@article{SickelAnkenbrandGrimmeretal.2015,
  author    = {Sickel, Wiebke and Ankenbrand, Markus J. and Grimmer, Gudrun and Holzschuh, Andrea and H{\"a}rtel, Stephan and Lanzen, Jonathan and Steffan-Dewenter, Ingolf and Keller, Alexander},
  title     = {Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach},
  series = {BMC Ecology},
  volume    = {15},
  journal   = {BMC Ecology},
  number    = {20},
  doi       = {10.1186/s12898-015-0051-y},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125730},
  year      = {2015},
  abstract  = {Background Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing. Results We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that remedies these issues. It uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run. It does not require further adapter ligation steps after amplification. We applied this protocol to 384 pollen samples collected by solitary bees and sequenced all samples together on a single Illumina MiSeq v2 flow cell. According to rarefaction curves, 2,000-3,000 high quality reads per sample were sufficient to assess the complete diversity of 95\% of the samples. We were able to detect 650 different plant taxa in total, of which 95\% were classified at the species level. Together with the laboratory protocol, we also present an update of the reference database used by the classifier software, which increases the total number of covered global plant species included in the database from 37,403 to 72,325 (93\% increase). Conclusions This study thus offers improvements for the laboratory and bioinformatical workflow to existing approaches regarding data quantity and quality as well as processing effort and cost-effectiveness. Although only tested for pollen samples, it is furthermore applicable to other research questions requiring plant identification in mixed and challenging samples.},
  language  = {en}
}
@phdthesis{MeirgebRother2015,
  author    = {Meir [geb. Rother], Juliane},
  title     = {Influence of oncolytic vaccinia viruses on metastases of human and murine tumors},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-118530},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Cancer is one of the leading causes of death. 90\% of all deaths are caused by the effects of metastases. It is of major importance to successfully treat the primary tumor and metastases. Tumors and metastases often differ in their properties and therefore, treatment is not always successful. In contrast, those therapeutic agents can even promote formation and growth of metastases. Hence, it is indispensable to find treatment options for metastatic disease. One promising candidate represents the oncolytic virus therapy with vaccinia viruses. The aim of this work was to analyze two cell lines regarding their metastatic abilities and to investigate whether oncolytic vaccinia viruses are useful therapy options. The cell lines used were the human cervical cancer cell line C33A implanted into immune-compromised mice and the murine melanoma cell line B16F10, implanted into immune-competent mice. The initial point of the investigations was the observation of enlarged lumbar und renal lymph nodes in C33A tumor-bearing mice 35 days post implantation of C33A cells subcutaneously into immune-compromised nude mice. Subsequently, the presence of human cells in enlarged lymph nodes was demonstrated by RT-PCR. To facilitate the monitoring of cancer cell spreading, the gene encoding for RFP was inserted into the genome of C33A cells. In cell culture experiments, it was possible to demonstrate that this insertion did not negatively affect the susceptibility of the cells to virus infection, replication and virus-mediated cell lysis. The analysis of the metastatic process in a xenografted mouse model revealed the continuous progression of lumbar (LN) and renal (RN) lymph node metastasis after C33A-RFP tumor cell implantation. The lymph node volume and the amount of RFP-positive LNs and RNs was increasing from week to week in accordance with the gain of the primary tumor volume. Moreover, the metastatic spread of cancer cells in lymph vessels between lumbar and renal lymph nodes was visualized. Additionally, the haematogenous way of cancer cell migration was demonstrated by RFP positive cancer cells in blood vessels. The haematogenous route of spreading was confirmed by detecting micrometastases in lungs of tumor bearing mice. The next step was to investigate whether the recombinant oncolytic vaccinia virus GLV-1h68 is a suitable candidate to cure the primary tumor and metastases. Therefore, GLV-1h68 was systemically injected into C33A-RFP tumor bearing mice 21 days after tumor cell implantation. It was demonstrated that the volume of the primary tumor was drastically reduced, and the volume and the amount of RFP positive lumbar and renal lymph nodes were significantly decreasing compared to the untreated control group. Subsequently, this process was analyzed further by investigating the colonization pattern in the C33A-RFP model. It was shown that first the primary tumor was colonized with highest detectable virus levels, followed by LN and RN lymph nodes. Histological analyses revealed the proliferative status of tumor cells in the tumor and lymph nodes, the amount of different immune cell populations and the vascular permeability in primary tumors and lymph nodes having an influence on the colonization pattern of the virus. Whereby, the vascular permeability seems to have a crucial impact on the preferential colonization of tumors compared to lymph node metastases in this tumor model. C33A turned out to be a useful model to study the formation and therapy of metastases. However, a metastatic model in which the influence of the immune system on tumors and especially on tumor therapy can be analyzed would be preferable. Therefore, the aim of the second part was to establish a syngeneic metastatic mouse model. Accordingly, the murine melanoma cell line B16F10 was analyzed in immunocompetent mice. First, the highly attenuated GLV 1h68 virus was compared to its parental strain LIVP 1.1.1 concerning infection, replication and cell lysis efficacy in cell culture. LIVP 1.1.1 was more efficient than GLV-1h68 and was subsequently used for following mouse studies. Comparative studies were performed, comparing two different implantation sites of the tumor cells, subcutaneously and footpad, and two different mouse strains, FoxN1 nude and C57BL/6 mice. Implantation into the footpad led to a higher metastatic burden in lymph nodes compared to the subcutaneous implantation site. Finally, the model of choice was the implantation of B16F10 into the footpad of immune-competent C57BL/6 mice. Furthermore, it was inevitable to deliver the virus as efficient as possible to the tumor and metastases. Comparison of two different injection routes, intravenously and intratumorally, revealed, that the optimal injection route was intratumorally. In summary, the murine B16F10 model is a promising model to study the effects of the immune system on vaccinia virus mediated therapy of primary tumors and metastases.},
  subject      = {Krebs <Medizin>},
  language  = {en}
}
@phdthesis{Brockmann2015,
  author    = {Brockmann, Markus},
  title     = {Inhibition von Aurora-A als neue Therapiestrategie gegen MYCN-amplifizierte Neuroblastome},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-135951},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Im Neuroblastom ist die Amplifikation des MYCN-Gens, das f{\"u}r den Transkriptionsfaktor N-Myc kodiert, der klinisch bedeutendste Faktor f{\"u}r eine schlechte Prognose. Als Mitglied der onkogenen Myc-Familie induziert N-Myc die Expression von Genen, die in vielen biologischen Prozessen wie Metabolismus, Zellzyklusprogression, Zellwachstum und Apoptose eine wichtige Rolle spielen. Die Deregulation der MYCN-Expression f{\"u}hrt zu einem charakteristischen Genexpressionsprofil und einem aggressiven Phenotyp in den Tumorzellen. In normalen neuronalen Vorl{\"a}uferzellen wird N-Myc gew{\"o}hnlich sehr schnell proteasomal abgebaut. W{\"a}hrend der Mitose wird N-Myc an Serin 62 phosphoryliert. Diese Phosphorylierung dient als Erkennungssignal f{\"u}r die Kinase GSK3β, die die Phosphorylierung an Threonin 58 katalysiert. Das Phosphodegron wird von Fbxw7, einer Komponente des E3-Ubiquitinligase-Komplex SCFFbxw7, erkannt. Die anschließende Ubiquitinierung induziert den proteasomalen Abbau des Proteins. Die Reduktion der N-Myc-Proteinlevel erm{\"o}glicht den neuronalen Vorl{\"a}uferzellen den Austritt aus dem Zellzyklus und f{\"u}hrt zu einer terminalen Differenzierung. In einem shRNA Screen konnte AURKA als essentielles Gen f{\"u}r die Proliferation MYCN-amplifizierter Neuroblastomzellen identifiziert werden. Eine Aurora-A-Depletion hatte jedoch keinen Einfluss auf das Wachstum nicht-amplifizierter Zellen. W{\"a}hrend dieser Doktorarbeit konnte gezeigt werden, dass Aurora-A speziell den Fbxw7-vermittelten Abbau verhindert und dadurch N-Myc stabilisiert. F{\"u}r die Stabilisierung ist zwar die Interaktion der beiden Proteine von entscheidender Bedeutung, {\"u}berraschenderweise spielt die Kinaseaktivit{\"a}t von Aurora-A jedoch keine Rolle. Zwei spezifische Aurora-A-Inhibitoren, MLN8054 und MLN8237, sind allerdings in der Lage, nicht nur die Kinaseaktivit{\"a}t zu hemmen, sondern auch die N-Myc-Proteinlevel zu reduzieren. Beide Molek{\"u}le induzieren eine Konformations{\"a}nderung in der Kinasedom{\"a}ne von Aurora-A. Diese ungew{\"o}hnliche strukturelle Ver{\"a}nderung hat zur Folge, dass der N-Myc/Aurora-A-Komplex dissoziiert und N-Myc mit Hilfe von Fbxw7 proteasomal abgebaut werden kann. In MYCN-amplifizierten Zellen f{\"u}hrt diese Reduktion an N-Myc zu einem Zellzyklusarrest in der G1-Phase. Die in vitro Daten konnten in einem transgenen Maus-Modell f{\"u}r das MYCN-amplifizierte Neuroblastom best{\"a}tigt werden. Die Behandlung mit MLN8054 und MLN8237 f{\"u}hrte in den Tumoren ebenfalls zu einer N-Myc-Reduktion. Dar{\"u}ber hinaus konnte ein prozentualer Anstieg an differenzierten Zellen, die vollst{\"a}ndige Tumorregression in der Mehrzahl der Neuroblastome und eine gesteigerte Lebenserwartung beobachtet werden. Insgesamt zeigen die in vitro und in vivo Daten, dass die spezifischen Aurora-A-Inhibitoren ein hohes therapeutisches Potential gegen das MYCN-amplifizierte Neuroblastom besitzen.},
  subject      = {N-Myc},
  language  = {de}
}
@article{RemmeleLutherBalkenholetal.2015,
  author    = {Remmele, Christian W. and Luther, Christian H. and Balkenhol, Johannes and Dandekar, Thomas and M{\"u}ller, Tobias and Dittrich, Marcus T.},
  title     = {Integrated inference and evaluation of host-fungi interaction networks},
  series = {Frontiers in Microbiology},
  volume    = {6},
  journal   = {Frontiers in Microbiology},
  number    = {764},
  doi       = {10.3389/fmicb.2015.00764},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148278},
  year      = {2015},
  abstract  = {Fungal microorganisms frequently lead to life-threatening infections. Within this group of pathogens, the commensal Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of invasive mycoses in Europe. A key capability for host invasion and immune response evasion are specific molecular interactions between the fungal pathogen and its human host. Experimentally validated knowledge about these crucial interactions is rare in literature and even specialized host pathogen databases mainly focus on bacterial and viral interactions whereas information on fungi is still sparse. To establish large-scale host fungi interaction networks on a systems biology scale, we develop an extended inference approach based on protein orthology and data on gene functions. Using human and yeast intraspecies networks as template, we derive a large network of pathogen host interactions (PHI). Rigorous filtering and refinement steps based on cellular localization and pathogenicity information of predicted interactors yield a primary scaffold of fungi human and fungi mouse interaction networks. Specific enrichment of known pathogenicity-relevant genes indicates the biological relevance of the predicted PHI. A detailed inspection of functionally relevant subnetworks reveals novel host fungal interaction candidates such as the Candida virulence factor PLB1 and the anti-fungal host protein APP. Our results demonstrate the applicability of interolog-based prediction methods for host fungi interactions and underline the importance of filtering and refinement steps to attain biologically more relevant interactions. This integrated network framework can serve as a basis for future analyses of high-throughput host fungi transcriptome and proteome data.},
  language  = {en}
}
@phdthesis{Czakai2015,
  author    = {Czakai, Kristin Bernadette},
  title     = {Interaktionen des humanpathogenen Pilzes Aspergillus fumigatus mit dem angeborenen Immunsystem und Thrombozyten},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-117496},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Pilze sind in unserer Umwelt allgegenw{\"a}rtig und besiedeln im Fall von Candida albicans (C. albicans) sogar bei {\"u}ber 50\% der Menschen die Schleimh{\"a}ute, w{\"a}hrend Sporen von Aspergillus fumigatus (A. fumigatus) t{\"a}glich {\"u}ber die Atmung in die Lunge des Menschen gelangen. Dennoch sind Erkrankungen, die durch diese zwei Pilze ausgel{\"o}st werden, bei gesunden Menschen selten. Ist jedoch das Immunsystem beeintr{\"a}chtigt, k{\"o}nnen diese Pilze zu systemischen und damit lebensbedrohlichen Erkrankungen wie der invasiven Aspergillose und der systemischen Candidiasis f{\"u}hren. F{\"u}r eine Verbesserung der Behandlung solcher Infektionen ist das genaue Verst{\"a}ndnis der Immunabwehrmechanismen entscheidend. Da A. fumigatus {\"u}ber die Lunge in den K{\"o}rper gelangt, wurden in dieser Arbeit die h{\"a}ufigsten Immunzellen der Lunge, die Makrophagen, und deren Immunantwort auf A. fumigatus untersucht. Parallel hierzu wurden dendritische Zellen (DCs) verwendet, die als Br{\"u}cke zwischen dem angeborenen und adaptiven Immunsystem wirken. Ein besonderes Augenmerk wurde hierbei auf A. fumigatus induzierte Genexpressions{\"a}nderungen und deren Regulationsmechanismen gelegt. Dabei wurden kurze, regulatorische RNAs, die sogenannten miRNAs, untersucht, die eine wichtige Rolle in der post-transkriptionalen Genregulation spielen. Bislang ist nur wenig {\"u}ber die miRNA-abh{\"a}ngigen Genregulationen in DCs, die auf eine Infektion mit A. fumigatus oder C. albicans reagieren, bekannt. Um alle durch A. fumigatus und C. albicans regulierten miRNAs zu identifizieren, wurden DCs mit A. fumigatus und C. albicans ko-kultiviert und anschließend eine Komplettsequenzierung der kurzen RNAs durchgef{\"u}hrt. Die Pilz-spezifische Induktion der miRNA-Regulation wurde zudem mit der miRNA-Regulation durch den bakteriellen Zellwandbestandteil Lipopolysaccharid verglichen. Durch die Stimulation mit Keimschl{\"a}uchen von A. fumigatus wurden die miRNAs miR-132-3p/5p, miR-155-5p, miR129-2-3p, miR-129-5p, miR-212-3p/5p und miR-9-5p in DCs induziert. Diese wurden ebenfalls durch C. albicans induziert, zudem noch die miRNAs miR-147a und miR-147b. Spezifisch f{\"u}r A. fumigatus war die Regulation der miR-129-2-3p. Neben dem miRNA-Profiling wurde auch das mRNA-Transkriptom {\"u}ber Microarrays analysiert und dadurch 18 potentielle Zielgene der Pilz-induzierten miRNAs identifiziert. Neben den Elementen der Translationsregulation wurden auch die Transkriptionsfaktoren untersucht. Als einziger unter den 60 regulierten Transkriptionsfaktoren zeigte KLF4 eine ver{\"a}nderte Expressionsrichtung in DCs, die mit Pilzen oder LPS behandelt waren. W{\"a}hrend die Stimulation mit LPS die Expression von KLF4 induzierte, wurde es durch die Pilze A. fumigatus und C. albicans reprimiert. In einer Untersuchung der unterschiedlichen A. fumigatus-Rezeptoren, wurde deren Einfluss auf die KLF4-Regulation gezeigt. W{\"a}hrend TLR4-Liganden KLF4 induzierten, f{\"u}hrten Liganden, die an die Rezeptoren TLR2/TLR1 und Dectin-1 binden, zu einer Reduktion von KLF4. Nach einem erfolgreich etablierten KLF4-knock-down mittels RNA-Interferenz wurden KLF4-Zielgene untersucht. W{\"a}hrend kein bzw. nur ein geringer Effekt auf die Genexpression von CCL2, RANTES, CXCL10 und TNF beobachtet wurde, sorgte der KLF4 knock-down f{\"u}r eine hoch signifikante Reduktion der IL6-Genexpression in LPS-stimulierten DCs. Um die KLF4-Regulation weiter zu untersuchen, wurde zudem eine weitere Zellpopulation des angeborenen Immunsystems, die Makrophagen, verwendet. Auch hier wurde die Immunantwort gegen A. fumigatus analysiert. Zudem wurde die Rolle der Thrombozyten als Immunmediatoren betrachtet. Zuerst wurde ein Zytokinprofil des pl{\"a}ttchenreichen Plasmas (PRP), das mit A. fumigatus stimuliert wurde, erstellt. In diesem konnte nur RANTES in hoher Konzentration nachgewiesen werden. Daraufhin wurde der Einfluss von PRP auf die Reifung von DCs, die Phagozytosef{\"a}higkeit von Makrophagen und DCs sowie der Einfluss von DCs und Makrophagen auf die metabolische Aktivit{\"a}t von A. fumigatus in An- und Abwesenheit von pl{\"a}ttchenreichem Plasma untersucht. Es konnte eine gering verst{\"a}rkte Reifung der DCs durch PRP gezeigt werden. Isolierte Thrombozyten konnten die Phagozytose von DCs steigern, w{\"a}hrend Makrophagen durch PRP verst{\"a}rkt Konidien phagozytierten. In einem genomweiten Transkriptomprofiling wurde die Immunantwort von DCs und Makrophagen verglichen. Zudem wurde untersucht, wie PRP die Immunantwort dieser Immunzellen beeinflusst. Es wurden 2 bzw. 24 Gene identifiziert, die signifikant in A. fumigatus-stimulierten DCs und Makrophagen reguliert waren. Hierbei wurde gezeigt, dass KLF4 durch die Zugabe von PRP herabreguliert wurde. Das zuvor beschriebene Zielgen IL6 wurde durch PRP in A. fumigatus-stimulierten DCs gegen{\"u}ber stimulierten DCs ohne PRP deutlich reduziert, wodurch sich eine immunmodulatorische F{\"a}higkeit des PRP zeigte. Die Induktion von IL-6, weiteren Zytokinen und der Reifemarker durch A. fumigatus in DCs wurden zudem in einem Booleschen Modell simuliert. Dieses Modell soll in Zukunft Vorhersagen {\"u}ber experimentelle Ergebnisse und dadurch eine optimale Versuchsvorbereitung erm{\"o}glichen.},
  subject      = {Aspergillus fumigatus},
  language  = {de}
}
@article{BrillMeyerRoessler2015,
  author    = {Brill, Martin F. and Meyer, Anneke and Roessler, Wolfgang},
  title     = {It takes two—coincidence coding within the dual olfactory pathway of the honeybee},
  series = {Frontiers in Physiology},
  volume    = {6},
  journal   = {Frontiers in Physiology},
  number    = {208},
  doi       = {10.3389/fphys.2015.00208},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-126179},
  year      = {2015},
  abstract  = {To rapidly process biologically relevant stimuli, sensory systems have developed a broad variety of coding mechanisms like parallel processing and coincidence detection. Parallel processing (e.g., in the visual system), increases both computational capacity and processing speed by simultaneously coding different aspects of the same stimulus. Coincidence detection is an efficient way to integrate information from different sources. Coincidence has been shown to promote associative learning and memory or stimulus feature detection (e.g., in auditory delay lines). Within the dual olfactory pathway of the honeybee both of these mechanisms might be implemented by uniglomerular projection neurons (PNs) that transfer information from the primary olfactory centers, the antennal lobe (AL), to a multimodal integration center, the mushroom body (MB). PNs from anatomically distinct tracts respond to the same stimulus space, but have different physiological properties, characteristics that are prerequisites for parallel processing of different stimulus aspects. However, the PN pathways also display mirror-imaged like anatomical trajectories that resemble neuronal coincidence detectors as known from auditory delay lines. To investigate temporal processing of olfactory information, we recorded PN odor responses simultaneously from both tracts and measured coincident activity of PNs within and between tracts. Our results show that coincidence levels are different within each of the two tracts. Coincidence also occurs between tracts, but to a minor extent compared to coincidence within tracts. Taken together our findings support the relevance of spike timing in coding of olfactory information (temporal code).},
  language  = {en}
}
@article{GamezViruesPerovićGossneretal.2015,
  author    = {G{\´a}mez-Viru{\´e}s, Sagrario and Perović, David J. and Gossner, Martin M. and B{\"o}rschig, Carmen and Bl{\"u}thgen, Nico and de Jong, Heike and Simons, Nadja K. and Klein, Alexandra-Maria and Krauss, Jochen and Maier, Gwen and Scherber, Christoph and Steckel, Juliane and Rothenw{\"o}hrer, Christoph and Steffan-Dewenter, Ingolf and Weiner, Christiane N. and Weisser, Wolfgang and Werner, Michael and Tscharntke, Teja and Westphal, Catrin},
  title     = {Landscape simplification filters species traits and drives biotic homogenization},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {8568},
  doi       = {10.1038/ncomms9568},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-141925},
  year      = {2015},
  abstract  = {Biodiversity loss can affect the viability of ecosystems by decreasing the ability of communities to respond to environmental change and disturbances. Agricultural intensification is a major driver of biodiversity loss and has multiple components operating at different spatial scales: from in-field management intensity to landscape-scale simplification. Here we show that landscape-level effects dominate functional community composition and can even buffer the effects of in-field management intensification on functional homogenization, and that animal communities in real-world managed landscapes show a unified response (across orders and guilds) to both landscape-scale simplification and in-field intensification. Adults and larvae with specialized feeding habits, species with shorter activity periods and relatively small body sizes are selected against in simplified landscapes with intense in-field management. Our results demonstrate that the diversity of land cover types at the landscape scale is critical for maintaining communities, which are functionally diverse, even in landscapes where in-field management intensity is high.},
  language  = {en}
}
@article{WaeldchenLehmannKleinetal.2015,
  author    = {W{\"a}ldchen, Sina and Lehmann, Julian and Klein, Teresa and van de Linde, Sebastian and Sauer, Markus},
  title     = {Light-induced cell damage in live-cell super-resolution microscopy},
  series = {Scientific Reports},
  volume    = {5},
  journal   = {Scientific Reports},
  number    = {15348},
  doi       = {10.1038/srep15348},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-145207},
  year      = {2015},
  abstract  = {Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20-24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of similar to 1 kW cm\(^{-2}\) at 640 nm for several minutes, the maximum dose at 405 nm is only similar to 50 J cm\(^{-2}\), emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.},
  language  = {en}
}
@phdthesis{Frank2015,
  author    = {Frank, Nicolas Clemens},
  title     = {Lokale axonale Wirkungen der CNTF-STAT3 Signalkaskade in Motoneuronen der pmn Maus - einem Mausmodel f{\"u}r die Amyotrophe Lateralsklerose},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121065},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {1. Zusammenfassung W{\"a}hrend der Embryogenese und nach Verletzungen von Nerven regulieren neurotrophe Faktoren Signalwege f{\"u}r Apoptose, Differenzierung, Wachstum und Regeneration von Neuronen. In vivo Experimente an neugeborenen Nagern haben gezeigt, dass der Verlust von Motoneuronen nach peripherer Nervenl{\"a}sion durch die Behandlung mit GDNF, BDNF, und CNTF reduziert werden kann In der pmn-Mausmutante, einem Modell f{\"u}r die Amyotrophe Lateralsklerose, f{\"u}hrt die Gabe von CNTF, nicht aber von GDNF zu einem verz{\"o}gerten Krankheitsbeginn und einem verlangsamten Fortschreiten der Motoneuronendegeneration. Ausl{\"o}ser der Motoneuronendegeneration in der pmn-Maus ist eine Mutation im Tubulin spezifischen Chaperon E (Tbce) Gen, das f{\"u}r eines von f{\"u}nf Tubulin spezifischen Chaperonen (TBCA-TBCE) kodiert und an der Bildung von -Tubulinheterodimeren beteiligt ist. Diese Arbeit sollte dazu beitragen, die CNTF-induzierten Signalwege zu entschl{\"u}sseln, die sich lindernd auf den progredienten Verlauf der Motoneuronendegeneration in der pmn-Maus auswirken. Prim{\"a}re pmn mutierte Motoneurone zeigen ein reduziertes Axonwachstum und eine erh{\"o}hte Anzahl axonaler Schwellungen mit einer anomalen H{\"a}ufung von Mitochondrien - ein fr{\"u}hes Erkennungsmerkmal bei ALS-Patienten. Die Applikation von CNTF nicht aber von BDNF oder GDNF, kann in vitro die beobachteten Wachstumsdefekte und das bidirektionale axonale Transportdefizit in pmn mutierten Motoneurone verhindern. Aus {\"a}lteren Untersuchungen war bekannt, dass CNTF {\"u}ber den dreiteiligen transmembranen Rezeptorkomplex, bestehend aus CNTFR, LIFR und gp130, Januskinasen aktiviert, die STAT3 an Tyrosin 705 phosphorylieren (pSTAT3Y705). Ich konnte beobachten, dass axonales fluoreszenzmarkiertes pSTAT3Y705 nach CNTF-Gabe nicht retrograd in den Nukleus transportiert wird. Stattdessen f{\"u}hrt die CNTF-induzierte Phosphorylierung von STAT3 an Tyrosin 705 zu einer transkriptionsunabh{\"a}ngigen lokalen Reaktion im Axon. Diese pSTAT3Y705 abh{\"a}ngige Reaktion ist notwendig und ausreichend, um das reduzierte Axonwachstum pmn mutierter Motoneurone zu beheben. Wie die Kombination einer CNTF Behandlung mit dem shRNA vermittelten knock-down von Stathmin in pmn mutierten Motoneuronen zeigt, zielt die CNTF-STAT3 Signalkaskade auf die Stabilisierung axonaler Mikrotubuli ab und wirkt sich positiv auf die anterograde und retrograde Mobilit{\"a}t von axonalen Mitochondrien aus. Interessanter Weise konnte ich außerdem feststellen, dass eine akute Gabe von CNTF das mitochondriale Membranpotential in Axonen prim{\"a}rer pmn mutierter und wildtypischer Motoneurone erh{\"o}ht und einen Anstieg von ATP ausl{\"o}st. Meine Beobachtungen legen nahe, dass CNTF unerwarteter Weise auch eine transiente Phosphorylierung an STAT3 Serin 727 (pSTAT3S727) ausl{\"o}st, die zur anschließenden Translokation von pSTAT3S727 in Mitochondrien f{\"u}hrt. Diese Ergebnisse zeigen, dass STAT3 mehrere lokale Ziele im Axon besitzt, n{\"a}mlich axonale Mikrotubuli und Mitochondrien.},
  subject      = {Motoneuron},
  language  = {de}
}
@article{FalibeneRocesRoessler2015,
  author    = {Falibene, Augustina and Roces, Flavio and R{\"o}ssler, Wolfgang},
  title     = {Long-term avoidance memory formation is associated with a transient increase in mushroom body synaptic complexes in leaf-cutting ants},
  series = {Frontiers in Behavioural Neuroscience},
  volume    = {9},
  journal   = {Frontiers in Behavioural Neuroscience},
  number    = {84},
  doi       = {10.3389/fnbeh.2015.00084},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148763},
  year      = {2015},
  abstract  = {Long-term behavioral changes related to learning and experience have been shown to be associated with structural remodeling in the brain. Leaf-cutting ants learn to avoid previously preferred plants after they have proved harmful for their symbiotic fungus, a process that involves long-term olfactory memory. We studied the dynamics of brain microarchitectural changes after long-term olfactory memory formation following avoidance learning in Acromyrmex ambiguus. After performing experiments to control for possible neuronal changes related to age and body size, we quantified synaptic complexes (microglomeruli, MG) in olfactory regions of the mushroom bodies (MB) at different times after learning. Long-term avoidance memory formation was associated with a transient change in MG densities. Two days after learning, MG density was higher than before learning. At days 4 and 15 after learning when ants still showed plant avoidance MG densities had decreased to the initial state. The structural reorganization of MG triggered by long-term avoidance memory formation clearly differed from changes promoted by pure exposure to and collection of novel plants with distinct odors. Sensory exposure by the simultaneous collection of several, instead of one, non-harmful plant species resulted in a decrease in MG densities in the olfactory lip. We hypothesize that while sensory exposure leads to MG pruning in the MB olfactory lip, the formation of long-term avoidance memory involves an initial growth of new MG followed by subsequent pruning.},
  language  = {en}
}
@article{FalibeneRocesRoessler2015,
  author    = {Falibene, Agustina and Roces, Flavio and R{\"o}ssler, Wolfgang},
  title     = {Long-term avoidance memory formation is associated with a transient increase in mushroom body synaptic complexes in leaf-cutting ants},
  series = {Frontiers in Behavioral Neuroscience},
  volume    = {9},
  journal   = {Frontiers in Behavioral Neuroscience},
  number    = {84},
  doi       = {10.3389/fnbeh.2015.00084},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125522},
  year      = {2015},
  abstract  = {Long-term behavioral changes related to learning and experience have been shown to be associated with structural remodeling in the brain. Leaf-cutting ants learn to avoid previously preferred plants after they have proved harmful for their symbiotic fungus, a process that involves long-term olfactory memory. We studied the dynamics of brain microarchitectural changes after long-term olfactory memory formation following avoidance learning in Acromyrmex ambiguus. After performing experiments to control for possible neuronal changes related to age and body size, we quantified synaptic complexes (microglomeruli, MG) in olfactory regions of the mushroom bodies (MBs) at different times after learning. Long-term avoidance memory formation was associated with a transient change in MG densities. Two days after learning, MG density was higher than before learning. At days 4 and 15 after learning—when ants still showed plant avoidance—MG densities had decreased to the initial state. The structural reorganization of MG triggered by long-term avoidance memory formation clearly differed from changes promoted by pure exposure to and collection of novel plants with distinct odors. Sensory exposure by the simultaneous collection of several, instead of one, non-harmful plant species resulted in a decrease in MG densities in the olfactory lip. We hypothesize that while sensory exposure leads to MG pruning in the MB olfactory lip, the formation of long-term avoidance memory involves an initial growth of new MG followed by subsequent pruning.},
  language  = {en}
}
@phdthesis{Zhu2015,
  author    = {Zhu, Ana Cheng},
  title     = {Metagenomic analysis of genetic variation in human gut microbial species},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-113890},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Microbial species (bacteria and archaea) in the gut are important for human health in various ways. Not only does the species composition vary considerably within the human population, but each individual also appears to have its own strains of a given species. While it is known from studies of bacterial pan-genomes, that genetic variation between strains can differ considerably, such as in Escherichia coli, the extent of genetic variation of strains for abundant gut species has not been surveyed in a natural habitat. This is mainly due to the fact that most of these species cannot be cultured in the laboratory. Genetic variation can range from microscale genomic rearrangements such as small nucleotide polymorphism (SNP) to macroscale large genomic rearrangements like structural variations. Metagenomics offers an alternative solution to study genetic variation in prokaryotes, as it involves DNA sequencing of the whole community directly from the environment. However, most metagenomic studies to date only focus on variation in gene abundance and hence are not able to characterize genetic variation (in terms of presence or absence of SNPs and genes) of gut microbial strains of individuals. The aim of my doctorate studies was therefore to study the extent of genetic variation in the genomic sequence of gut prokaryotic species and its phenotypic effects based on: (1) the impact of SNP variation in gut bacterial species, by focusing on genes under selective pressure and (2) the gene content variation (as a proxy for structural variation) and their effect on microbial species and the phenotypic traits of their human host. In the first part of my doctorate studies, I was involved in a project in which we created a catalogue of 10.3 million SNPs in gut prokaryotic species, based on metagenomes. I used this to perform the first SNP-based comparative study of prokaryotic species evolution in a natural habitat. Here, I found that strains of gut microbial species in different individuals evolve at more similar rates than the strains within an individual. In addition, I found that gene evolution can be uncoupled from the evolution of its originating species, and that this could be related to selective pressure such as diet, exemplified by galactokinase gene (galK). Despite the individuality (i.e. uniqueness of each individual within the studied metagenomic dataset) in the SNP profile of the gut microbiota that we found, for most cases it is not possible to link SNPs with phenotypic differences. For this reason I also used gene content as a proxy to study structural variation in metagenomes. In the second part of my doctorate studies, I developed a methodology to characterize the variability of gene content in gut bacterial species, using metagenomes. My approach is based on gene deletions, and was applied to abundant species (demonstrated using a set of 11 species). The method is sufficiently robust as it captures a similar range of gene content variability as has been detected in completely sequenced genomes. Using this procedure I found individuals differ by an average of 13\% in their gene content of gut bacterial strains within the same species. Interestingly no two individuals shared the same gene content across bacterial species. However, this variation corresponds to a lower limit, as it is only accounts for gene deletion and not insertions. This large variation in the gene content of gut strain was found to affect important functions, such as polysaccharide utilization loci (PULs) and capsular polysaccharide synthesis (CPS), which are related with digestion of dietary fibers. In summary, I have shown that metagenomics based approaches can be robust in characterizing genetic variation in gut bacterial species. I also illustrated, using examples both for SNPs and gene content (galK, PULs and CPS), that this genetic variation can be used to predict the phenotypic characteristics of the microbial species, as well as predicting the phenotype of their human host (for example, their capacity to digest different food components). Overall, the results of my thesis highlight the importance of characterizing the strains in the gut microbiome analogous to the emerging variability and importance of human genomics.},
  subject      = {Darmflora},
  language  = {en}
}
@phdthesis{Graver2015,
  author    = {Graver, Shannon},
  title     = {Molecular and cellular cross talk between angiogenic, immune and DNA mismatch repair pathways},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-108302},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {VEGF is a main driver of tumor angiogenesis, playing an important role not only in the formation of new blood vessels, but also acts as a factor for cell migration, proliferation, survival and apoptosis. Angiogenesis is a universal function shared by most solid tumors and its inhibition was thought to have the potential to work across a broad patient population. Clinical evidence has shown that inhibiting pathological angiogenesis only works in a subset of patients and the identification of those patients is an important step towards personalized cancer care. The first approved antiangiogenic therapy was bevacizumab (Avastin®), a monoclonal antibody targeting VEGF in solid tumors including CRC, BC, NSCLC, RCC and others. In addition to endothelial cells, VEGF receptors are present on a number of different cell types including tumor cells, monocytes and macrophages. The work presented in this thesis looked at the in vitro cellular changes in tumor cells and leukocytes in response to the inhibition of VEGF signaling with the use of bevacizumab. In the initial experiments, VEGF was induced by hypoxia in tumor cells to evaluate changes in survival, proliferation, migration and changes in gene or protein expression. There was a minimal direct response of VEGF inhibition in tumor cells that could be attributed to bevacizumab treatment, with minor variations in some of the cell lines screened but no uniform or specific response noted. MMR deficiency often results in microsatellite instability (MSI) in tumors, as opposed to microsatellite stable (MSS) tumors, and accounts for up to 15\% of colorectal carcinomas (CRCs). It has been suggested in clinical data that MMR deficient tumors responded better to bevacizumab regimens, therefore further research used isogenic paired CRC tumor cell lines (MMR deficient and proficient). Furthermore, a DNA damaging agent was added to the treatment regimen, the topoisomerase inhibitor SN-38 (the active metabolite of irinotecan). Inhibiting VEGF using bevacizumab significantly inhibited the ability of MMR deficient tumor cells to form anchor dependent colonies, however conversely, bevacizumab treatment before damaging cells with SN-38, showed a significant increase in colony numbers. Moreover, VEGF inhibition by bevacizumab pretreatment also significantly increased the mutation fraction in MMR deficient cells as measured by transiently transfecting a dinucleotide repeat construct, suggesting VEGF signaling may have an intrinsic role in MMR deficient cells. A number of pathways were analyzed in addition to changes in gene expression profiles resulting in the identification of JNK as a possible VEGF targeted pathway. JUN expression was also reduced in these conditions reinforcing this hypothesis, however the intricate molecular mechanisms remain to be elucidated. In order to remain focused on the clinical application of the findings, it was noted that some cytokines were differentially regulated by bevacizumab between MMR proficient and deficient cells. Treatment regimens employed in vitro attempted to mimic the clinical setting by inducing DNA damage, then allowing cells to recover with or without VEGF using bevacizumab treatment. Inflammatory cytokines, CCL7 and CCL8, were found to have higher expression in the MMR deficient cell line with bevacizumab after DNA damage, therefore the cross talk via tumor derived factors to myeloid cells was analyzed. Gene expression changes in monocytes induced by tumor conditioned media showed CCL18 to be a bevacizumab regulated gene by MMR deficient cells and less so in MMR proficient cells. CCL18 has been described as a prognostic marker in gastric, colorectal and ovarian cancers, however the significance is dependent on tumor type. CCL18 primarily exerts its function on the adaptive immune system to trigger a TH2 response in T cells, but is also described to increase non-specific phagocytosis. The results of this study did show an increase in the phagocytic activity of macrophages in the presence of bevacizumab that was significantly more apparent in MMR deficient cells. Furthermore, after DNA damage MMR deficient cells treated with bevacizumab released a cytokine mix that induced monocyte migration in a bevacizumab dependent manner, showing a functional response with the combination of MMR deficiency and bevacizumab. In summary, the work in this thesis has shown evidence of immune cell modulation that is specific to MMR deficient tumor cells that may translate into a marker for the administration of bevacizumab in a clinical setting. VEGF ist ein zentraler Regulator der Tumor-Angiogenese, und spielt eine wichtige Rolle nicht nur in der Bildung von neuen Blutgef{\"a}ßen, sondern ist auch f{\"u}r die Migration, Proliferation, das {\"U}berleben und Apoptose von Tumorzellen essentiell. Angiogenese ist eine der universellen Funktionen, welche das Wachstum der meisten soliden Tumoren charakterisiert. Eine der klassischen therapeutischen Ideen wurde auf der Basis entwickelt, dass die spezifische Hemmung der Angiogenese das Potenzial hat in einer breiten Patientenpopulation einen klinischen Effekt zu zeigen. Die klinische Erfahrung und Anwendung hat jedoch gezeigt, dass die Hemmung der pathologischen Angiogenese nur in einem Teil der Patienten einen therapeutischen Nutzen aufweist. Somit stellt die Identifikation derjenigen Patienten, welche von der anti-angiogenen Therapie profitieren, einen wichtiger Schritt zur personalisierten Krebsbehandlung dar. Die erste zugelassene antiangiogene Therapie war Bevacizumab (Avastin®), ein monoklonaler Antik{\"o}rper gegen VEGF, welcher unter anderem in soliden Tumoren wie CRC, BC, nicht-kleinzelligem Lungenkrebs (NSCLC) und dem Nierenzellkarzinom angewandt wird. VEGF-Rezeptoren befinden sich nicht nur auf Endothelzellen, sondern sind auch auf einer Anzahl von verschiedenen Zelltypen, einschließlich Tumorzellen, Monozyten und Makrophagen nachweisbar. Die in dieser Arbeit vorgestellten Ergebnisse befassen sich mit den zellul{\"a}ren Ver{\"a}nderungen an Tumorzellen und Leukozyten als Reaktion auf die Hemmung der VEGF-Signalkaskade durch Bevacizumab in-vitro. In den Initialen Experimenten wurde VEGF durch Hypoxie in Tumorzellen induziert und Ver{\"a}nderungen der {\"U}berlebensrate, der Proliferation, Migration als auch in der Gen- oder Protein-Expression gemessen. Es konnte eine minimale direkte Reaktion der VEGF-Hemmung auf Tumorzellen beobachtet werden, welche auf die Bevacizumab Behandlung zur{\"u}ckgef{\"u}hrt werden k{\"o}nnte. Es zeigten sich aber auch geringf{\"u}gige Abweichungen in einigen der verwendeten Zellinien, die keine einheitliche Interpretation erlauben oder auf eine uniformelle Reaktion hinweisen w{\"u}rden. Das ph{\"a}notypische Korrelat einer „Mismatch" Reparatur (MMR)-Defizienz ist die Mikrosatelliteninstabilit{\"a}t im Gegensatz zu mikrosatellitenstabilen Tumoren und findet sich bei bis zu 15\% der kolorektalen Karzinomen (CRC) wieder. Klinischen Daten deuten daraufhin, dass Bevacizumab besser in MMR-defizienten Tumoren wirkt. Daher wurden die weiteren Untersuchungen in gepaarten MMR stabilen und MMR instabilen CRC-Tumorzelllinien (MMR defizient und kompetent) durchgef{\"u}hrt. Weiterhin wurde ein DNA-sch{\"a}digendes Agens, SN-38, ein Topoisomerase-Inhibitor (der aktive Metabolit von Irinotecan) dem Behandlungsschema zugef{\"u}gt. Es zeigte sich, dass die Hemmung von VEGF mittels Bevacizumab die F{\"a}higkeit der MMR defizienten Tumorzellen Kolonien zu bilden signifikant inhibiert. Im Gegensatz dazu, hatte die Behandlung von Bevacizumab vor der Zugabe des DNA sch{\"a}digenden Agens zu einer vermehrten Kolonienzahl gef{\"u}hrt. Außerdem erh{\"o}hte die Vorbehandlung mit Bevacizumab deutlich die Mutationsrate in MMR-defizienten Zellen, was durch die transiente Transfektion eines Dinukleotid-Repeat-Konstrukts nachgewiesen werden konnte. Dies deutete darauf hin, dass VEGF eine intrinsische Rolle in der Signalkaskade des MMR-Systems haben k{\"o}nnte. Deshalb wurde eine Anzahl von Signalalkaskaden zus{\"a}tzlich zu Ver{\"a}nderungen von Genexpressionsprofilen untersucht und JNK als m{\"o}gliche Verbindungsstelle der beiden Signalkaskaden, VEGF und MMR, identifiziert. Diese Hypothese wurde zus{\"a}tzlich unterst{\"u}tzt durch die Tatsache, dass die JUN Expression unter diesen experimentellen Bedingungen reduziert war. Die Aufkl{\"a}rung der komplexen molekularen Mechanismen der potentiellen Interaktion bleibt zuk{\"u}nftigen Untersuchungen vorbehalten. In Hinblick auf die klinische Konsequenz der erhaltenen Ergebnisse war es auff{\"a}llig, dass einige Zytokine durch Bevacizumab in den MMR defizienten Zellen im Gegensatz zu den MMR kompetenten Zellen unterschiedlich reguliert wurden. Die in-vitro verwendeten Behandlungsschemata waren den klinisch zur Anwendung kommenden Protokollen nachempfunden. Zuerst wurde ein DNA-Schaden gesetzt, und den Zellen erm{\"o}glicht, sich mit oder ohne Bevacizumab zu erholen. Es konnte gezeigt werden, dass die inflammatorischen Zytokine CCL7 und CCL8 eine h{\"o}here Expression in der MMR-defiziente Zelllinie in Kombination mit Bevacizumab aufweisen. Daher wurde ein m{\"o}glicher Crosstalk zwischen von Tumorzellen sezernierten Faktoren und myeloischen Zellen weiter verfolgt. Ver{\"a}nderungen der Genexpression in Monozyten durch Tumorzell- konditionierte Medien zeigte CCL18 als ein Bevacizumab reguliertes Gen in MMR-defizienten Zellen, aber nicht in MMR kompetenten Zellen. CCL18 {\"u}bt seine Funktion prim{\"a}r im adaptiven Immunsystems aus um eine TH2-Antwort in T-Zellen auszul{\"o}sen Ausserdem wird eine Erh{\"o}hung der nicht-spezifische Phagozytose als weitere Funktion beschrieben. CCL18 wurde bereits als prognostischer Marker in Magen-, Dickdarm- und Eierstockkrebsarten beschrieben; die klinische Bedeutung ist jedoch abh{\"a}ngig von Tumortyp. Die Ergebnisse dieser Arbeit zeigen, dass eine Erh{\"o}hung der phagozytischen Aktivit{\"a}t von Makrophagen in Gegenwart von Bevacizumab wesentlich deutlicher in MMR-defizienten Zellen ausgepr{\"a}gt war. Weiterhin wurde gefunden, dass nach DNA-Sch{\"a}digung in Bevacizumab behandelten MMR-defizienten Zellen Zytokine freigesetzt werden, welche eine Monozytenmigration in einer Bevacizumab-abh{\"a}ngigen Weise induzieren. Dies weist auf eine funktionelle Interaktion von MMR-Defizienz und Bevacizumab hin. Zus{\"a}tzlich zeigen die Ergebnisse dieser Arbeit eine Immunzellmodulation, die spezifisch f{\"u}r Mismatch-Reparatur defiziente Tumorzellen ist und in der klinischen Praxis als Marker f{\"u}r die Verabreichung von Bevacizumab verwendet werden k{\"o}nnte.},
  subject      = {Vascular endothelial Growth Factor},
  language  = {en}
}
@article{AdolfiCarreiraJesusetal.2015,
  author    = {Adolfi, Mateus C. and Carreira, Ana C. O. and Jesus, L{\´a}zaro W. O. and Bogerd, Jan and Funes, Rejane M. and Schartl, Manfred and Sogayar, Mari C. and Borella, Maria I.},
  title     = {Molecular cloning and expression analysis of dmrt1 and sox9 during gonad development and male reproductive cycle in the lambari fish, Astyanax altiparanae},
  series = {Reproductive Biology and Endocrinology},
  volume    = {13},
  journal   = {Reproductive Biology and Endocrinology},
  number    = {2},
  doi       = {10.1186/1477-7827-13-2},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-126486},
  year      = {2015},
  abstract  = {Background The dmrt1 and sox9 genes have a well conserved function related to testis formation in vertebrates, and the group of fish presents a great diversity of species and reproductive mechanisms. The lambari fish (Astyanax altiparanae) is an important Neotropical species, where studies on molecular level of sex determination and gonad maturation are scarce. Methods Here, we employed molecular cloning techniques to analyze the cDNA sequences of the dmrt1 and sox9 genes, and describe the expression pattern of those genes during development and the male reproductive cycle by qRT-PCR, and related to histology of the gonad. Results Phylogenetic analyses of predicted amino acid sequences of dmrt1 and sox9 clustered A. altiparanae in the Ostariophysi group, which is consistent with the morphological phylogeny of this species. Studies of the gonad development revealed that ovary formation occurred at 58 days after hatching (dah), 2 weeks earlier than testis formation. Expression studies of sox9 and dmrt1 in different tissues of adult males and females and during development revealed specific expression in the testis, indicating that both genes also have a male-specific role in the adult. During the period of gonad sex differentiation, dmrt1 seems to have a more significant role than sox9. During the male reproductive cycle dmrt1 and sox9 are down-regulated after spermiation, indicating a role of these genes in spermatogenesis. Conclusions For the first time the dmrt1 and sox9 were cloned in a Characiformes species. We show that both genes have a conserved structure and expression, evidencing their role in sex determination, sex differentiation and the male reproductive cycle in A. altiparanae. These findings contribute to a better understanding of the molecular mechanisms of sex determination and differentiation in fish.},
  language  = {en}
}
@article{WilliamsChagtaiAlcaideGermanetal.2015,
  author    = {Williams, Richard D. and Chagtai, Tasnim and Alcaide-German, Marisa and Apps, John and Wegert, Jenny and Popov, Sergey and Vujanic, Gordan and Van Tinteren, Harm and Van den Heuvel-Eibrink, Marry M and Kool, Marcel and De Kraker, Jan and Gisselsson, David and Graf, Norbert and Gessler, Manfred and Pritchard-Jones, Kathy},
  title     = {Multiple mechanisms of MYCN dysregulation in Wilms tumour},
  series = {Oncotarget},
  volume    = {6},
  journal   = {Oncotarget},
  number    = {9},
  doi       = {10.18632/oncotarget.3377},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143471},
  pages     = {7232-7243},
  year      = {2015},
  abstract  = {Genomic gain of the proto-oncogene transcription factor gene MYCN is associated with poor prognosis in several childhood cancers. Here we present a comprehensive copy number analysis of MYCN in Wilms tumour (WT), demonstrating that gain of this gene is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. Using whole exome and gene-specific sequencing, together with methylation and expression profiling, we show that MYCN is targeted by other mechanisms, including a recurrent somatic mutation, P44L, and specific DNA hypomethylation events associated with MYCN overexpression in tumours with high risk histologies. We describe parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumours of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolve over time. We report a second bilateral case in which MYCN gain is a germline aberration. Our results suggest a significant role for MYCN dysregulation in the molecular biology of Wilms tumour. We conclude that MYCN gain is prognostically significant, and suggest that the novel P44L somatic variant is likely to be an activating mutation.},
  language  = {en}
}
@article{ElkonLoayzaPuchKorkmazetal.2015,
  author    = {Elkon, Ran and Loayza-Puch, Fabricio and Korkmaz, Gozde and Lopes, Rui and van Breugel, Pieter C and Bleijerveld, Onno B and Altelaar, AF Maarten and Wolf, Elmar and Lorenzin, Francesca and Eilers, Martin and Agami, Reuven},
  title     = {Myc coordinates transcription and translation to enhance transformation and suppress invasiveness},
  series = {EMBO reports},
  volume    = {16},
  journal   = {EMBO reports},
  number    = {12},
  doi       = {10.15252/embr.201540717},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150373},
  pages     = {1723-1736},
  year      = {2015},
  abstract  = {c-Myc is one of the major human proto-oncogenes and is often associated with tumor aggression and poor clinical outcome. Paradoxically, Myc was also reported as a suppressor of cell motility, invasiveness, and metastasis. Among the direct targets of Myc are many components of the protein synthesis machinery whose induction results in an overall increase in protein synthesis that empowers tumor cell growth. At present, it is largely unknown whether beyond the global enhancement of protein synthesis, Myc activation results in translation modulation of specific genes. Here, we measured Myc-induced global changes in gene expression at the transcription, translation, and protein levels and uncovered extensive transcript-specific regulation of protein translation. Particularly, we detected a broad coordination between regulation of transcription and translation upon modulation of Myc activity and showed the connection of these responses to mTOR signaling to enhance oncogenic transformation and to the TGFβ pathway to modulate cell migration and invasiveness. Our results elucidate novel facets of Myc-induced cellular responses and provide a more comprehensive view of the consequences of its activation in cancer cells.},
  language  = {en}
}
@phdthesis{Hoecherl2015,
  author    = {H{\"o}cherl, Nicole},
  title     = {Nesting behaviour of the paper wasp Polistes dominula - with special focus on thermoregulatory mechanisms},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-132681},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Wasps of the genus Polistes comprise over 200 species and are nearly cosmopolitan. They show a lack of physiological caste differentiation and are therefore considered as primitively eusocial. Furthermore, paper wasps are placed between the solitary living Eumenidae and the highly social organized Vespinae. Hence, they are often called a "key genus" for understanding the evolution of sociality. Particularly, Polistes dominula, with its small easy manageable nests and its frequent occurrence and wide distribution range is often the subject of studies. In Europe, the invasion of this species into northern regions is on the rise. Since little was known about the nesting behaviour of P. dominula in Central Europe, the basic principles about nesting were investigated in W{\"u}rzburg, Germany (latitude 49°) by conducting a comprehensive field-study spanning three consecutive years. Furthermore, the thermoregulation of individual wasps in their natural habitat had not yet been investigated in detail. Therefore, their ability to respond to external hazards with elevated thorax temperatures was tested. In addition, different types of nest thermoregulation were investigated using modern methods such as infrared thermography and temperature data logger. In the present work, the investigation of basic nesting principles revealed that foundress groups (1-4 foundresses) and nests are smaller and that the nesting season is shorter in the W{\"u}rzburg area than in other regions. The mean size of newly founded nests was 83 cells and the average nesting season was around 4.6 months. The queens neither preferred single (54\%) nor multiple founding (46\%) in this study. The major benefit of multiple founding is an increased rate of survival. During the three years of observation, only 47\% of single-foundress colonies survived, whereas 100\% of colonies that were built by more than two queens, survived. However, an influence of the number of foundresses on the productivity of colonies in terms of number of cells and pupae per nest has not shown up. However, the length of the nesting season as well as the nest sizes varied strongly depending on the climatic conditions of the preceding winter during the three consecutive years. In order to investigate the thermoregulatory mechanisms of individual adult P. dominula wasps, I presented artificial threats by applying smoke or carbon dioxide simulating fire and predator attacks, respectively, and monitored the thorax temperature of wasps on the nest using infrared thermography. The results clearly revealed that P. dominula workers recognized smoke and CO2 and reacted almost instantaneously and simultaneously with an increase of their thorax temperature. The maximal thorax temperature was reached about 65 s after the application of both stressors, but subsequently the wasps showed a different behaviour pattern. They responded to a longer application of smoke with moving to the exit and fled, whereas in case of CO2 the wasps started flying and circling the nest without trying to escape. No rise of the thorax temperature was detectable after an air blast was applied or in wasps resting on the nest. Additionally, the thorax temperatures of queens were investigated during dominance battles. I found that the thorax temperature of the dominant queens rose up to 5°C compared to that of subordinate queens that attacked the former. The study of active mechanisms for nest thermoregulation revealed no brood incubation or clustering behaviour of P. dominula. Furthermore, I found out that wing fanning for cooling the nest was almost undetectable (4 documented cases). However, I could convincingly record that water evaporation is most effective for nest cooling. By the direct comparison of active (with brood and adults) and non-active (without brood and adults) nests, the start of cooling by water evaporation was detected above maximum outside temperatures of 25°C or at nest temperatures above 35°C. The powerful role of water in nest cooling was manifested by an average decrease of temperature of a single cell of about 8°C and a mean duration of 7 min until the cell reached again its initial temperature. The investigation of passive thermoregulatory mechanisms revealed that the nest site choice as well as nest orientation appears to be essential for P. dominula wasps. Furthermore, I was able to show that the architecture of the nests plays an important role. Based on the presented results, it can be assumed that the vertical orientation of cells helps maintaining the warmth of nests during the night, whereas the pedicel assists in cooling the nest during the day.},
  subject      = {Franz{\"o}sische Feldwespe},
  language  = {en}
}
@article{KarulinCaspellDittrichetal.2015,
  author    = {Karulin, Alexey Y. and Caspell, Richard and Dittrich, Marcus and Lehmann, Paul V.},
  title     = {Normal distribution of CD8+ T-cell-derived ELISPOT counts within replicates justifies the reliance on parametric statistics for identifying positive responses},
  series = {Cells},
  volume    = {4},
  journal   = {Cells},
  number    = {1},
  doi       = {10.3390/cells4010096},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-149968},
  pages     = {96-111},
  year      = {2015},
  abstract  = {Accurate assessment of positive ELISPOT responses for low frequencies of antigen-specific T-cells is controversial. In particular, it is still unknown whether ELISPOT counts within replicate wells follow a theoretical distribution function, and thus whether high power parametric statistics can be used to discriminate between positive and negative wells. We studied experimental distributions of spot counts for up to 120 replicate wells of IFN-γ production by CD8+ T-cell responding to EBV LMP2A (426 - 434) peptide in human PBMC. The cells were tested in serial dilutions covering a wide range of average spot counts per condition, from just a few to hundreds of spots per well. Statistical analysis of the data using diagnostic Q-Q plots and the Shapiro-Wilk normality test showed that in the entire dynamic range of ELISPOT spot counts within replicate wells followed a normal distribution. This result implies that the Student t-Test and ANOVA are suited to identify positive responses. We also show experimentally that borderline responses can be reliably detected by involving more replicate wells, plating higher numbers of PBMC, addition of IL-7, or a combination of these. Furthermore, we have experimentally verified that the number of replicates needed for detection of weak responses can be calculated using parametric statistics.},
  language  = {en}
}
@article{GaoNagpalSchneideretal.2015,
  author    = {Gao, Shiqiang and Nagpal, Jatin and Schneider, Martin W. and Kozjak-Pavlovic, Vera and Nagel, Georg and Gottschalk, Alexander},
  title     = {Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {8046},
  doi       = {10.1038/ncomms9046},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148197},
  year      = {2015},
  abstract  = {Cyclic GMP (cGMP) signalling regulates multiple biological functions through activation of protein kinase G and cyclic nucleotide-gated (CNG) channels. In sensory neurons, cGMP permits signal modulation, amplification and encoding, before depolarization. Here we implement a guanylyl cyclase rhodopsin from Blastocladiella emersonii as a new optogenetic tool (BeCyclOp), enabling rapid light-triggered cGMP increase in heterologous cells (Xenopus oocytes, HEK293T cells) and in Caenorhabditis elegans. Among five different fungal CyclOps, exhibiting unusual eight transmembrane topologies and cytosolic N-termini, BeCyclOp is the superior optogenetic tool (light/dark activity ratio: 5,000; no cAMP production; turnover (20 °C) ~17 cGMPs\(^{-1}\)). Via co-expressed CNG channels (OLF in oocytes, TAX-2/4 in C. elegans muscle), BeCyclOp photoactivation induces a rapid conductance increase and depolarization at very low light intensities. In O\(_2\)/CO\(_2\) sensory neurons of C. elegans, BeCyclOp activation evokes behavioural responses consistent with their normal sensory function. BeCyclOp therefore enables precise and rapid optogenetic manipulation of cGMP levels in cells and animals.},
  language  = {en}
}
@article{TsaiGrimmChaoetal.2015,
  author    = {Tsai, Yu-Chen and Grimm, Stefan and Chao, Ju-Lan and Wang, Shih-Chin and Hofmeyer, Kerstin and Shen, Jie and Eichinger, Fred and Michalopoulou, Theoni and Yao, Chi-Kuang and Chang, Chih-Hsuan and Lin, Shih-Han and Sun, Y. Henry and Pflugfelder, Gert O.},
  title     = {Optomotor-blind negatively regulates Drosophila eye development by blocking Jak/STAT signaling},
  series = {PLoS ONE},
  volume    = {10},
  journal   = {PLoS ONE},
  number    = {3},
  doi       = {10.1371/journal.pone.0120236},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143577},
  pages     = {e0120236},
  year      = {2015},
  abstract  = {Organ formation requires a delicate balance of positive and negative regulators. In Drosophila eye development, wingless (wg) is expressed at the lateral margins of the eye disc and serves to block retinal development. The T-box gene optomotor-blind (omb) is expressed in a similar pattern and is regulated by Wg. Omb mediates part of Wg activity in blocking eye development. Omb exerts its function primarily by blocking cell proliferation. These effects occur predominantly in the ventral margin. Our results suggest that the primary effect of Omb is the blocking of Jak/STAT signaling by repressing transcription of upd which encodes the Jak receptor ligand Unpaired.},
  language  = {en}
}