay between intermediate toxicity and pathway regulation in the metabolic pathways of over 5000 sequenced prokaryotes. Moreover, using the lipopolysaccharide biosynthesis in Escherichia coli as an example, we show how knowledge about the relation of regulation, kinetic efficiency and intermediate toxicity can be used to identify drug targets, which control endogenous toxic metabolites and prevent microbial growth. Beyond prokaryotes, we discuss the potential of our findings for the development of antifungal drugs.}, language = {en} } @article{WanzekSchwindtCapraetal.2017, author = {Wanzek, Katharina and Schwindt, Eike and Capra, John A. and Paeschke, Katrin}, title = {Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {13}, doi = {10.1093/nar/gkx467}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170577}, pages = {7796-7806}, year = {2017}, abstract = {The regulation of replication is essential to preserve genome integrity. Mms1 is part of the E3 ubiquitin ligase complex that is linked to replication fork progression. By identifying Mms1 binding sites genome-wide in Saccharomyces cerevisiae we connected Mms1 function to genome integrity and replication fork progression at particular G-rich motifs. This motif can form G-quadruplex (G4) structures in vitro. G4 are stable DNA structures that are known to impede replication fork progression. In the absence of Mms1, genome stability is at risk at these G-rich/G4 regions as demonstrated by gross chromosomal rearrangement assays. Mms1 binds throughout the cell cycle to these G-rich/G4 regions and supports the binding of Pif1 DNA helicase. Based on these data we propose a mechanistic model in which Mms1 binds to specific G-rich/G4 motif located on the lagging strand template for DNA replication and supports Pif1 function, DNA replication and genome integrity.}, language = {en} } @phdthesis{Iltzsche2017, author = {Iltzsche, Fabian}, title = {The Role of DREAM/MMB-mediated mitotic gene expression downstream of mutated K-Ras in lung cancer}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154108}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {The evolutionary conserved Myb-MuvB (MMB) multiprotein complex has an essential role in transcriptional activation of mitotic genes. MMB target genes as well as the MMB associated transcription factor B-Myb and FoxM1 are highly expressed in a range of different cancer types. The elevated expression of these genes correlates with an advanced tumor state and a poor prognosis. This suggests that MMB could contribute to tumorigenesis by mediating overexpression of mitotic genes. Although MMB has been extensively characterized biochemically, the requirement for MMB to tumorigenesis in vivo remains largely unknown and has not been tested directly so far. In this study, conditional knockout of the MMB core member Lin9 inhibits tumor formation in vivo in a mouse model of lung cancer driven by oncogenic K-Ras and loss of p53. The incomplete recombination observed within tumors points towards an enormous selection pressure against the complete loss of Lin9. RNA interference (RNAi)-mediated depletion of Lin9 or the MMB associated subunit B-Myb provides evidence that MMB is required for the expression of mitotic genes in lung cancer cells. Moreover, it was demonstrated that proliferation of lung cancer cells strongly depends on MMB. Furthermore, in this study, the relationship of MMB to the p53 tumor suppressor was investigated in a primary lung cancer cell line with restorable p53 function. Expression analysis revealed that mitotic genes are downregulated after p53 re-expression. Moreover, activation of p53 induces formation of the repressive DREAM complex and results in enrichment of DREAM at mitotic gene promoters. Conversely, MMB is displaced at these promoters. Based on these findings the following model is proposed: In p53-negative cells, mitogenic stimuli foster the switch from DREAM to MMB. Thus, mitotic genes are overexpressed and may promote chromosomal instability and tumorigenesis. This study provides evidence that MMB contributes to the upregulation of G2/M phase-specific genes in p53-negative cells and suggests that inhibition of MMB (or its target genes) might be a strategy for treatment of lung cancer.}, subject = {Nicht-kleinzelliges Bronchialkarzinom (NSCLC)}, language = {en} }