TY - THES A1 - Orf, Isabel T1 - Photorespiratory metabolism in the cyanobacterial model Synechocystis sp. strain PCC 6803 BT - a systems biology approach Y1 - 2016 ER - TY - THES A1 - Reinecke, Antje Adriana T1 - Impact of protein structure on the mechanics and assembly of mytilus byssal threads Y1 - 2016 ER - TY - THES A1 - Breuer, David T1 - The plant cytoskeleton as a transportation network T1 - Modellierung des pflanzliche Zytoskeletts als Transportnetzwerk N2 - The cytoskeleton is an essential component of living cells. It is composed of different types of protein filaments that form complex, dynamically rearranging, and interconnected networks. The cytoskeleton serves a multitude of cellular functions which further depend on the cell context. In animal cells, the cytoskeleton prominently shapes the cell's mechanical properties and movement. In plant cells, in contrast, the presence of a rigid cell wall as well as their larger sizes highlight the role of the cytoskeleton in long-distance intracellular transport. As it provides the basis for cell growth and biomass production, cytoskeletal transport in plant cells is of direct environmental and economical relevance. However, while knowledge about the molecular details of the cytoskeletal transport is growing rapidly, the organizational principles that shape these processes on a whole-cell level remain elusive. This thesis is devoted to the following question: How does the complex architecture of the plant cytoskeleton relate to its transport functionality? The answer requires a systems level perspective of plant cytoskeletal structure and transport. To this end, I combined state-of-the-art confocal microscopy, quantitative digital image analysis, and mathematically powerful, intuitively accessible graph-theoretical approaches. This thesis summarizes five of my publications that shed light on the plant cytoskeleton as a transportation network: (1) I developed network-based frameworks for accurate, automated quantification of cytoskeletal structures, applicable in, e.g., genetic or chemical screens; (2) I showed that the actin cytoskeleton displays properties of efficient transport networks, hinting at its biological design principles; (3) Using multi-objective optimization, I demonstrated that different plant cell types sustain cytoskeletal networks with cell-type specific and near-optimal organization; (4) By investigating actual transport of organelles through the cell, I showed that properties of the actin cytoskeleton are predictive of organelle flow and provided quantitative evidence for a coordination of transport at a cellular level; (5) I devised a robust, optimization-based method to identify individual cytoskeletal filaments from a given network representation, allowing the investigation of single filament properties in the network context. The developed methods were made publicly available as open-source software tools. Altogether, my findings and proposed frameworks provide quantitative, system-level insights into intracellular transport in living cells. Despite my focus on the plant cytoskeleton, the established combination of experimental and theoretical approaches is readily applicable to different organisms. Despite the necessity of detailed molecular studies, only a complementary, systemic perspective, as presented here, enables both understanding of cytoskeletal function in its evolutionary context as well as its future technological control and utilization. N2 - Das Zytoskelett ist ein notwendiger Bestandteil lebender Zellen. Es besteht aus verschiedenen Arten von Proteinfilamenten, die ihrerseits komplexe, sich dynamisch reorganisierende und miteinander verknüpfte Netzwerke bilden. Das Zytoskelett erfüllt eine Vielzahl von Funktionen in der Zelle. In Tierzellen bestimmt das Aktin-Zytoskelett maßgeblich die mechanischen Zelleigenschaften und die Zellbewegung. In Pflanzenzellen hingegen kommt dem Aktin-Zytoskelett eine besondere Bedeutung in intrazellulären Transportprozessen zu, bedingt insbesondere durch die starre pflanzliche Zellwand sowie die Zellgröße. Als wesentlicher Faktor für Zellwachstum und somit auch die Produktion von Biomasse, ist Zytoskelett-basierter Transport daher von unmittelbarer ökologischer und ökonomischer Bedeutung. Während das Wissen über die molekularen Grundlagen Zytoskelett-basierter Transportprozesse beständig wächst, sind die zugrunde liegenden Prinzipien zellweiter Organisation bisher weitgehend unbekannt. Diese Dissertation widmet sich daher folgender Frage: Wie hängt die komplexe Architektur des pflanzlichen Zytoskeletts mit seiner intrazellulären Transportfunktion zusammen? Eine Antwort auf diese Frage erfordert eine systemische Perspektive auf Zytoskelettstruktur und -transport. Zu diesem Zweck habe ich Mikroskopiedaten mit hoher raumzeitlicher Auflösung sowie Computer-gestützte Bildanalysen und mathematische Ansätzen der Graphen- und Netzwerktheorie kombiniert. Die vorliegende Dissertation umfasst fünf meiner Publikationen, die sich einem systemischen Verständnis des pflanzlichen Zytoskeletts als Transportnetzwerk widmen: (1) Dafür habe ich Bilddaten-basierte Netzwerkmodelle entwickelt, die eine exakte und automatisierte Quantifizierung der Architektur des Zytoskeletts ermöglichen. Diese Quantifizierung kann beispielsweise in genetischen oder chemischen Versuchen genutzt werden und für eine weitere Erforschung der genetischen Grundlagen und möglicher molekularer Interaktionspartner des Zytoskeletts hilfreich sein; (2) Ich habe nachgewiesen, dass das pflanzliche Aktin-Zytoskelett Eigenschaften effizienter Transportnetzwerk aufweist und Hinweise auf seine evolutionären Organisationsprinzipien liefert; (3) Durch die mathematische Optimierung von Transportnetzwerken konnte ich zeigen, dass unterschiedliche Pflanzenzelltypen spezifische und optimierte Organisationsstrukturen des Aktin-Zytoskeletts aufweisen; (4) Durch quantitative Analyse des Transports von Organellen in Pflanzenzellen habe ich nachgewiesen, dass sich Transportmuster ausgehend von der Struktur des Aktin-Zytoskeletts vorhersagen lassen. Dabei spielen sowohl die Organisation des Zytoskeletts auf Zellebene als auch seine Geometrie eine zentrale Rolle. (5) Schließlich habe ich eine robuste, optimierungs-basierte Methode entwickelt, die es erlaubt, individuelle Filamente eines Aktin-Netzwerks zu identifizieren. Dadurch ist es möglich, die Eigenschaften einzelner Zytoskelettfilamente im zellulären Kontext zu untersuchen. Die im Zuge dieser Dissertation entwickelten Methoden wurden frei und quelloffen als Werkzeuge zur Beantwortung verwandter Fragestellung zugänglich gemacht. Insgesamt liefern die hier präsentierten Ergebnisse und entwickelten Methoden quantitative, systemische Einsichten in die Transportfunktion des Zytoskeletts. Die hier etablierte Kombination von experimentellen und theoretischen Ansätzen kann, trotz des Fokusses auf das pflanzliche Zytoskelett, direkt auf andere Organismen angewendet werden. Als Ergänzung molekularer Studien bildet ein systemischer Blickwinkel, wie er hier entwickelt wurde, die Grundlage für ein Verständnis sowohl des evolutionären Kontextes als auch zukünftiger Kontroll- und Nutzungsmöglichkeiten des pflanzlichen Zytoskeletts. KW - systems biology KW - mathematical modeling KW - cytoskeleton KW - plant science KW - graph theory KW - image analysis KW - Systembiologie KW - mathematische Modellierung KW - Zytoskelett KW - Zellbiologie KW - Graphtheorie KW - Bildanalyse Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93583 ER - TY - THES A1 - Makower, Katharina T1 - The roles of secondary metabolites in microcystis inter-strain interactions T1 - Die Rolle von Sekundärmetaboliten in den Wechselbeziehungen zwischen Microcystis-Stämmen N2 - Among the bloom-forming and potentially harmful cyanobacteria, the genus Microcystis represents a most diverse taxon, on the genomic as well as on morphological and secondary metabolite levels. Microcystis communities are composed of a variety of diversified strains. The focus of this study lies on potential interactions between Microcystis representatives and the roles of secondary metabolites in these interaction processes. The role of secondary metabolites functioning as signaling molecules in the investigated interactions is demonstrated exemplary for the prevalent hepatotoxin microcystin. The extracellular and intracellular roles of microcystin are tested in microarray-based transcriptomic approaches. While an extracellular effect of microcystin on Microcystis transcription is confirmed and connected to a specific gene cluster of another secondary metabolite in this study, the intracellularly occurring microcystin is related with several pathways of the primary metabolism. A clear correlation of a microcystin knockout and the SigE-mediated regulation of carbon metabolism is found. According to the acquired transcriptional data, a model is proposed that postulates the regulating effect of microcystin on transcriptional regulators such as the alternative sigma factor SigE, which in return captures an essential role in sugar catabolism and redox-state regulation. For the purpose of simulating community conditions as found in the field, Microcystis colonies are isolated from the eutrophic lakes near Potsdam, Germany and established as stably growing under laboratory conditions. In co-habitation simulations, the recently isolated field strain FS2 is shown to specifically induce nearly immediate aggregation reactions in the axenic lab strain Microcystis aeruginosa PCC 7806. In transcriptional studies via microarrays, the induced expression program in PCC 7806 after aggregation induction is shown to involve the reorganization of cell envelope structures, a highly altered nutrient uptake balance and the reorientation of the aggregating cells to a heterotrophic carbon utilization, e.g. via glycolysis. These transcriptional changes are discussed as mechanisms of niche adaptation and acclimation in order to prevent competition for resources. N2 - Die Gattung Microcystis stellt unter den blüten-bildenden Cyanobakterien ein Taxon besonderer Diversität dar. Dies gilt sowohl für die Genomstruktur als auch für morphologische Charakteristika und Sekundärmetabolite. Microcystis-Communities weisen eine Zusammensetzung aus einer Vielzahl von diversifizierten Stämmen auf. Das Hauptaugenmerk dieser Arbeit lag darauf, potentielle Wechselwirkungen zwischen Microcystis-Vertretern zu charakterisieren und die Rolle von Sekundärmetaboliten in Interaktions-Prozessen zu untersuchen. Die Rolle von Sekundärmetaboliten als Signalstoffe in Microcystis-Interaktionen wurde exemplarisch für das Hepatotoxin Microcystin demonstriert. Sowohl die extrazelluläre als auch die intrazellulare Funktion von Microcystin wurde anhand von Microarray-basierten Transkriptomstudien getestet. Dabei konnte eine extrazelluläre Wirkung von Microcystin bestätigt werden und mit der Transkription eines spezifischen anderen Sekundärmetaboliten in Verbindung gebracht werden. Intrazellulär vorkommendes Microcystin wurde hingegen mit verschiedenen Stoffwechselwegen des Primärstoffwechsels verknüpft. Es konnte ein deutlicher Zusammenhang zwischen einem Microcystin-Knockout und der SigE-vermittelten Regulation des Kohlenstoffmetabolismus festgestellt werden. Anhand der erworbenen Transkriptionsdaten wurde ein Modell vorgeschlagen, das eine regulierende Wirkung von Microcystin auf Transkriptionsfaktoren wie den alternativen Sigmafaktor SigE postuliert, welcher seinerseits eine zentrale Rolle in Zuckerabbauprozessen und zellulärer Redoxregulation einnimmt. Mit dem Ziel, Community-ähnliche Bedingungen zu simulieren, wurden Microcystis-Freiland-Kolonien aus eutrophen Gewässern in der Umgebung von Potsdam isoliert und ein stabiles Wachstum unter Laborbedingungen etabliert. Es konnte gezeigt werden, dass der frisch isolierte Freilandstamm FS2 spezifisch eine starke Zellaggregation in Microcystis aeruginosa PCC 7806 (einem axenischen Labortstamm) auslösen konnte. In Transkriptionsstudien mit Hilfe von Microarrays wurden Expressionsprogramme gefunden, die sowohl einen Umbau von Zellhüllstrukturen, als auch einen stark veränderten transmembranen Nährstofftransport beinhalteten. Darüber hinaus konnte in den aggregierenden PCC 7806-Zellen eine Verlagerung zu heterotrophen Kohlenstoffabbauprozessen wie der Glykolyse gefunden werden. Die transkriptionellen Veränderungen wurden als Akklimationsmechanismen zur Positionierung in ökologische Nischen diskutiert, um Konkurrenzen um Ressourcen zu vermeiden. KW - microcystis KW - microcystin KW - secondary metabolites KW - transcriptomics KW - interactions KW - Sekundärmetabolite KW - Transkriptomik KW - Wechselwirkungen Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93916 ER - TY - THES A1 - Shahnejat-Bushehri, Sara T1 - Unravelling the role of the Arabidopsis NAC transcription factor JUNGBRUNNEN1 (JUB1) for the regulation of growth and stress responses Y1 - 2016 ER - TY - JOUR A1 - Klauschies, Toni A1 - Vasseur, David A. A1 - Gaedke, Ursula T1 - Trait adaptation promotes species coexistence in diverse predator and prey communities JF - Ecology and evolution N2 - Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator–prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to pre- vious studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species. KW - Coadaptation KW - equalizing and stabilizing mechanisms KW - maintenance of functional diversity KW - niche and fitness differences KW - supersaturated species coexistence KW - trait convergence and divergence Y1 - 2016 U6 - https://doi.org/10.1002/ece3.2172 SN - 2045-7758 PB - John Wiley & Sons, Inc. ER - TY - GEN A1 - Klauschies, Toni A1 - Vasseur, David A. A1 - Gaedke, Ursula T1 - Trait adaptation promotes species coexistence in diverse predator and prey communities N2 - Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator–prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to previous studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 227 KW - Coadaptation KW - equalizing and stabilizing mechanisms KW - maintenance of functional diversity KW - niche and fitness differences KW - supersaturated species coexistence KW - trait convergence and divergence Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-91498 SN - 1866-8372 ER - TY - THES A1 - Bartholomäus, Alexander T1 - Analyzing Transcriptional and Translational Control in E. coli using Deep-Seq Data Y1 - 2016 ER - TY - GEN A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Kaufmann, Kerstin T1 - Efficient multiplex mutagenesis by RNA‑guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene N2 - Background: The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its ‘endogenous’ environment. Results: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable largefragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions: Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 224 KW - RNA-guided Cas9 KW - Multiplex mutagenesis KW - Large fragment deletion KW - Germline transmission Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-90895 ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Kaufmann, Kerstin T1 - Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene JF - Plant methods N2 - Background The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its ‘endogenous’ environment. Results Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants. KW - RNA-guided Cas9 KW - Multiplex mutagenesis KW - Large fragment deletion KW - Germline transmission Y1 - 2016 U6 - https://doi.org/10.1186/s13007-016-0125-7 SN - 1746-4811 VL - 12 SP - 1 EP - 9 PB - BioMed Central CY - London ER -