TY  - THES
A1  - Bertho, Sylvain
T1  - Biochemical and molecular characterization of an original master sex determining gene in Salmonids
T1  - Biochemische und molekulare Charakterisierung des Mastergens bei der Sex-bestimmung in Salmoniden
N2  - 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.
N2  - Le développement du sexe est un processus fondamental et versatile qui forme la morphologie, la physiologie et le comportement des animaux. Le processus de développement sous-jacent est composé de la détermination et de la différentiation du sexe. Les mécanismes de détermination du sexe sont extrêment labile parmi les taxons. Les signaux initiaux du processus de détermination du sexe sont souvent génétiques et nommés gènes de détermination du sexe. Ces gènes sont exprimés dans la gonade bipotente et font pencher l’équilibre vers un programme de développement permettant la formation soit d’un testicule soit d’un ovaire. Les poissons représentent un large et fascinant groupe de vertébrés pour étudier les processus de détermination et de différentiation du sexe. A l’heure actuelle, parmi les gènes de détermination connus, trois familles de gènes nommément sox, dmrt and les facteurs TGF-β gouvernent ce processus de développement. Comme exception à cette règle, sdY  « sexually dimorphic on the Y » n’appartient à aucune de ces familles puisqu’il provient d’une duplication/évolution d’un gène ancestral de l’immunité, c’est-à-dire d’un facteur lié à l’interféron, irf9. sdY est le gène maître de la détermination du sexe chez les salmonidés, un groupe de poissons incluant des espèces tel que la truite arc-en-ciel et le saumon Altantique. L’étude présentée avait pour but de premièrement caractériser les propriétés de la protéine SdY. Les résultats indiquent que SdY est localisée de façon prédominante dans le cytoplasme testés dans diverses cellules de poissons et de mammifères et confirmé par des différentes méthodes. Une analyse in silico prédictive a révélé que SdY est composé d’un core β-sandwich entouré par trois hélices-α ainsi que des caractéristiques lui conférant un site d’interaction protéine-protéine. Deuxièment, l’étude avait pour but de comprendre comment SdY pouvait entraîner  la différentiation testiculaire. SdY est une version tronquée divergente de Irf9 qui a conservé le domaine protéine-protéine mais a perdu le domaine d’interaction à l’ADN présent dans le gène ancestral. Il a été proposé que SdY entraîne la différentiation testiculaire par interaction(s) protéine-protéine. Afin d’évaluer cette hypothèse, un crible double-hybride en système levure a révélé une forte proportion de facteurs de transcription incluant les protéines fox. En utilisant de nombreuses méthodes au niveau cellulaire et biochimique, nous avons confirmé une interaction entre SdY et Foxl2, un facteur majeur impliqué dans la différentiation ovarienne et gardien de son identité. De façon intéressante, l’interaction de SdY avec Foxl2 conduit à une translocation nucléaire de SdY à partir du cytoplasme. De plus, le mécanisme de translocation de SdY est spécifique à la protéine Foxl2 et dans une moindre mesure à Foxl3 parmi les protéines Fox de poissons ou bien des protéines FoxL2 de mammifères. Puis, nous avons montré que cette interaction permet la stabilisation de SdY et empêche sa dégradation. Enfin, pour mieux décrypter l’action de SdY, nous avons utilisé comme modèle une version mutée qui a été identifiée dans une population naturelle de saumon Chinook avec des individus XY femelles. Les résultats montrent que la mutation induit un défaut de conformation local menant à une protéine mal-repliée et à sa dégradation. De plus, la version mutée compromet l’interaction avec Foxl2 définissant un seuil minimal d’induction de la différentiation testiculaire.  Les résultats de ma thèse pris dans leur ensemble proposent  que SdY pourrait entraîner la différentiation testiculaire chez les salmonidés en empêchant Foxl2 d’induire la différentiation ovarienne. Les recherches doivent se poursuivre dans le but de comprendre comment l’interaction SdY avec Foxl2 fonctionne in vivo.
N2  - Sexuelle Entwicklung ist ein grundlegender und vielfältiger Prozess, der die Morphologie, Physiologie und das Verhalten von Tieren gestaltet. Der zugrundeliegende Entwicklungsprozess besteht aus der Geschlechtsbestimmung und der Geschlechtsdifferenzierung. Die Mechanismen der Geschlechtsbestimmung sind sehr instabil zwischen verschiedenen Arten. Die Auslöser des Prozesses der Geschlechtsbestimmung sind oft genetischen Ursprungs wie geschlechtsbestimmende Gene. Diese Gene werden in den bipotentialen Gonaden exprimiert und steuern die Balance eines entwicklungsgemäßen Programms, das die Differenzierung zum Testis oder Ovar erlaubt. Fische repräsentieren eine umfangreiche und faszinierende Gruppe von Vertebraten, um die Mechanismen der Geschlechtsbestimmung und –differenzierung zu untersuchen. Bislang ist bekannt, dass –unter den bekannten geschlechtsbestimmenden Genen- die drei Gen-Familien sox, dmrt und die TGFß-Faktoren dieses Entwicklungsprogramm steuern. Als Ausnahme von dieser Regel ist sdY „sexually dimorphic on the Y“ keiner dieser Familien zugehörig da es von der Duplikation / Evolution eines Vorgänger-Gens, das mit Immunität wie z.B. interferon related factor9, irf9, in Verbindung steht, herrührt. sdY ist das Mastergen der Geschlechtsbestimmung in Salmoniden, die als Gruppe von Fischen Arten wie die Regenbogenforelle und den Atlantischen Lachs umfassen. Das Ziel der vorliegenden Arbeit war es zunächst die Eigenschaften des SdY Proteins zu charakterisieren. Die Ergebnisse zeigen, dass SdY vor allem im Zytoplasma lokalisiert ist. Dies wurde in verschiedenen Fischen und Säugetier Zelllinien untersucht und mit Hilfe verschiedener Methoden bestätigt. Prädiktive in silico Analysen zeigten, dass SdY aus einem ß-sandwich Kern besteht, der von drei α-Helices umgeben ist sowie spezifischen Eigenschaften für eine putative Protein-Protein Interaktion Stelle. Das zweite Ziel der vorliegenden Arbeit war es, zu verstehen, wie SdY die testikuläre Differenzierung auslösen könnte. SdY ist eine verkürzte, divergente Version von Irf9, das eine konservierte Protein-Protein Domäne aufweist, jedoch seine DNA Interaktion Domäne a seines Vorläufer Gens verloren hat. Daher wurde angenommen, dass SdY die testikuläre Differenzierung durch Protein-Protein Interaktion initiieren könnte. Um diese Hypothese zu bestätigen führten wir zuerst einen Yeast Two-Hybrid Screen durch, der einen hohen Anteil an Transkriptionsfaktoren darunter fox Proteine zeigte. Unter Einsatz verschiedener biochemischer und zellulärer Methoden bestätigten wir eine Interaktion zwischen SdY und Foxl2, einem wesentlichen Transkriptionsfaktor, der in die Differenzierung und die Erhaltung der Identität der Ovarien involviert ist. Interessanterweise führt die Interaktion von SdY mit Foxl2 zu einer nukleären Translokation von SdY aus dem Zytoplasma. Außerdem wurde festgestellt, dass dieser SdY Translokations-Mechanismus für das Fisch Foxl2 und in einem geringerem Maße für Foxl3 spezifisch ist aber nicht für andere Fox Proteine oder Säuger FoxL2. Des Weiteren haben wir herausgefunden, dass diese Interaktion die Stabilisierung von SdY ermöglicht und sein Abbau verhindert. Zuletzt haben wir ein Modell einer mutierten Version von SdY benutzt, die in XY Weibchen der natürlichen Population der Königslachse identifiziert wurde, um die Wirkung von SdY besser zu entschlüsseln. Die Ergebnisse zeigen, dass diese Mutation einen lokalen Konformationsdefekt verursacht, der zu fehlgefalteten Proteinen und einem raschen Abbau führt. Darüber hinaus beeinträchtigt die mutierte Version die Interaktion mit FoxL2 und definiert einen minimalen Grenzwert, um die testikuläre Differenzierung zu induzieren. Insgesamt deuten die Ergebnisse meiner Dissertation darauf hin, dass SdY die testikuläre Differenzierung in Salmoniden auslöst, indem es verhindert, dass Foxl2 die Differenzierung der Ovarien fördert. In Zukunft soll erforscht werden, wie sich die Interaktion von SdY und Foxl2 in-vivo auswirkt.
KW  - Fish Sex determination
KW  - gonad development
KW  - SdY
KW  - salmonids
KW  - Lachsartige <Familie>
KW  - Geschlechtsdifferenzierung
KW  - Molekulargenetik
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-139130
ER  - 
TY  - JOUR
A1  - Seren, Ümit
A1  - Grimm, Dominik
A1  - Fitz, Joffrey
A1  - Weigel, Detlef
A1  - Nordborg, Magnus
A1  - Borgwardt, Karsten
A1  - Korte, Arthur
T1  - AraPheno: a public database for Arabidopsis thaliana phenotypes
JF  - Nucleic Acids Research
N2  - Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map.
KW  - phenotype
KW  - arabidopsis
KW  - genotype
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147909
VL  - 45
IS  - D1
ER  - 
TY  - JOUR
A1  - Otto, Christoph
A1  - Hahlbrock, Theresa
A1  - Eich, Kilian
A1  - Karaaslan, Ferdi
A1  - Jürgens, Constantin
A1  - Germer, Christoph-Thomas
A1  - Wiegering, Armin
A1  - Kämmerer, Ulrike
T1  - Antiproliferative and antimetabolic effects behind the anticancer property of fermented wheat germ extract
JF  - BMC Complementary and Alternative Medicine
N2  - Background
Fermented wheat germ extract (FWGE) sold under the trade name Avemar exhibits anticancer activity in vitro and in vivo. Its mechanisms of action are divided into antiproliferative and antimetabolic effects. Its influcence on cancer cell metabolism needs further investigation. One objective of this study, therefore, was to further elucidate the antimetabolic action of FWGE. The anticancer compound 2,6-dimethoxy-1,4-benzoquinone (DMBQ) is the major bioactive compound in FWGE and is probably responsible for its anticancer activity. The second objective of this study was to compare the antiproliferative properties in vitro of FWGE and the DMBQ compound.

Methods
The IC\(_{50}\) values of FWGE were determined for nine human cancer cell lines after 24 h of culture. The DMBQ compound was used at a concentration of 24 μmol/l, which is equal to the molar concentration of DMBQ in FWGE. Cell viability, cell cycle, cellular redox state, glucose consumption, lactic acid production, cellular ATP levels, and the NADH/NAD\(^+\) ratio were measured.

Results
The mean IC\(_{50}\) value of FWGE for the nine human cancer cell lines tested was 10 mg/ml. Both FWGE (10 mg/ml) and the DMBQ compound (24 μmol/l) induced massive cell damage within 24 h after starting treatment, with changes in the cellular redox state secondary to formation of intracellular reactive oxygen species. Unlike the DMBQ compound, which was only cytotoxic, FWGE exhibited cytostatic and growth delay effects in addition to cytotoxicity. Both cytostatic and growth delay effects were linked to impaired glucose utilization which influenced the cell cycle, cellular ATP levels, and the NADH/NAD\(^+\) ratio. The growth delay effect in response to FWGE treatment led to induction of autophagy.

Conclusions
FWGE and the DMBQ compound both induced oxidative stress-promoted cytotoxicity. In addition, FWGE exhibited cytostatic and growth delay effects associated with impaired glucose utilization which led to autophagy, a possible previously unknown mechanism behind the influence of FWGE on cancer cell metabolism.
KW  - cytostatic
KW  - FWGE
KW  - benzoquinone
KW  - cancer cells
KW  - reactive oxygen species
KW  - autophagy
KW  - cytotoxicity
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146013
VL  - 16
IS  - 160
ER  - 
TY  - JOUR
A1  - Schwarz, Roland F.
A1  - Tamuri, Asif U.
A1  - Kultys, Marek
A1  - King, James
A1  - Godwin, James
A1  - Florescu, Ana M.
A1  - Schultz, Jörg
A1  - Goldman, Nick
T1  - ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
JF  - Nucleic Acids Research
N2  - 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).
KW  - visualization
KW  - multiple sequence alignments
KW  - phylogenetic trees
KW  - Alvis
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166374
VL  - 44
IS  - 8
ER  - 
TY  - JOUR
A1  - Chen, Jiangtian
A1  - Reiher, Wencke
A1  - Hermann-Luibl, Christiane
A1  - Sellami, Azza
A1  - Cognigni, Paola
A1  - Kondo, Shu
A1  - Helfrich-Förster, Charlotte
A1  - Veenstra, Jan A.
A1  - Wegener, Christian
T1  - Allatostatin A Signalling in Drosophila Regulates Feeding and Sleep and Is Modulated by PDF
JF  - PLoS Genetics
N2  - Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations. The circadian system and peptidergic signals are important components of this modulation, but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep. We show that specific thermogenetic activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and enteroendocrine cells reduces feeding and promotes sleep in the fruit fly Drosophila. The effects of AstA cell activation are mediated by AstA peptides with receptors homolog to galanin receptors subserving similar and apparently conserved functions in vertebrates. We further identify the PLP neurons as a downstream target of the neuropeptide pigment-dispersing factor (PDF), an output factor of the circadian clock. PLP neurons are contacted by PDF-expressing clock neurons, and express a functional PDF receptor demonstrated by cAMP imaging. Silencing of AstA signalling and continuous input to AstA cells by tethered PDF changes the sleep/activity ratio in opposite directions but does not affect rhythmicity. Taken together, our results suggest that pleiotropic AstA signalling by a distinct neuronal and enteroendocrine AstA cell subset adapts the fly to a digestive energy-saving state which can be modulated by PDF.
KW  - neurons
KW  - neuroimaging
KW  - circadian rhythms
KW  - food consumption
KW  - sleep
KW  - biological locomotion
KW  - Drosophila melanogaster
KW  - signal peptides
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-178170
VL  - 12
IS  - 9
ER  - 
TY  - JOUR
A1  - Becker, Nils
A1  - Kucharski, Robert
A1  - Rössler, Wolfgang
A1  - Maleszka, Ryszard
T1  - Age‐dependent transcriptional and epigenomic responses to light exposure in the honey bee brain
JF  - FEBS Open Bio
N2  - Light is a powerful environmental stimulus of special importance in social honey bees that undergo a behavioral transition from in-hive to outdoor foraging duties. Our previous work has shown that light exposure induces structural neuronal plasticity in the mushroom bodies (MBs), a brain center implicated in processing inputs from sensory modalities. Here, we extended these analyses to the molecular level to unravel light-induced transcriptomic and epigenomic changes in the honey bee brain. We have compared gene expression in brain compartments of 1- and 7-day-old light-exposed honey bees with age-matched dark-kept individuals. We have found a number of differentially expressed genes (DEGs), both novel and conserved, including several genes with reported roles in neuronal plasticity. Most of the DEGs show age-related changes in the amplitude of light-induced expression and are likely to be both developmentally and environmentally regulated. Some of the DEGs are either known to be methylated or are implicated in epigenetic processes suggesting that responses to light exposure are at least partly regulated at the epigenome level. Consistent with this idea light alters the DNA methylation pattern of bgm, one of the DEGs affected by light exposure, and the expression of microRNA miR-932. This confirms the usefulness of our approach to identify candidate genes for neuronal plasticity and provides evidence for the role of epigenetic processes in driving the molecular responses to visual stimulation.
KW  - DNA methylation
KW  - insect brain
KW  - light-induced gene expression
KW  - microRNA
KW  - neuronal plasticity
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147080
VL  - 6
IS  - 7
ER  - 
TY  - JOUR
A1  - Rosenbaum, Corinna
A1  - Schick, Martin Alexander
A1  - Wollborn, Jakob
A1  - Heider, Andreas
A1  - Scholz, Claus-Jürgen
A1  - Cecil, Alexander
A1  - Niesler, Beate
A1  - Hirrlinger, Johannes
A1  - Walles, Heike
A1  - Metzger, Marco
T1  - Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo
JF  - PLoS One
N2  - Background
Enteric glial cells (EGCs) are the main constituent of the enteric nervous system and share similarities with astrocytes from the central nervous system including their reactivity to an inflammatory microenvironment. Previous studies on EGC pathophysiology have specifically focused on mucosal glia activation and its contribution to mucosal inflammatory processes observed in the gut of inflammatory bowel disease (IBD) patients. In contrast knowledge is scarce on intestinal inflammation not locally restricted to the mucosa but systemically affecting the intestine and its effect on the overall EGC network.

Methods and Results
In this study, we analyzed the biological effects of a systemic LPS-induced hyperinflammatory insult on overall EGCs in a rat model in vivo, mimicking the clinical situation of systemic inflammation response syndrome (SIRS). Tissues from small and large intestine were removed 4 hours after systemic LPS-injection and analyzed on transcript and protein level. Laser capture microdissection was performed to study plexus-specific gene expression alterations. Upon systemic LPS-injection in vivo we observed a rapid and dramatic activation of Glial Fibrillary Acidic Protein (GFAP)-expressing glia on mRNA level, locally restricted to the myenteric plexus. To study the specific role of the GFAP subpopulation, we established flow cytometry-purified primary glial cell cultures from GFAP promotor-driven EGFP reporter mice. After LPS stimulation, we analyzed cytokine secretion and global gene expression profiles, which were finally implemented in a bioinformatic comparative transcriptome analysis. Enriched GFAP+ glial cells cultured as gliospheres secreted increased levels of prominent inflammatory cytokines upon LPS stimulation. Additionally, a shift in myenteric glial gene expression profile was induced that predominantly affected genes associated with immune response.

Conclusion and Significance
Our findings identify the myenteric GFAP-expressing glial subpopulation as particularly susceptible and responsive to acute systemic inflammation of the gut wall and complement knowledge on glial involvement in mucosal inflammation of the intestine.
KW  - gene expression
KW  - gastrointestinal tract
KW  - inflammatory bowel disease
KW  - central nervous system
KW  - systemic inflammatory response syndrome
KW  - inflammation
KW  - astrocytes
KW  - cytokines
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146544
VL  - 11
IS  - 3
ER  - 
TY  - JOUR
A1  - Xu, Li
A1  - He, Jianzheng
A1  - Kaiser, Andrea
A1  - Gräber, Nikolas
A1  - Schläger, Laura
A1  - Ritze, Yvonne
A1  - Scholz, Henrike
T1  - A Single Pair of Serotonergic Neurons Counteracts Serotonergic Inhibition of Ethanol Attraction in Drosophila
JF  - PLoS ONE
N2  - 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.
KW  - attraction
KW  - ethanol
KW  - Drosophila melanogaster
KW  - serotonin transporter
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166762
VL  - 11
IS  - 12
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Steffan-Dewenter, Ingolf
A1  - Härtel, Stephan
A1  - Helfrich-Förster, Charlotte
T1  - A new device for monitoring individual activity rhythms of honey bees reveals critical effects of the social environment on behavior
JF  - Journal of Comparative Physiology A
N2  - 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.
KW  - Social entrainment
KW  - Foragers
KW  - Nurses
KW  - Locomotor activity
KW  - Temperature rhythms
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188030
VL  - 202
IS  - 8
ER  - 
TY  - THES
A1  - Hackl, Thomas
T1  - A draft genome for the Venus flytrap, Dionaea muscipula : Evaluation of assembly strategies for a complex Genome – Development of novel approaches and bioinformatics solutions
T1  - Ein Genom für die Venus Fliegenfalle, Dionaea muscipula
N2  - 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.
N2  - Die Venus Fliegenfalle, D. muscipula fasziniert aufgrund ihres karnivoren Lebensstil
und ihrer hochspezialisierten Fallen Biologen schon seit der Zeit von Charles Darwins.
Das Ziel des D. muscipula Genomprojekts ist es, neue Einblicke in den genomischen
Grundlagen dieser besonderen Pflanze zu gewinnen.
Die diploide Venus Fliegenfalle verfügt mit eine geschätzten Größe von 2.6 bp
bis 3Gbp über ein vergleichsweise großes Genom, das zudem zu über 70% aus
repetitiven Regionen besteht. Sequenzierung und Assembly von Genomen dieser
Größenordnung stellen selbst mit neusten technischen und informatischen Methoden
eine große Herausforderung dar. Zum ersten mal sequenziert und assembliert wurde
das Genom 2011 durch das BGI (Beijing Genomics Institute). Meine Arbeit am
Genom der Fliegenfalle begann mit der Analyse des 3.7Gbp großen Assemblies,
welches wir vom BGI erhalten haben. Mit meinen Untersuchungen könnte ich zeigen,
dass das Assembly stark fragmentiert und gleichzeitig durch überrepräsentierte
repetitive Sequenzen stark aufgebläht ist. Darüberhinaus beinhaltet es gerade ein
mal eine drittel der erwarteten Gene in Volllänge, wodurch es für die weiter Analyse
ungeeignet ist.
In meiner weiteren Arbeit habe ich mich daher darauf konzentriert, unsere Sequenzierungsund
Assemblierungsstrategie zu verfeinern um ein stärker zusammenhängendes und
vollständigeres Assembly zu erhalten. Dafür war es notwendig die Qualität der Sequenzierdaten
so wie den Assemblierungsprozess selbst zu optimieren, und Programme zu
entwickeln, die eine Verbesserung der Daten und eine Analyse der Zwischenergebnisse
ermöglichen. So wurden etwa zur neue Bibliotheken von nicht-polymorphen
DNA-Proben sequenziert um die Heterogenität im Datensatz zu verringern. Um die
Kontinuität der Assemblies zu verbessern und Probleme mit der Heterozygosität der
Daten zu lösen habe ich eine Reihe verschiedener Assemblierungsprogramme getestet.
Dabei zeigte sich, dass das Programm ALLPATHS-LG am besten geeignet ist für die
Assemblierung von D. muscipula Daten. Durch den Einsatz von digitaler Normalisierung
konnte ich den Bedarf an Computerressourcen für einzelne Assemblierungen
deutlich reduzieren und gleichzeitig die Kontinuität der Assemblies deutlich erhöhen.
Zur besseren Auflösung repetitiver Strukturen im Genom, habe ich auf eine neu
entwickelte Sequenziertechnologie von PacBio zurückgegriffen, die deutlich länger
Sequenzen erzeugt. Um die neuen Daten trotz ihrer hohen Fehlerrate von 15%
für Assemblierungen nutzen zu können, entwickelte ich das Korrekturprogramm
proovread (Hackl et al., 2014). proovread nutzt kurze Illumina Sequenzen mit hoher Sequenziertiefe um innerhalb eines iterativen Prozess Fehler in PacBio Daten ausfindig
zu machen und zu korrigieren. Das Programm erreicht dabei eine bessere Genauigkeit
und eine höhere Sensitivität als vergleichbare Software. Darüber hinaus erlaubt sein
flexibles Design auch Datensätze in der Größenordung des Fliegenfallengenoms
effizient auf großen Rechenclustern zu bearbeiten.
Neben dem Assemblierungsprozess an sich, stellt auch die Analyse von Assemblies
großer Genome eine Herausforderung dar. Klassische Methoden basieren oft auf
der rechenintensiven Berechnung von Alignments zwischen Sequenzierdaten und
Assembly. Um vergleichbare Analysen deutlich schneller generieren zu können, habe
ich Programme entwickelt die auf der Auswertung von k-mer Häufigkeiten beruhen,
und die gewonnenen Ergebnisse in übersichtlichen Graphiken darstellen.
Durch Kombination der so gewonnenen Einblicke und der verschiedenen Erkenntnisse
bezüglich der Optimierung es Assemblierungsprozesses, war es mir am Ende
möglich, ein Assembly von hoher Qualität für das Genom der Venus Fliegenfalle
zu rekonstruieren. Dieses habe ich weiter verfeinert, unter anderem durch das Entfernen
heterozygoter Sequenzen und durch das Flicken von Lücken mit Hilfe von
PacBio Daten. Das so erstelle Assembly besteht aus 86 × 103 Sequenzen und hat
eine Gesamtgröße von 1.45Gbp. Der Unterschied zur erwarteten Genomgröße
lässt sich dabei gut durch kollabierte repetitive Regionen erklären. Gleichzeitig untermauert
ein hoher Anteil an Volllängengenen im Assembly die Interpretation, dass das
vorliegende Assembly eine vollständiges und umfassendes Abbild der D. muscipula
Genom zeigt, und dass es sich damit als gute Grundlage für weitere Untersuchungen
zur Biologie dieser faszinierenden Pflanze eignet.
KW  - Venusfliegenfalle
KW  - genome assembly
KW  - repeats
KW  - heterozygosity
KW  - pacbio correction
KW  - Genom
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-133149
ER  -