@phdthesis{Baleka2019, author = {Baleka, Sina Isabelle}, title = {Palaeogenetic analyses of extinct Elephantidae from temperate and subtropical climates}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 114}, year = {2019}, language = {en} } @phdthesis{Behm2019, author = {Behm, Laura Vera Johanna}, title = {Thermoresponsive Zellkultursubstrate f{\"u}r zeitlich-r{\"a}umlich gesteuertes Auswachsen neuronaler Zellen}, doi = {10.25932/publishup-43619}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436196}, school = {Universit{\"a}t Potsdam}, pages = {VII, 105}, year = {2019}, abstract = {Ein wichtiges Ziel der Neurowissenschaften ist das Verst{\"a}ndnis der komplexen und zugleich faszinierenden, hochgeordneten Vernetzung der Neurone im Gehirn, welche neuronalen Prozessen, wie zum Beispiel dem Wahrnehmen oder Lernen wie auch Neuropathologien zu Grunde liegt. F{\"u}r verbesserte neuronale Zellkulturmodelle zur detaillierten Untersuchung dieser Prozesse ist daher die Rekonstruktion von geordneten neuronalen Verbindungen dringend erforderlich. Mit Oberfl{\"a}chenstrukturen aus zellattraktiven und zellabweisenden Beschichtungen k{\"o}nnen neuronale Zellen und ihre Neuriten in vitro strukturiert werden. Zur Kontrolle der neuronalen Verbindungsrichtung muss das Auswachsen der Axone zu benachbarten Zellen dynamisch gesteuert werden, zum Beispiel {\"u}ber eine ver{\"a}nderliche Zug{\"a}nglichkeit der Oberfl{\"a}che. In dieser Arbeit wurde untersucht, ob mit thermoresponsiven Polymeren (TRP) beschichtete Zellkultursubstrate f{\"u}r eine dynamische Kontrolle des Auswachsens neuronaler Zellen geeignet sind. TRP k{\"o}nnen {\"u}ber die Temperatur von einem zellabweisenden in einen zellattraktiven Zustand geschaltet werden, womit die Zug{\"a}nglichkeit der Oberfl{\"a}che f{\"u}r Zellen dynamisch gesteuert werden kann. Die TRP-Beschichtung wurde mikrostrukturiert, um einzelne oder wenige neuronale Zellen zun{\"a}chst auf der Oberfl{\"a}che anzuordnen und das Auswachsen der Zellen und Neuriten {\"u}ber definierte TRP-Bereiche in Abh{\"a}ngigkeit der Temperatur zeitlich und r{\"a}umlich zu kontrollieren. Das Protokoll wurde mit der neuronalen Zelllinie SH-SY5Y etabliert und auf humane induzierte Neurone {\"u}bertragen. Die Anordnung der Zellen konnte bei Kultivierung im zellabweisenden Zustand des TRPs f{\"u}r bis zu 7 Tage aufrecht erhalten werden. Durch Schalten des TRPs in den zellattraktiven Zustand konnte das Auswachsen der Neuriten und Zellen zeitlich und r{\"a}umlich induziert werden. Immunozytochemische F{\"a}rbungen und Patch-Clamp-Ableitungen der Neurone demonstrierten die einfache Anwendbarkeit und Zellkompatibilit{\"a}t der TRP-Substrate. Eine pr{\"a}zisere r{\"a}umliche Kontrolle des Auswachsens der Zellen sollte durch lokales Schalten der TRP-Beschichtung erreicht werden. Daf{\"u}r wurden Mikroheizchips mit Mikroelektroden zur lokalen Jouleschen Erw{\"a}rmung der Substratoberfl{\"a}che entwickelt. Zur Evaluierung der generierten Temperaturprofile wurde eine Temperaturmessmethode entwickelt und die erhobenen Messwerte mit numerisch simulierten Werten abgeglichen. Die Temperaturmessmethode basiert auf einfach zu applizierenden Sol-Gel-Schichten, die den temperatursensitiven Fluoreszenzfarbstoff Rhodamin B enthalten. Sie erm{\"o}glicht oberfl{\"a}chennahe Temperaturmessungen in trockener und w{\"a}ssriger Umgebung mit hoher Orts- und Temperaturaufl{\"o}sung. Numerische Simulationen der Temperaturprofile korrelierten gut mit den experimentellen Daten. Auf dieser Basis konnten Geometrie und Material der Mikroelektroden hinsichtlich einer lokal stark begrenzten Temperierung optimiert werden. Ferner wurden f{\"u}r die Kultvierung der Zellen auf den Mikroheizchips eine Zellkulturkammer und Kontaktboard f{\"u}r die elektrische Kontaktierung der Mikroelektroden geschaffen. Die vorgestellten Ergebnisse demonstrieren erstmalig das enorme Potential thermoresponsiver Zellkultursubstrate f{\"u}r die zeitlich und r{\"a}umlich gesteuerte Formation geordneter neuronaler Verbindungen in vitro. Zuk{\"u}nftig k{\"o}nnte dies detaillierte Studien zur neuronalen Informationsverarbeitung oder zu Neuropathologien an relevanten, humanen Zellmodellen erm{\"o}glichen.}, language = {de} } @phdthesis{Brechun2019, author = {Brechun, Katherine E.}, title = {Development and application of genetic networks for engineering photo-controlled proteins}, doi = {10.25932/publishup-43092}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430924}, school = {Universit{\"a}t Potsdam}, pages = {xxiv, 195}, year = {2019}, abstract = {Light-switchable proteins are being used increasingly to understand and manipulate complex molecular systems. The success of this approach has fueled the development of tailored photo-switchable proteins, to enable targeted molecular events to be studied using light. The development of novel photo-switchable tools has to date largely relied on rational design. Complementing this approach with directed evolution would be expected to facilitate these efforts. Directed evolution, however, has been relatively infrequently used to develop photo-switchable proteins due to the challenge presented by high-throughput evaluation of switchable protein activity. This thesis describes the development of two genetic circuits that can be used to evaluate libraries of switchable proteins, enabling optimization of both the on- and off-states. A screening system is described, which permits detection of DNA-binding activity based on conditional expression of a fluorescent protein. In addition, a tunable selection system is presented, which allows for the targeted selection of protein-protein interactions of a desired affinity range. This thesis additionally describes the development and characterization of a synthetic protein that was designed to investigate chromophore reconstitution in photoactive yellow protein (PYP), a promising scaffold for engineering photo-controlled protein tools.}, language = {en} } @phdthesis{Canitz2019, author = {Canitz, Julia}, title = {Genome and karyotype evolution underlying speciation and diversification of electric organ discharges in African weakly electric fish (Campylomormyrus, Mormyridae, Teleostei)}, school = {Universit{\"a}t Potsdam}, pages = {111}, year = {2019}, abstract = {The African weakly electric fish genus Campylomormyrus is a well-investigated fish group of the species-rich family Mormyridae. They are able to generate species-specific electric organ discharges (EODs) which vary in their waveform characteristics including polarity, phase umber and duration. In mormyrid species EODs are used for communication, species discrimination and mate recognition, and it is thought hat they serve as pre-zygotic isolation mechanism driving sympatric speciation by promoting assortative mating. The EOD diversification, its volutionary effects and the link to species divergence have been examined histologically, behaviorally, and genetically. Molecular analyses are a major tool to identify species and their phenotypic traits by studying the underlying genes. The genetic variability between species further provides information from which evolutionary processes, such as speciation, can be deduced. Hence, the ultimate aim of this study is the investigation of genetic variability within the African weakly electric fish genus Campylomormyrus to better understand their sympatric speciation and comprehend their evolutionary drivers. In order to extend the current knowledge and gain more insights into its species history, karyological and genomic approaches are being pursued considering species differences. Previous studies have shown that species with different EOD duration have specific gene expression patterns and single nucleotide polymorphisms (SNPs). As EODs play a crucial role during the evolution of Campylomormyrus species, the identification of its underlying genes may suggest how the EOD diversity evolved and whether this trait is based on a complex network of genetic processes or is regulated by only a few genes. The results obtained in this study suggest that genes with non-synonymous SNPs, which are exclusive to C. tshokwe with an elongated EOD, have frequent functions ssociated with tissue morphogenesis and transcriptional regulation. Therefore, it is proposed that these processes likely co-determine EOD characteristics of Campylomormyrus species. Furthermore, genome-wide analyses confirm the genetic difference among most Campylomormyrus species. In contrast, the same analyses reveal genetic similarity among individuals of the alces-complex showing different EOD waveforms. It is therefore hypothesized that the low genetic variability and high EOD diversity represents incipient sympatric speciation. The karyological description of a Campylomormyrus species provides crucial information about chromosome number and shapes. Its diploid chromosome number of 2n=48 supports the conservation of this trait within Mormyridae. Differences have been detected in the number of bi-armed chromosomes which is unusually high compared to other mormyrid species. This high amount can be due to chromosome rearrangements which could cause genetic incompatibility and reproductive isolation. Hence an alternative hypothesis regarding processes which cause sympatric speciation is that chromosome differences are involved in the speciation process of Campylomormyrus by acting as postzygotic isolation mechanism. In summary, the karyological and genomic investigations conducted in this study contributed to the increase of knowledge about Campylomormyrus species, to the solution of some existing ambiguities like phylogenetic relationships and to the raising of new hypothesis explaining the sympatric speciation of those African weakly electric fish. This study provides a basis for future genomic research to obtain a complete picture for causes and results of evolutionary processes in Campylomormyrus.}, language = {en} } @phdthesis{Devkar2019, author = {Devkar, Vikas Suresh}, title = {Functional characterization of NAC transcription factors ATAF1 and SITAF1 in growth and abiotic stress tolerance in tomato}, school = {Universit{\"a}t Potsdam}, year = {2019}, language = {en} } @phdthesis{Ehrlich2019, author = {Ehrlich, Elias}, title = {On the role of trade-offs in predator-prey interactions}, doi = {10.25932/publishup-43063}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430631}, school = {Universit{\"a}t Potsdam}, pages = {192}, year = {2019}, abstract = {Predation drives coexistence, evolution and population dynamics of species in food webs, and has strong impacts on related ecosystem functions (e.g. primary production). The effect of predation on these processes largely depends on the trade-offs between functional traits in the predator and prey community. Trade-offs between defence against predation and competitive ability, for example, allow for prey speciation and predator-mediated coexistence of prey species with different strategies (defended or competitive), which may stabilize the overall food web dynamics. While the importance of such trade-offs for coexistence is widely known, we lack an understanding and the empirical evidence of how the variety of differently shaped trade-offs at multiple trophic levels affect biodiversity, trait adaptation and biomass dynamics in food webs. Such mechanistic understanding is crucial for predictions and management decisions that aim to maintain biodiversity and the capability of communities to adapt to environmental change ensuring their persistence. In this dissertation, after a general introduction to predator-prey interactions and tradeoffs, I first focus on trade-offs in the prey between qualitatively different types of defence (e.g. camouflage or escape behaviour) and their costs. I show that these different types lead to different patterns of predator-mediated coexistence and population dynamics, by using a simple predator-prey model. In a second step, I elaborate quantitative aspects of trade-offs and demonstrates that the shape of the trade-off curve in combination with trait-fitness relationships strongly affects competition among different prey types: Either specialized species with extreme trait combinations (undefended or completely defended) coexist, or a species with an intermediate defence level dominates. The developed theory on trade-off shapes and coexistence is kept general, allowing for applications apart from defence-competitiveness trade-offs. Thirdly, I tested the theory on trade-off shapes on a long-term field data set of phytoplankton from Lake Constance. The measured concave trade-off between defence and growth governs seasonal trait changes of phytoplankton in response to an altering grazing pressure by zooplankton, and affects the maintenance of trait variation in the community. In a fourth step, I analyse the interplay of different tradeoffs at multiple trophic levels with plankton data of Lake Constance and a corresponding tritrophic food web model. The results show that the trait and biomass dynamics of the different three trophic levels are interrelated in a trophic biomass-trait cascade, leading to unintuitive patterns of trait changes that are reversed in comparison to predictions from bitrophic systems. Finally, in the general discussion, I extract main ideas on trade-offs in multitrophic systems, develop a graphical theory on trade-off-based coexistence, discuss the interplay of intra- and interspecific trade-offs, and end with a management-oriented view on the results of the dissertation, describing how food webs may respond to future global changes, given their trade-offs.}, language = {en} } @phdthesis{Farhan2019, author = {Farhan, Muhammad}, title = {Multifunctional reprogrammable actuators based on polymer networks with crystallizable segments}, school = {Universit{\"a}t Potsdam}, year = {2019}, abstract = {Soft polymeric materials, which can change their shape reversibly in response to external stimuli, can serve as actuating components in robotic systems. Besides electroactive polymers (EAP), hydrogels and liquid crystalline elastomers (LCE), crosslinked crystallizable shape-memory polymers networks have been introduced recently as reprogrammable thermo-reversible actuators. The integration of additional functions in such materials will lead to multifunctional polymeric actuators, which meet the complex requirements of modern robotic applications. The primary aim of this thesis was to achieve multifunctional reprogrammable thermo-reversible actuators based on thermoplastic polymers. Here, three different actuators providing additional functionalities such as surface modification capability (i), self-healing capability (ii) or a tailorable non-response function enabling noncontinuous multi-step motions (iii) were realized. At first, it was hypothesized that surface modifiable polymeric actuators (i) can be achieved by crosslinking of crystallizable thermoplastic terpolymers having reactive moieties, where subsequent thermomechanical programming enables reversible actuations while the sustained reactive groups allow post surface modification. For the second actuator type (ii) it was hypothesized that self-healing during reprogramming of polymeric actuators prepared by crosslinking of crystallizable linear homopolymers, can be achieved by adjusting the amount of freely interpenetrating extractable polymer moieties. Finally, it was hypothesized that thermo-reversible actuators providing a non-response function (iii) and thus enable multistep motions upon continuous normal stimulation, can be achieved by a crosslinked blend of two thermoplastic polymers with co-continuous morphology having a well-separated melting and crystallization transitions. In addition, these actuators can be physically reprogrammed by heating above all melting transitions to provide a different actuating shape. In this study, surface functionalizable actuators were realized from crosslinked poly[(ethylene)-co-(ethyl acrylate)-co-(maleic anhydride)] (cPEEAMA) based networks. Here crystallizable polyethylene (PE) segments should serve as actuation segments, ethyl acrylate (EA) provides elasticity to the system required for deformation, while reactive maleic anhydride (MA) will be used as chemically modifiable entities for post surface modification. Networks with varied crosslink density were prepared and its effect on thermomechanical properties as well as actuation performance was analyzed. Cyclic thermomechanical experiments were employed to investigate the actuation capability, which revealed a reversible actuation (ε׳rev) between 5 and 15\%. Fourier-transform infrared spectroscopy (FTIR) measurements confirmed that MA groups were sustained at the sample surface after processing and programming, which could be modified by reaction with ethylene diamine. Such amine functionalization allows the attachment of bioactive molecules to the actuator surface, which might provide a route to actuating substrates for biotechnology. Self-healable actuating materials were realized by poly(ε-caprolactone) (PCL) polymer networks with extractable linear PCL fractions of 5 to 60 wt\%. A detailed evaluation of the actuation capabilities by cyclic experiments revealed the highest reversible change in strain of Δε = 24\% for the cPCL network with 30 wt\% of linear polymer. The thermal treatment of damaged samples resulted in the healing of the network when heated to 80 °C. Here a linear polymer fraction ≥ 30 wt\% was necessary to achieve a self-healing efficiency of ≥ 50\%. The application of such high temperatures erases the programmed actuator shape and at the same time allows to reprogram a new actuating shape. Such sustainable actuators with self-healing function are of great interest for future robotic devices. Afore mentioned actuators operate continuously between two shapes and their movements can only be interrupted when the temperature is stopped. To overcome this limitation, noncontinuously responding actuators enabling multi-step actuation were realized from crosslinked blend networks prepared from PCL and poly[(ethylene)-co-(vinyl acetate)] (PEVA). These polymers (PCL and PEVA) were selected due to their immiscible character, where crystallizable PE and PCL segments provide two different actuation units, while vinyl acetate (VA) segment enabled sufficient elasticity of the system. A gap of 20 K in the melting and crystallization temperature of PE and PCL was achieved by selecting PEVA with 5 wt\% VA content (cPCL-PEVA5) providing a co-continuous phase morphology. Cyclic thermomechanical investigations were employed to investigate noncontinuous actuation, which revealed a high Δε = 25\% with a similar contribution from PCL and PE actuation units with a non-response region in the temperature range from 50 to 71 °C in heating step and 30 to 60 °C in cooling step. The actuation related to PCL part changed from 13 to 2\% by altering the heating and cooling rates from 3 to 10 K·min-1. Free-standing reversible noncontinuous actuation was realized by rotating demonstrator which exhibits reversible angle change in a custom-made setup. For this purpose, cPCL-PEVA5 stripe was programmed by twisting and reversible rotational actuation was realized from 0 to 180° while pausing in the 90° position during non-response. These blends can be physically programmed to perform reversible noncontinuous actuations, while the programmed geometry can be erased by heating it to temperature above all melting transitions. By physically reprogramming of the material various different actuation modes can be obtained. Such a noncontinuous actuator would be relevant for designing interruptive actuating soft robots at continuous trigger signals.}, language = {en} } @phdthesis{Ferrari2019, author = {Ferrari, Camilla}, title = {Comparative transcriptomic studies to predict gene function and investigate the evolution of diurnal regulation}, pages = {147}, year = {2019}, language = {en} } @phdthesis{Goktas2019, author = {Goktas, Melis}, title = {Coiled coils as molecular force sensors for the extracellular matrix}, doi = {10.25932/publishup-42749}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427493}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 124}, year = {2019}, abstract = {Kraft spielt eine fundamentale Rolle bei der Regulation von biologischen Prozessen. Zellen messen mechanische Eigenschaften der extrazellul{\"a}ren Matrix und benutzen diese Information zur Regulierung ihrer Funktion. Dazu werden im Zytoskelett Kr{\"a}fte generiert und auf extrazellul{\"a}re Rezeptor-Ligand Wechselwirkungen {\"u}bertragen. Obwohl der grundlegende Einfluss von mechanischen Signalen f{\"u}r das Zellschicksal eindeutig belegt ist, sind die auf molekularer Ebene wirkenden Kr{\"a}fte kaum bekannt. Zur Messung dieser Kr{\"a}fte wurden verschiedene molekulare Kraftsensoren entwickelt, die ein mechanisches Inputsignal aufnehmen und in einen optischen Output (Fluoreszenz) umwandeln. Diese Arbeit etabliert einen neuen Kraftsensor-Baustein, der die mechanischen Eigenschaften der extrazellul{\"a}ren Matrix nachbildet. Dieser Baustein basiert auf nat{\"u}rlichen Matrixproteinen, sogenannten coiled coils (CCs), die α-helikale Strukturen im Zytoskelett und der Matrix formen. Eine Serie an CC-Heterodimeren wurde konzipiert und mittels Einzelmolek{\"u}l-Kraftspektroskopie und Molekulardynamik-Simulationen charakterisiert. Es wurde gezeigt, dass eine anliegende Scherkraft die Entfaltung der helikalen Struktur induziert. Die mechanische Stabilit{\"a}t (Separation der CC Helices) wird von der CC L{\"a}nge und der Zuggeschwindigkeit bestimmt. Im Folgenden wurden 2 CCs unterschiedlicher L{\"a}nge als Kraftsensoren verwendet, um die Adh{\"a}sionskr{\"a}fte von Fibroblasten und Endothelzellen zu untersuchen. Diese Kraftsensoren deuten an, dass diese Zelltypen unterschiedlich starke Kr{\"a}ften generieren und mittels Integrin-Rezeptoren auf einen extrazellul{\"a}ren Liganden (RGD-Peptid) {\"u}bertragen. Dieses neue CC-basierte Sensordesign ist ein leistungsstarkes Werkzeug zur Betrachtung zellul{\"a}rer Kraftwahrnehmungsprozesse auf molekularer Ebene, das neue Erkenntnisse {\"u}ber die involvierten Mechanismen und Kr{\"a}fte an der Zell-Matrix-Schnittstelle erm{\"o}glicht. Dar{\"u}ber hinaus wird dieses Sensordesign auch Anwendung bei der Entwicklung mechanisch kontrollierter Biomaterialien finden. Dazu k{\"o}nnen mechanisch charakterisierte, und mit einem Fluoreszenzreporter versehene, CCs in Hydrogele eingef{\"u}gt werden. Dies erlaubt die Untersuchung der Zusammenh{\"a}nge zwischen molekularer und makroskopischer Mechanik und er{\"o}ffnet neue M{\"o}glichkeiten zur Diskriminierung von lokalen und globalen Faktoren, die die zellul{\"a}re Antwort auf mechanische Signale bestimmen.}, language = {en} } @phdthesis{GonzalezdelaCruz2019, author = {Gonzalez de la Cruz, Jorge}, title = {Metabolic engineering of Saccharomyces cerevisiae for formatotrophic growth}, school = {Universit{\"a}t Potsdam}, pages = {96}, year = {2019}, language = {en} } @phdthesis{Grafe2019, author = {Grafe, Marianne Erika}, title = {Analysis of supramolecular assemblies of NE81, the first lamin protein in a non-metazoan organism}, doi = {10.25932/publishup-44180}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441802}, school = {Universit{\"a}t Potsdam}, pages = {V, 94}, year = {2019}, abstract = {Lamine sind Proteine an der inneren Kernh{\"u}lle und bilden zusammen mit verbundenen Proteinen die nukle{\"a}re Lamina. Dieses Netzwerk sorgt f{\"u}r die Stabilit{\"a}t des Zellkerns und unterst{\"u}tzt die Organisation des Zell-Zytoskeletts. Zus{\"a}tzlich sind Lamine und ihre verbundenen Proteine in viele Prozesse wie Genregulation und Zelldifferenzierung involviert. Bis 2012 war der Stand der Forschung, dass nur bei mehrzelligen Organismen eine nukle{\"a}re Lamina zu finden ist. NE81 ist das erste lamin-{\"a}hnliche Protein, das in einem nicht-mehrzelligen Organismus (Dictyostelium discoideum) entdeckt wurde. Es hat viele Eigenschaften und Strukturmerkmale mit Laminen gemeinsam. Dazu z{\"a}hlt der dreiteilige Aufbau des Proteins, eine Phosphorylierungsstelle f{\"u}r ein Zellzyklus-abh{\"a}ngiges Enzym, ein Kernlokalisationssignal, wodurch das Protein in den Kern transportiert wird, sowie eine C-terminale Sequenz zur Verankerung des Proteins in der Kernh{\"u}lle. In dieser Arbeit wurden verschiedene Methoden zur vereinfachten Untersuchung von Laminstrukturen getestet, um zu zeigen, dass sich NE81 wie bereits bekannte Lamin-Proteine verh{\"a}lt und supramolekulare Netzwerke aus Laminfilamenten bildet. Zur Analyse der Struktur supramolekularer Anordnungen wurde das Protein durch Entfernen des Kernlokalisationssignals auf der {\"a}ußeren Kernh{\"u}lle von Dictyostelium gebildet. Die anschließende Untersuchung der Oberfl{\"a}che der Kerne mit einem Rasterelektronenmikroskop zeigte, dass NE81 Strukturen in der Gr{\"o}ße von Laminen bildet, allerdings nicht in regelm{\"a}ßigen filament{\"o}sen Anordnungen. Um die Entstehung der Laminfilamente zu untersuchen, wurde l{\"o}sliches NE81 aus Dictyostelium aufgereinigt und mit verschiedenen mikroskopischen Methoden untersucht. Dabei wurde festgestellt, dass NE81 unter Niedrigsalz-Bedingungen d{\"u}nne, fadenf{\"o}rmige Strukturen und Netzwerke ausbildet, die denen von S{\"a}ugetier-Laminen sehr {\"a}hnlich sind. Die Mutation der Phosphorylierungsstelle von NE81 zu einer imitierenden dauerhaften Phosphorylierung von NE81 in der Zelle, zeigte zun{\"a}chst ein gel{\"o}stes Protein, das {\"u}berraschenderweise unter Blaulichtbestrahlung der Zelle wieder lamin-{\"a}hnliche Anordnungen formte. Die Ergebnisse dieser Arbeit zeigen, dass NE81 echte Laminstrukturen ausbilden kann und hebt Dictyostelium als Nicht-S{\"a}ugetier-Modellorganismus mit einer gut charakterisierten Kernh{\"u}lle, mit allen relevanten, aus tierischen Zellen bekannten Proteinen, hervor.}, language = {en} } @phdthesis{Guislain2019, author = {Guislain, Alexis}, title = {Eco-physiological consequences of fluctuating light on phytoplankton}, doi = {10.25932/publishup-46927}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-469272}, school = {Universit{\"a}t Potsdam}, pages = {161}, year = {2019}, abstract = {Phytoplankton growth depends not only on the mean intensity but also on the dynamics of the light supply. The nonlinear light-dependency of growth is characterized by a small number of basic parameters: the compensation light intensity PARcompμ, where production and losses are balanced, the growth efficiency at sub-saturating light αµ, and the maximum growth rate at saturating light µmax. In surface mixed layers, phytoplankton may rapidly move between high light intensities and almost darkness. Because of the different frequency distribution of light and/or acclimation processes, the light-dependency of growth may differ between constant and fluctuating light. Very few studies measured growth under fluctuating light at a sufficient number of mean light intensities to estimate the parameters of the growth-irradiance relationship. Hence, the influence of light dynamics on µmax, αµ and PARcompμ are still largely unknown. By extension, accurate modelling predictions of phytoplankton development under fluctuating light exposure remain difficult to make. This PhD thesis does not intend to directly extrapolate few experimental results to aquatic systems - but rather improving the mechanistic understanding of the variation of the light-dependency of growth under light fluctuations and effects on phytoplankton development. In Lake TaiHu and at the Three Gorges Reservoir (China), we incubated phytoplankton communities in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Phytoplankton at fixed depths received only the diurnal changes in light (defined as constant light regime), while phytoplankton received rapidly fluctuating light by superimposing the vertical light gradient on the natural sinusoidal diurnal sunlight. The vertically moved samples followed a circular movement with 20 min per revolution, replicating to some extent the full overturn of typical Langmuir cells. Growth, photosynthesis, oxygen production and respiration of communities (at Lake TaiHu) were measured. To complete these investigations, a physiological experiment was performed in the laboratory on a toxic strain of Microcystis aeruginosa (FACBH 1322) incubated under 20 min period fluctuating light. Here, we measured electron transport rates and net oxygen production at a much higher time resolution (single minute timescale). The present PhD thesis provides evidence for substantial effects of fluctuating light on the eco-physiology of phytoplankton. Both experiments performed under semi-natural conditions in Lake TaiHu and at the Three Gorges Reservoir gave similar results. The significant decline in community growth efficiencies αµ under fluctuating light was caused for a great share by different frequency distribution of light intensities that shortened the effective daylength for production. The remaining gap in community αµ was attributed to species-specific photoacclimation mechanisms and to light-dependent respiratory losses. In contrast, community maximal growth rates µmax were similar between incubations at constant and fluctuating light. At daily growth saturating light supply, differences in losses for biosynthesis between the two light regimes were observed. Phytoplankton experiencing constant light suffered photo-inhibition - leading to photosynthesis foregone and additional respiratory costs for photosystems repair. On the contrary, intermittent exposure to low and high light intensities prevented photo-inhibition of mixed algae but forced them to develop alternative light strategy. They better harvested and exploited surface irradiance by enhancing their photosynthesis. In the laboratory, we showed that Microcystis aeruginosa increased its oxygen consumption by dark respiration in the light few minutes only after exposure to increasing light intensities. More, we proved that within a simulated Langmuir cell, the net production at saturating light and the compensation light intensity for production at limiting light are positively related. These results are best explained by an accumulation of photosynthetic products at increasing irradiance and mobilization of these fresh resources by rapid enhancement of dark respiration for maintenance and biosynthesis at decreasing irradiance. At the daily timescale, we showed that the enhancement of photosynthesis at high irradiance for biosynthesis of species increased their maintenance respiratory costs at limiting light. Species-specific growth at saturating light µmax and compensation light intensity for growth PARcompμ of species incubated in Lake TaiHu were positively related. Because of this species-specific physiological tradeoff, species displayed different light affinities to limiting and saturating light - thereby exhibiting a gleaner-opportunist tradeoff. In Lake TaiHu, we showed that inter-specific differences in light acquisition traits (µmax and PARcompμ) allowed coexis¬tence of species on a gradient of constant light while avoiding competitive exclusion. More interestingly we demonstrated for the first time that vertical mixing (inducing fluctuating light supply for phytoplankton) may alter or even reverse the light utilization strategies of species within couple of days. The intra-specific variation in traits under fluctuating light increased the niche space for acclimated species, precluding competitive exclusion. Overall, this PhD thesis contributes to a better understanding of phytoplankton eco-physiology under fluctuating light supply. This work could enhance the quality of predictions of phytoplankton development under certain weather conditions or climate change scenarios.}, language = {en} } @phdthesis{Gupta2019, author = {Gupta, Saurabh}, title = {Deciphering stress acclimation mechanisms in plants with extreme abiotic stress tolerence using genomics approaches}, school = {Universit{\"a}t Potsdam}, pages = {161}, year = {2019}, language = {en} } @phdthesis{He2019, author = {He, Hai}, title = {Exploring and engineering formaldehyde assimilation}, doi = {10.25932/publishup-47386}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-473867}, school = {Universit{\"a}t Potsdam}, pages = {vi, 105}, year = {2019}, abstract = {Increasing concerns regarding the environmental impact of our chemical production have shifted attention towards possibilities for sustainable biotechnology. One-carbon (C1) compounds, including methane, methanol, formate and CO, are promising feedstocks for future bioindustry. CO2 is another interesting feedstock, as it can also be transformed using renewable energy to other C1 feedstocks for use. While formaldehyde is not suitable as a feedstock due to its high toxicity, it is a central intermediate in the process of C1 assimilation. This thesis explores formaldehyde metabolism and aims to engineer formaldehyde assimilation in the model organism Escherichia coli for the future C1-based bioindustry. The first chapter of the thesis aims to establish growth of E. coli on formaldehyde via the most efficient naturally occurring route, the ribulose monophosphate pathway. Linear variants of the pathway were constructed in multiple-gene knockouts strains, coupling E. coli growth to the activities of the key enzymes of the pathway. Formaldehyde-dependent growth was achieved in rationally designed strains. In the final strain, the synthetic pathway provides the cell with almost all biomass and energy requirements. In the second chapter, taking advantage of the unique feature of its reactivity, formaldehyde assimilation via condensation with glycine and pyruvate by two promiscuous aldolases was explored. Facilitated by these two reactions, the newly designed homoserine cycle is expected to support higher yields of a wide array of products than its counterparts. By dividing the pathway into segments and coupling them to the growth of dedicated strains, all pathway reactions were demonstrated to be sufficiently active. The work paves a way for future implementation of a highly efficient route for C1 feedstocks into commodity chemicals. In the third chapter, the in vivo rate of the spontaneous formaldehyde tetrahydrofolate condensation to methylene-tetrahydrofolate was assessed in order to evaluate its applicability as a biotechnological process. Tested within an E. coli strain deleted in essential genes for native methylene-tetrahydrofolate biosynthesis, the reaction was shown to support the production of this essential intermediate. However, only low growth rates were observed and only at high formaldehyde concentrations. Computational analysis dependent on in vivo evidence from this strain deduced the slow rate of this spontaneous reaction, thus ruling out its substantial contribution to growth on C1 feedstocks. The reactivity of formaldehyde makes it highly toxic. In the last chapter, the formation of thioproline, the condensation product of cysteine and formaldehyde, was confirmed to contribute this toxicity effect. Xaa-Pro aminopeptidase (PepP), which genetically links with folate metabolism, was shown to hydrolyze thioproline-containing peptides. Deleting pepP increased strain sensitivity to formaldehyde, pointing towards the toxicity of thioproline-containing peptides and the importance of their removal. The characterization in this study could be useful in handling this toxic intermediate. Overall, this thesis identified challenges related to formaldehyde metabolism and provided novel solutions towards a future bioindustry based on sustainable C1 feedstocks in which formaldehyde serves as a key intermediate.}, language = {en} } @phdthesis{Hoang2019, author = {Hoang, Yen}, title = {De novo binning strategy to analyze and visualize multi-dimensional cytometric data}, doi = {10.25932/publishup-44307}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-443078}, school = {Universit{\"a}t Potsdam}, pages = {vii, 81, xxxii}, year = {2019}, abstract = {Since half a century, cytometry has been a major scientific discipline in the field of cytomics - the study of system's biology at single cell level. It enables the investigation of physiological processes, functional characteristics and rare events with proteins by analysing multiple parameters on an individual cell basis. In the last decade, mass cytometry has been established which increased the parallel measurement to up to 50 proteins. This has shifted the analysis strategy from conventional consecutive manual gates towards multi-dimensional data processing. Novel algorithms have been developed to tackle these high-dimensional protein combinations in the data. They are mainly based on clustering or non-linear dimension reduction techniques, or both, often combined with an upstream downsampling procedure. However, these tools have obstacles either in comprehensible interpretability, reproducibility, computational complexity or in comparability between samples and groups. To address this bottleneck, a reproducible, semi-automated cytometric data mining workflow PRI (pattern recognition of immune cells) is proposed which combines three main steps: i) data preparation and storage; ii) bin-based combinatorial variable engineering of three protein markers, the so called triploTs, and subsequent sectioning of these triploTs in four parts; and iii) deployment of a data-driven supervised learning algorithm, the cross-validated elastic-net regularized logistic regression, with these triploT sections as input variables. As a result, the selected variables from the models are ranked by their prevalence, which potentially have discriminative value. The purpose is to significantly facilitate the identification of meaningful subpopulations, which are most distinguish between two groups. The proposed workflow PRI is exemplified by a recently published public mass cytometry data set. The authors found a T cell subpopulation which is discriminative between effective and ineffective treatment of breast carcinomas in mice. With PRI, that subpopulation was not only validated, but was further narrowed down as a particular Th1 cell population. Moreover, additional insights of combinatorial protein expressions are revealed in a traceable manner. An essential element in the workflow is the reproducible variable engineering. These variables serve as basis for a clearly interpretable visualization, for a structured variable exploration and as input layers in neural network constructs. PRI facilitates the determination of marker levels in a semi-continuous manner. Jointly with the combinatorial display, it allows a straightforward observation of correlating patterns, and thus, the dominant expressed markers and cell hierarchies. Furthermore, it enables the identification and complex characterization of discriminating subpopulations due to its reproducible and pseudo-multi-parametric pattern presentation. This endorses its applicability as a tool for unbiased investigations on cell subsets within multi-dimensional cytometric data sets.}, language = {en} } @phdthesis{Hornick2019, author = {Hornick, Thomas}, title = {Impact of climate change effects on diversity and function of pelagic heterotrophic bacteria studied in large-scale mesocosm facilities}, doi = {10.25932/publishup-42893}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428936}, school = {Universit{\"a}t Potsdam}, pages = {199}, year = {2019}, abstract = {Seit der Industriellen Revolution steigt die Konzentration von Kohlenstoffdioxid (CO2) und anderen Treibhausgasen in der Erdatmosph{\"a}re stetig an, wodurch wesentliche Prozesse im Erdsystem beeinflusst werden. Dies wird mit dem Begriff „Klimawandel" umschrieben. Aquatische {\"O}kosysteme sind sehr stark davon betroffen, da sie als Integral vieler Prozesse in einer Landschaft fungieren. Ziel dieser Doktorarbeit war zu bestimmen, wie verschiedene Auswirkungen des Klimawandels die Gemeinschaftsstruktur und Aktivit{\"a}t von heterotrophen Bakterien in Gew{\"a}ssern ver{\"a}ndert, welche eine zentrale Rolle bei biogeochemischen Prozessen einnehmen. Diese Arbeit konzentriert sich auf zwei Aspekte des Klimawandels: (1) Ozeane nehmen einen Großteil des atmosph{\"a}rischen CO2 auf, welches im Meerwasser das chemische Gleichgewicht des Karbonatsystems verschiebt („Ozeanversauerung"). (2) Durch kontinuierlichen Anstieg der Erdoberfl{\"a}chentemperatur werden Ver{\"a}nderungen im Klimasystem der Erde vorhergesagt, welche u. a. die H{\"a}ufigkeit und Heftigkeit von episodischen Wetterereignissen (z.B. St{\"u}rme) verst{\"a}rken wird. Insbesondere Sommer-St{\"u}rme sind dabei in der Lage die sommerliche Temperaturschichtung der Wassers{\"a}ule in Seen zu zerst{\"o}ren. Beide Effekte des Klimawandels k{\"o}nnen weitreichende Auswirkungen auf Wasserchemie/-physik sowie die Verteilung von Organismen haben, was mittels Mesokosmen simuliert wurde. Dabei untersuchten wir den Einfluss der Ozeanversauerung auf heterotrophe bakterielle Prozesse in der Ostsee bei geringen Konzentrationen an gel{\"o}sten N{\"a}hrstoffen. Unsere Ergebnisse zeigen, dass Ozeanversauerungseffekte in Kombination mit N{\"a}hrstofflimitation indirekt das Wachstum von heterotrophen Bakterien durch ver{\"a}nderte trophische Interaktionen beeinflussen k{\"o}nnen und potentiell zu einer Erh{\"o}hung der Autotrophie des {\"O}kosystems f{\"u}hren. In einer weiteren Studie analysierten wir, wie Ozeanversauerung die Umsetzung und Qualit{\"a}t gel{\"o}sten organischen Materials (DOM) durch heterotrophe Bakterien beeinflussen kann. Die Ergebnisse weisen jedoch darauf hin, dass {\"A}nderungen in der DOM-Qualit{\"a}t durch heterotrophe bakterielle Prozesse mit zunehmender Ozeanversauerung unwahrscheinlich sind. Desweiteren wurde der Einfluss eines starken Sommer-Sturmes auf den stratifizierten, oligotroph-mesotrophen Stechlinsee simuliert. Mittels oberfl{\"a}chlicher Durchmischung in Mesokosmen wurde die bestehende Thermokline zerst{\"o}rt und die durchmischte Oberfl{\"a}chenwasserschicht vergr{\"o}ßert. Dies {\"a}nderte die physikalischen und chemischen Gradienten innerhalb der Wassers{\"a}ule. Effekte der Einmischung von Tiefenwasser {\"a}nderten in der Folge die Zusammensetzung der bakteriellen Gemeinschaftsstruktur und stimulierten das Wachstum filament{\"o}ser Cyanobakterien, die zu einer Cyanobakterien-Bl{\"u}te f{\"u}hrte und so maßgeblich die metabolischen Prozesse von heterotrophen Bakterien bestimmte. Unsere Studie gibt ein mechanistisches Verst{\"a}ndnis, wie Sommer-St{\"u}rme bakterielle Gemeinschaften und Prozesse f{\"u}r l{\"a}ngere Zeit w{\"a}hrend der sommerlichen Stratifizierung beeinflussen k{\"o}nnen. Die in dieser Arbeit pr{\"a}sentierten Ergebnisse zeigen Ver{\"a}nderungen bakterieller Gemeinschaften und Prozesse, welche mit dem einhergehenden Klimawandel erwartet werden k{\"o}nnen. Diese sollten bei Beurteilung klimarelevanter Fragen hinsichtlich eines zuk{\"u}nftigen Gew{\"a}sser-managements Ber{\"u}cksichtigung finden.}, language = {en} } @phdthesis{JadhavSudam2019, author = {Jadhav Sudam, Sagar}, title = {Metabolic regulation and key genes of tomato secondary metabolism}, doi = {10.25932/publishup-42447}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-424478}, school = {Universit{\"a}t Potsdam}, pages = {x, 149}, year = {2019}, abstract = {Domestication syndrome has resulted in the large loss of genetic variation of crop plants. Because of such genetic loss, productivity of various beneficial secondary (specialized) metabolites that protect against abiotic/biotic stresses, has been narrowed in many domesticated crops. Many key regulators or structural genes of secondary metabolic pathways in the domesticated as well as wild tomatoes are still largely unknown. In recent studies, metabolic quantitative trait loci (mQTL) analysis using the population of introgression lines (ILs), each containing a single introgression from Solanum pennellii (wild tomato) in the genetic background of domesticated tomato (M82, Solanum lycopersicum), has been used for investigation of metabolic regulation and key genes involved in both primary and secondary metabolism. In this thesis, three research projects, i) understanding of metabolic linkage between branched chain amino acids (BCAAs) and secondary metabolism using antisense lines of BCAAs metabolic genes, ii) investigation of novel key genes involved in tomato secondary metabolism and fruit ripening, iii) mapping of drought stress responsive mQTLs in tomato, are presented and discussed. In the first part, metabolic linkage between leucine and secondary metabolism is investigated by analyzing antisense lines of four key genes (ketol-acid reductoisomerase, KARI; dihydroxy-acid dehydratase, DHAD; isopropylmalate dehydratase, IPMD and branched chain aminotransferases1, BCAT1) found previously in mQTL of leucine contents. Obtained results indicate that KARI might be a rate limiting enzyme for iC5 acyl-sucrose synthesis in young leaf but not in red ripe fruits. By integrating obtained results with previous reports, inductive metabolic linkage between BCAAs and other secondary metabolic pathways at DHAD transcriptional levels in fruit is proposed. In the second part, candidate genes that are involved in secondary metabolism and fruit ripening in tomato were found by the approach of expression quantitative trait loci (eQTL) analysis. To predict functions of those candidate genes, functional validation by virus induced gene silencing and transient overexpression were performed. Results obtained by analyzing T0 overexpression and artificial miRNA lines for some of those candidates confirm their predicted functions, for example involved in fruit ripening (WD40, Solyc04g005020) and iC5 acyl-sucrose synthesis (P450, Solyc03g111940). In the third part, mapping of drought stress responsive mQTLs was performed using 57 S. pennellii ILs population. Evaluation of genetic architecture of mQTL analysis resulted in identifying drought responsive ILs (11-2, 8-3-1, 10-1-1 and 3-1). Location of well characterized regulators in these ILs helped to filter potential new key genes involved in drought stress tolerance. Obtained results suggests us our approaches could be viable for narrowing down potential candidates involved in creating interspecific variation in secondary metabolite content and at the level of fruit ripening.}, language = {en} } @phdthesis{Jantzen2019, author = {Jantzen, Friederike}, title = {Genetic basis and adaptive significance of repeated scent loss in selfing Capsella species}, doi = {10.25932/publishup-43525}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435253}, school = {Universit{\"a}t Potsdam}, pages = {124}, year = {2019}, abstract = {Floral scent is an important way for plants to communicate with insects, but scent emission has been lost or strongly reduced during the transition from pollinator-mediated outbreeding to selfing. The shift from outcrossing to selfing is not only accompanied by scent loss, but also by a reduction in other pollinator-attracting traits like petal size and can be observed multiple times among angiosperms. These changes are summarized by the term selfing syndrome and represent one of the most prominent examples of convergent evolution within the plant kingdom. In this work the genus Capsella was used as a model to study convergent evolution in two closely related selfers with separate transitions to self-fertilization. Compared to their outbreeding ancestor C. grandiflora, the emission of benzaldehyde as main compound of floral scent is lacking or strongly reduced in the selfing species C. rubella and C. orientalis. In C. rubella the loss of benzaldehyde was caused by mutations to cinnamate:CoA ligase CNL1, but the biochemical basis and evolutionary history of this loss remained unknown, together with the genetic basis of scent loss in C. orientalis. Here, a combination of plant transformations, in vitro enzyme assays, population genetics and quantitative genetics has been used to address these questions. The results indicate that CNL1 has been inactivated twice independently by point mutations in C. rubella, leading to a loss of benzaldehyde emission. Both inactivated haplotypes can be found around the Mediterranean Sea, indicating that they arose before the species´ geographical spread. This study confirmed CNL1 as a hotspot for mutations to eliminate benzaldehyde emission, as it has been suggested by previous studies. In contrast to these findings, CNL1 in C. orientalis remains active. To test whether similar mechanisms underlie the convergent evolution of scent loss in C. orientalis a QTL mapping approach was used and the results suggest that this closely related species followed a different evolutionary route to reduce floral scent, possibly reflecting that the convergent evolution of floral scent is driven by ecological rather than genetic factors. In parallel with studying the genetic basis of repeated scent loss a method for testing the adaptive value of individual selfing syndrome traits was established. The established method allows estimating outcrossing rates with a high throughput of samples and detects successfully insect-mediated outcrossing events, providing major advantages regarding time and effort compared to other approaches. It can be applied to correlate outcrossing rates with differences in individual traits by using quasi-isogenic lines as demonstrated here or with environmental or morphological parameters. Convergent evolution can not only be observed for scent loss in Capsella but also for the morphological evolution of petal size. Previous studies detected several QTLs underlying the petal size reduction in C. orientalis and C. rubella, some of them shared among both species. One shared QTL is PAQTL1 which might map to NUBBIN, a growth factor. To better understand the morphological evolution and genetic basis of petal size reduction, this QTL was studied. Mapping this QTL to a gene might identify another example for a hotspot gene, in this case for the convergent evolution of petal size.}, language = {en} } @phdthesis{Jehle2019, author = {Jehle, Franziska}, title = {Tracking self-assembly of hierarchically structured soft matter}, school = {Universit{\"a}t Potsdam}, pages = {88}, year = {2019}, language = {en} } @phdthesis{Kagel2019, author = {Kagel, Heike}, title = {Light-induced pH cycle}, doi = {10.25932/publishup-43435}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434353}, school = {Universit{\"a}t Potsdam}, pages = {VI, 118}, year = {2019}, abstract = {Background Many biochemical reactions depend on the pH of their environment and some are strongly accelerated in an acidic surrounding. A classical approach to control biochemical reactions non-invasivly is by changing the temperature. However, if the pH could be controlled by optical means using photo-active chemicals, this would mean to be able to accelerate suitable biochemical reactions. Optically switching the pH can be achieved by using photoacids. A photoacid is a molecule with a functional group that releases a proton upon irradiation with the suitable wavelength, acidifying the environmental aqueous surrounding. A major goal of this work was to establish a non-invasive method of optically controlling the pH in aqueous solutions, offering the opportunity to enhance the known chemical reactions portfolio. To demonstrate the photo-switchable pH cycling we chose an enzymatic assay using acid phosphatase, which is an enzyme with a strong pH dependent activity. Results In this work we could demonstrate a light-induced, reversible control of the enzymatic activity of acid phosphatase non-invasivly. To successfully conduct those experiments a high power LED array was designed and built, suitable for a 96 well standard microtiter plate, not being commercially available. Heat management and a lateral ventilation system to avoid heat accumulation were established and a stable light intensity achieved. Different photoacids were characterised and their pH dependent absorption spectra recorded. By using the reversible photoacid G-acid as a proton donor, the pH can be changed reversibly using high power UV 365 nm LEDs. To demonstrate the pH cycling, acid phosphatase with hydrolytic activity under acidic conditions was chosen. An assay using the photoacid together with the enzyme was established, also providing that G-acid does not inhibit acid phosphatase. The feasibility of reversibly regulating the enzyme's pH dependent activity by optical means was demonstrated, by controlling the enzymatic activity with light. It was demonstrated that the enzyme activity depends on the light exposure time only. When samples are not illuminated and left in the dark, no enzymatic activity was recorded. The process can be rapidly controlled by simply switching the light on and off and should be applicable to a wide range of enzymes and biochemical reactions. Conclusions Reversible photoacids offer a light-dependent regulation of pH, making them extremely attractive for miniaturizable, non-invasive and time-resolved control of biochemical reactions. Many enzymes have a sharp pH dependent activity, thus the established setup in this thesis could be used for a versatile enzyme portfolio. Even though the demonstrated photo-switchable strategy could also be used for non-enzymatic assays, greatly facilitating the assay establishment. Photoacids have the potential for high throughput methods and automation. We demonstrated that it is possible to control photoacids using commonly available LEDs, making their use in highly integrated devices and instruments more attractive. The successfully designed 96 well high power UV LED array presents an opportunity for general combinatorial analysis in e.g. photochemistry, where a high light intensity is needed for the investigation of various reactions.}, language = {en} } @phdthesis{Kolk2019, author = {Kolk, Jens}, title = {The long-term legacy of historical land cover changes}, doi = {10.25932/publishup-43939}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439398}, school = {Universit{\"a}t Potsdam}, pages = {196}, year = {2019}, abstract = {Over the last years there is an increasing awareness that historical land cover changes and associated land use legacies may be important drivers for present-day species richness and biodiversity due to time-delayed extinctions or colonizations in response to historical environmental changes. Historically altered habitat patches may therefore exhibit an extinction debt or colonization credit and can be expected to lose or gain species in the future. However, extinction debts and colonization credits are difficult to detect and their actual magnitudes or payments have rarely been quantified because species richness patterns and dynamics are also shaped by recent environmental conditions and recent environmental changes. In this thesis we aimed to determine patterns of herb-layer species richness and recent species richness dynamics of forest herb layer plants and link those patterns and dynamics to historical land cover changes and associated land use legacies. The study was conducted in the Prignitz, NE-Germany, where the forest distribution remained stable for the last ca. 100 years but where a) the deciduous forest area had declined by more than 90 per cent (leaving only remnants of "ancient forests"), b) small new forests had been established on former agricultural land ("post-agricultural forests"). Here, we analyzed the relative importance of land use history and associated historical land cover changes for herb layer species richness compared to recent environmental factors and determined magnitudes of extinction debt and colonization credit and their payment in ancient and post-agricultural forests, respectively. We showed that present-day species richness patterns were still shaped by historical land cover changes that ranged back to more than a century. Although recent environmental conditions were largely comparable we found significantly more forest specialists, species with short-distance dispersal capabilities and clonals in ancient forests than in post-agricultural forests. Those species richness differences were largely contingent to a colonization credit in post-agricultural forests that ranged up to 9 species (average 4.7), while the extinction debt in ancient forests had almost completely been paid. Environmental legacies from historical agricultural land use played a minor role for species richness differences. Instead, patch connectivity was most important. Species richness in ancient forests was still dependent on historical connectivity, indicating a last glimpse of an extinction debt, and the colonization credit was highest in isolated post-agricultural forests. In post-agricultural forests that were better connected or directly adjacent to ancient forest patches the colonization credit was way smaller and we were able to verify a gradual payment of the colonization credit from 2.7 species to 1.5 species over the last six decades.}, language = {en} } @phdthesis{Kowalski2019, author = {Kowalski, Gabriele Joanna}, title = {Animal movement patterns across habitats}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2019}, language = {en} } @phdthesis{Kuecuekgoeze2019, author = {K{\"u}{\c{c}}{\"u}kg{\"o}ze, G{\"o}khan}, title = {Purification and characterization of mouse aldehyde oxidases}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 125}, year = {2019}, abstract = {Mouse aldehyde oxidases (mAOXs) have a homodimeric structure and belong to xanthine oxidase family of molybdo-flavoenzymes. In general, each dimer is characterized by three subdomains: a 20 kDa N-terminal 2x[2Fe2S] cluster containing domain, a 40 kDa central FAD-containing domain and an 85 kDa C-terminal molybdenum cofactor (Moco) containing domain. Aldehyde oxidases have a broad substrate specificity including the oxidation of different aldehydes and N-heterocyclic compounds. AOX enzymes are present in mainly all eukaryotes. Four different homologs of AOX were identified to be present with varying numbers among species and rodents like mice and rats contain the highest number of AOX isoenzymes. There are four identified homologs in mouse named mAOX1, mAOX3, mAOX2, and mAOX4. The AOX homologs in mice are expressed in a tissue-specific manner. Expression of mAOX1 and mAOX3 are almost superimposable and predominantly synthesized in liver, lung, and testis. The richest source of mAOX4 is the Harderian gland, which is found within the eye's orbit in tetrapods. Expression of mAOX2 is strictly restricted to the Bowman's gland, the main secretory organ of the nasal mucosa. In this study, the four catalytically active mAOX enzymes were expressed in a heterologous expression system in Escherichia coli and purified in a catalytically active form. Thirty different structurally related aromatic, aliphatic and N-heterocyclic compounds were used as substrates, and the kinetic parameters of all four mAOX enzymes were directly compared. The results showed that all enzymes can catalyze a broad range of substrates. Generally, no major differences between mAOX1, mAOX3 and mAOX2 were identified and the substrate specificity of mAOX1, mAOX3, and mAOX2 was broader compared to that of mAOX4 since mAOX4 showed no activity with substrates like methoxy-benzaldehydes, phenanthridine, N1-methyl-nicotinamide, and cinnamaldehyde and 4-(dimethylamino)cinnamaldehyde. We investigated differences at the flavin site of the mAOX enzymes by measuring the ability of the four mAOX enzymes to oxidize NADH in the absence of oxygen. NADH was able to reduce only mAOX3. The four mouse AOXs are also characterized by quantitative differences in their ability to produce superoxide radicals. mAOX2 is the enzyme generating the largest rate of superoxide radicals of around 40\% in relation to moles of substrate converted and it is followed by mAOX1 with a ratio of 30\%. To understand the factors that contribute to the substrate specificity of mAOX4, site-directed mutagenesis was applied to substitute amino acids in the substrate-binding funnel by the ones present in mAOX1, mAOX3, and mAOX2. The amino acids Val1016, Ile1018 and Met1088 were selected as targets. An increase in activity was obtained by the amino acid exchange M1088V in the active site identified to be specific for mAOX4, to the amino acid identified in mAOX3.}, language = {en} } @phdthesis{Langhammer2019, author = {Langhammer, Maria}, title = {Simulating biodiversity responses to land use mosaics in agricultural landscapes}, school = {Universit{\"a}t Potsdam}, year = {2019}, language = {en} } @phdthesis{LozadaGobilard2019, author = {Lozada Gobilard, Sissi Donna}, title = {From genes to communities: Assessing plant diversity and connectivity in kettle holes as metaecosystems in agricultural landscapes}, doi = {10.25932/publishup-43768}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437684}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 147}, year = {2019}, abstract = {Species assembly from a regional pool into local metacommunities and how they colonize and coexist over time and space is essential to understand how communities response to their environment including abiotic and biotic factors. In highly disturbed landscapes, connectivity of isolated habitat patches is essential to maintain biodiversity and the entire ecosystem functioning. In northeast Germany, a high density of the small water bodies called kettle holes, are good systems to study metacommunities due to their condition as "aquatic islands" suitable for hygrophilous species that are surrounded by in unsuitable matrix of crop fields. The main objective of this thesis was to infer the main ecological processes shaping plant communities and their response to the environment, from biodiversity patterns and key life-history traits involved in connectivity using ecological and genetic approaches; and to provide first insights of the role of kettle holes harboring wild-bee species as important mobile linkers connecting plant communities in this insular system. t a community level, I compared plant diversity patterns and trait composition in ephemeral vs. permanent kettle holes). My results showed that types of kettle holes act as environmental filers shaping plant diversity, community-composition and trait-distribution, suggesting species sorting and niche processes in both types of kettle holes. At a population level, I further analyzed the role of dispersal and reproductive strategies of four selected species occurring in permanent kettle holes. Using microsatellites, I found that breeding system (degree of clonality), is the main factor shaping genetic diversity and genetic divergence. Although, higher gene flow and lower genetic differentiation among populations in wind vs. insect pollinated species was also found, suggesting that dispersal mechanisms played a role related to gene flow and connectivity. For most flowering plants, pollinators play an important role connecting communities. Therefore, as a first insight of the potential mobile linkers of these plant communities, I investigated the diversity wild-bees occurring in these kettle holes. My main results showed that local habitat quality (flower resources) had a positive effect on bee diversity, while habitat heterogeneity (number of natural landscape elements surrounding kettle holes 100-300m), was negatively correlated. This thesis covers from genetic flow at individual and population level to plant community assembly. My results showed how patterns of biodiversity, dispersal and reproduction strategies in plant population and communities can be used to infer ecological processes. In addition, I showed the importance of life-history traits and the relationship between species and their abiotic and biotic interactions. Furthermore, I included a different level of mobile linkers (pollinators) for a better understanding of another level of the system. This integration is essential to understand how communities respond to their surrounding environment and how disturbances such as agriculture, land-use and climate change might affect them. I highlight the need to integrate many scientific areas covering from genes to ecosystems at different spatiotemporal scales for a better understanding, management and conservation of our ecosystems.}, language = {en} } @phdthesis{Luzarowski2019, author = {Luzarowski, Marcin}, title = {Development and application of biochemical approaches for characterisation of the protein-protein-metabolite interactome in model organisms' A. thaliana and S. cerevisiae}, school = {Universit{\"a}t Potsdam}, pages = {123}, year = {2019}, language = {en} } @phdthesis{LopezGarcia2019, author = {L{\´o}pez Garc{\´i}a, Patricia}, title = {Coiled coils as mechanical building blocks}, doi = {10.25932/publishup-42956}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429568}, school = {Universit{\"a}t Potsdam}, pages = {xi, 130}, year = {2019}, abstract = {The natural abundance of Coiled Coil (CC) motifs in cytoskeleton and extracellular matrix proteins suggests that CCs play an important role as passive (structural) and active (regulatory) mechanical building blocks. CCs are self-assembled superhelical structures consisting of 2-7 α-helices. Self-assembly is driven by hydrophobic and ionic interactions, while the helix propensity of the individual helices contributes additional stability to the structure. As a direct result of this simple sequence-structure relationship, CCs serve as templates for protein design and sequences with a pre-defined thermodynamic stability have been synthesized de novo. Despite this quickly increasing knowledge and the vast number of possible CC applications, the mechanical function of CCs has been largely overlooked and little is known about how different CC design parameters determine the mechanical stability of CCs. Once available, this knowledge will open up new applications for CCs as nanomechanical building blocks, e.g. in biomaterials and nanobiotechnology. With the goal of shedding light on the sequence-structure-mechanics relationship of CCs, a well-characterized heterodimeric CC was utilized as a model system. The sequence of this model system was systematically modified to investigate how different design parameters affect the CC response when the force is applied to opposing termini in a shear geometry or separated in a zipper-like fashion from the same termini (unzip geometry). The force was applied using an atomic force microscope set-up and dynamic single-molecule force spectroscopy was performed to determine the rupture forces and energy landscape properties of the CC heterodimers under study. Using force as a denaturant, CC chain separation is initiated by helix uncoiling from the force application points. In the shear geometry, this allows uncoiling-assisted sliding parallel to the force vector or dissociation perpendicular to the force vector. Both competing processes involve the opening of stabilizing hydrophobic (and ionic) interactions. Also in the unzip geometry, helix uncoiling precedes the rupture of hydrophobic contacts. In a first series of experiments, the focus was placed on canonical modifications in the hydrophobic core and the helix propensity. Using the shear geometry, it was shown that both a reduced core packing and helix propensity lower the thermodynamic and mechanical stability of the CC; however, with different effects on the energy landscape of the system. A less tightly packed hydrophobic core increases the distance to the transition state, with only a small effect on the barrier height. This originates from a more dynamic and less tightly packed core, which provides more degrees of freedom to respond to the applied force in the direction of the force vector. In contrast, a reduced helix propensity decreases both the distance to the transition state and the barrier height. The helices are 'easier' to unfold and the remaining structure is less thermodynamically stable so that dissociation perpendicular to the force axis can occur at smaller deformations. Having elucidated how canonical sequence modifications influence CC mechanics, the pulling geometry was investigated in the next step. Using one and the same sequence, the force application points were exchanged and two different shear and one unzipping geometry were compared. It was shown that the pulling geometry determines the mechanical stability of the CC. Different rupture forces were observed in the different shear as well as in the unzipping geometries, suggesting that chain separation follows different pathways on the energy landscape. Whereas the difference between CC shearing and unzipping was anticipated and has also been observed for other biological structures, the observed difference for the two shear geometries was less expected. It can be explained with the structural asymmetry of the CC heterodimer. It is proposed that the direction of the α-helices, the different local helix propensities and the position of a polar asparagine in the hydrophobic core are responsible for the observed difference in the chain separation pathways. In combination, these factors are considered to influence the interplay between processes parallel and perpendicular to the force axis. To obtain more detailed insights into the role of helix stability, helical turns were reinforced locally using artificial constraints in the form of covalent and dynamic 'staples'. A covalent staple bridges to adjacent helical turns, thus protecting them against uncoiling. The staple was inserted directly at the point of force application in one helix or in the same terminus of the other helix, which did not experience the force directly. It was shown that preventing helix uncoiling at the point of force application reduces the distance to the transition state while slightly increasing the barrier height. This confirms that helix uncoiling is critically important for CC chain separation. When inserted into the second helix, this stabilizing effect is transferred across the hydrophobic core and protects the force-loaded turns against uncoiling. If both helices were stapled, no additional increase in mechanical stability was observed. When replacing the covalent staple with a dynamic metal-coordination bond, a smaller decrease in the distance to the transition was observed, suggesting that the staple opens up while the CC is under load. Using fluorinated amino acids as another type of non-natural modification, it was investigated how the enhanced hydrophobicity and the altered packing at the interface influences CC mechanics. The fluorinated amino acid was inserted into one central heptad of one or both α-helices. It was shown that this substitution destabilized the CC thermodynamically and mechanically. Specifically, the barrier height was decreased and the distance to the transition state increased. This suggests that a possible stabilizing effect of the increased hydrophobicity is overruled by a disturbed packing, which originates from a bad fit of the fluorinated amino acid into the local environment. This in turn increases the flexibility at the interface, as also observed for the hydrophobic core substitution described above. In combination, this confirms that the arrangement of the hydrophobic side chains is an additional crucial factor determining the mechanical stability of CCs. In conclusion, this work shows that knowledge of the thermodynamic stability alone is not sufficient to predict the mechanical stability of CCs. It is the interplay between helix propensity and hydrophobic core packing that defines the sequence-structure-mechanics relationship. In combination, both parameters determine the relative contribution of processes parallel and perpendicular to the force axis, i.e. helix uncoiling and uncoiling-assisted sliding as well as dissociation. This new mechanistic knowledge provides insight into the mechanical function of CCs in tissues and opens up the road for designing CCs with pre-defined mechanical properties. The library of mechanically characterized CCs developed in this work is a powerful starting point for a wide spectrum of applications, ranging from molecular force sensors to mechanosensitive crosslinks in protein nanostructures and synthetic extracellular matrix mimics.}, language = {en} } @phdthesis{Neukranz2019, author = {Neukranz, Yannika}, title = {MOCS3 and its role in molybdenum cofactor biosynthesis, tRNA thiolation and other cellular pathways in humans}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2019}, language = {en} } @phdthesis{Neumann2019, author = {Neumann, Bettina}, title = {Bioelectrocatalytic activity of surface-confined heme catalysts}, school = {Universit{\"a}t Potsdam}, pages = {116}, year = {2019}, language = {en} } @phdthesis{Nguyen2019, author = {Nguyen, Manh Duy Linh}, title = {Reproduction, development and reproductive isolation barriers of the mormyrid fish (genus Campylomormyrus, Teleostei)}, doi = {10.25932/publishup-43719}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437197}, school = {Universit{\"a}t Potsdam}, pages = {121}, year = {2019}, abstract = {Weakly electric mormyrid fish comprise about 200 species. 15 species of the genus Campylomormyrus have been described. These are very diverse concerning the trunk-like snout and the shape and duration of the electric organ discharge (EOD) and the anatomy of the electric organ. In this dissertation data on the reproduction in captivity of four species and on the ontogeny of the EOD and the EO of three species are presented. Reproduction of the four species C. compressirostris, C. rhynchophorus, C. tshokwe and C. numenius: Cyclical reproduction was provoked by changing only water conductivity (C): decreasing C led to gonadal recrudescence, an increase induced gonad regression. Data on the reproduction and development of three species are presented (in C. numenius gonad development could only be achieved in males). Agonistic behavior in the C. tshokwe pair forced us to divide the breeding tank; therefore, only ovipositions occurred. However, injection of an artificial GnRH hormone allowed us to obtain ripe eggs and sperm and to perform successful artificial reproduction. All three species (C. compressirostris, C. rhynchophorus, C. tshokwe) are indeterminate fractional spawners. Spawnings/ovipositions occurred during the second half of the night; no parental care was observed; no special spawning substrates were necessary. C. compressirostris successfully spawned in breeding groups, C. rhynchophorus as pair. Spawning intervals ranged from 6 to 66 days in C. rhynchophorus, 10-75 days in C. tshokwe, and 18 days in C. compressirostris (calculated values). Fecundities (eggs per fractional spawning) ranged from 70 to 1570 eggs in C. rhynchophorus, 100-1192 in C. tshokwe, and 38-246 in C. compressirostris. All three species produce yolky, slightly sticky eggs. Egg diameter ranges from 2.3-3.0 mm. Hatching occurred on day 3, feeding started on day 11. Transition from larval to juvenile stage occurred at around 20 mm total length (TL). At this size C. rhynchophorus developed a higher body than the two other species and differences between the species in the melanin pigmentation of the unpaired fins occurred. Between 32 and 35 mm TL the upper and lower jaws developed. C. compressirostris and C. tamandua are similar in morphology and both produce short EODs of ca. 150-200 μs duration. Both species reproduce easily in captivity. We tried to obtain natural hybrids in two breeding groups, 1) four males of C. compressirostris and three females of C. tamandua and 2) six females of C. compressirostris and four males of C. tamandua. In both combinations several times oviposition occurred, however, we never found fertilized eggs. In subsequent experiments, not described here, we obtained hybrids between these two species by means of artificial reproduction. Ontogeny of the EOD and the EO: The Campylomormyrus species are very diverse both concerning the shape and the duration of their EODs. There are species with very short EODs, e.g. C. compressirostris duration, a species with an EOD length of about 4-8 ms duration (C. tshokwe) and species with very long EODs of about 25 ms duration (e.g. C. rhynchophorus). Due to the successful breeding of the three species in captivity, we were able to investigate in detail the ontogeny of the EOD. Larvae of the three species C. compressirostris, C. tshokwe and C. rhynchophorus first produce a biphasic larval EOD typical for these small larvae. The first activity of the adult electric organ in the caudal peduncle is a biphasic juvenile EOD. Juvenile C. compressirostris and C. tshokwe start out with a short biphasic EOD of about 160 - 200 μs duration at sizes between 25 mm (C. compressirostris) and 37 mm (C. tshokwe). Adult C. compressirostris show an EOD identical to that of the juvenile. In C. tshokwe, the juvenile EOD changes continuously during development both concerning duration, amplitude increase and shape. 18 cm long C. tshokwe still do not yet produce an EOD typical for the adult fish. Juveniles of C. rhynchophorus produce at 33 mm total length a juvenile biphasic EOD, however, of longer duration (about 640 μs) than the two species mentioned above. This juvenile EOD changes continuously both in form, amplitude increase and duration with growth until the adult EOD waveform appears at about 15 cm body length. In juveniles about seven cm long the triphasic feature of the EOD starts to develop due to the appearance of a second head positive phase. Specific EOD stages are produced in relation to size and not to age. Individual differences in the EOD both concerning shape and duration are very small. The basic anatomy of the electrocytes is very similar in all three species: the main stalk which receives the innervation, is located at the caudal face of the electrocyte. Membrane penetrations of the stalks do not occur. However, there are differences in the fine structure of the electrocytes in the three species. Papillae, proliferations of the membrane, which increase the surface area of the electrocyte and are thought to incrase the EOD-duration, are only found in C. tshokwe and C. rhynchophorus. In these two species in addition, holes develop in the electrocytes during ontogeny. This might also have an impact on EOD duration.}, language = {en} } @phdthesis{Numberger2019, author = {Numberger, Daniela}, title = {Urban wastewater and lakes as habitats for bacteria and potential vectors for pathogens}, doi = {10.25932/publishup-43709}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437095}, school = {Universit{\"a}t Potsdam}, pages = {VI, 130}, year = {2019}, abstract = {Wasser ist lebensnotwendig und somit eine essentielle Ressource. Jedoch sind unsere S{\"u}ßwasser-Ressourcen begrenzt und ihre Erhaltung daher besonders wichtig. Verschmutzungen mit Chemikalien und Krankheitserregern, die mit einer wachsenden Bev{\"o}lkerung und Urbanisierung einhergehen, verschlechtern die Qualit{\"a}t unseres S{\"u}ßwassers. Außerdem kann Wasser als {\"U}bertragungsvektor f{\"u}r Krankheitserreger dienen und daher wasserb{\"u}rtige Krankheiten verursachen. Der Leibniz-Forschungsverbund INFECTIONS'21 untersuchte innerhalb der interdisziplin{\"a}ren Forschungsgruppe III - „Wasser", Gew{\"a}sser als zentralen Mittelpunkt f{\"u}r Krankheiterreger. Dabei konzentrierte man sich auf Clostridioides difficile sowie avi{\"a}re Influenza A-Viren, von denen angenommen wird, dass sie in die Gew{\"a}sser ausgeschieden werden. Ein weiteres Ziel bestand darin, die bakterielle Gemeinschaften eines Kl{\"a}rwerkes der deutschen Hauptstadt Berlin zu charakterisieren, um anschließend eine Bewertung des potentiellen Gesundheitsrisikos geben zu k{\"o}nnen. Bakterielle Gemeinschaften des Roh- und Klarwassers aus dem Kl{\"a}rwerk unterschieden sich signifikant voneinander. Der Anteil an Darm-/F{\"a}kalbakterien war relativ niedrig und potentielle Darmpathogene wurden gr{\"o}ßtenteils aus dem Rohwasser entfernt. Ein potentielles Gesundheitsrisiko konnte allerdings von potentiell pathogenen Legionellen wie L. lytica festgestellt werden, deren relative Abundanz im Klarwasser h{\"o}her war als im Rohwasser. Es wurden außerdem drei C. difficile-Isolate aus den Kl{\"a}rwerk-Rohwasser und einem st{\"a}dtischen Badesee in Berlin (Weisser See) gewonnen und sequenziert. Die beiden Isolate aus dem Kl{\"a}rwerk tragen keine Toxin-Gene, wohingegen das Isolat aus dem See Toxin-Gene besitzt. Alle drei Isolate sind sehr nah mit humanen St{\"a}mmen verwandt. Dies deutet auf ein potentielles, wenn auch sporadisches Gesundheitsrisiko hin. (Avi{\"a}re) Influenza A-Viren wurden in 38.8\% der untersuchten Sedimentproben mittels PCR detektiert, aber die Virusisolierung schlug fehl. Ein Experiment mit beimpften Wasser- und Sedimentproben zeigte, dass f{\"u}r die Isolierung aus Sedimentproben eine relativ hohe Viruskonzentration n{\"o}tig ist. In Wasserproben ist jedoch ein niedriger Titer an Influenza A-Viren ausreichend, um eine Infektion auszul{\"o}sen. Es konnte zudem auch festgestellt werden, dass sich „Madin-Darby Canine Kidney (MDCK)―-Zellkulturen im Gegensatz zu embryonierten H{\"u}hnereiern besser eignen, um Influenza A-Viren aus Sediment zu isolieren. Zusammenfassend l{\"a}sst sich sagen, dass diese Arbeit m{\"o}gliche Gesundheitsrisiken aufgedeckt hat, wie etwa durch Legionellen im untersuchten Berliner Kl{\"a}rwerk, deren relative Abundanz in gekl{\"a}rtem Abwasser h{\"o}her ist als im Rohwasser. Desweiteren wird indiziert, dass Abwasser und Gew{\"a}sser als Reservoir und Vektor f{\"u}r pathogene Organismen dienen k{\"o}nnen, selbst f{\"u}r nicht-typische Wasser-Pathogene wie C. difficile.}, language = {en} } @phdthesis{Paraskevopoulou2019, author = {Paraskevopoulou, Sofia}, title = {Adaptive genetic variation and responses to thermal stress in brachionid rotifers}, pages = {IV, 177}, year = {2019}, abstract = {The importance of cryptic diversity in rotifers is well understood regarding its ecological consequences, but there remains an in depth comprehension of the underlying molecular mechanisms and forces driving speciation. Temperature has been found several times to affect species spatio-temporal distribution and organisms' performance, but we lack information on the mechanisms that provide thermal tolerance to rotifers. High cryptic diversity was found recently in the freshwater rotifer "Brachionus calyciflorus", showing that the complex comprises at least four species: B. calyciflorus sensu stricto (s.s.), B. fernandoi, B. dorcas, and B. elevatus. The temporal succession among species which have been observed in sympatry led to the idea that temperature might play a crucial role in species differentiation. The central aim of this study was to unravel differences in thermal tolerance between species of the former B. calyciflorus species complex by comparing phenotypic and gene expression responses. More specifically, I used the critical maximum temperature as a proxy for inter-species differences in heat-tolerance; this was modeled as a bi-dimensional phenotypic trait taking into consideration the intention and the duration of heat stress. Significant differences on heat-tolerance between species were detected, with B. calyciflorus s.s. being able to tolerate higher temperatures than B. fernandoi. Based on evidence of within species neutral genetic variation, I further examined adaptive genetic variability within two different mtDNA lineages of the heat tolerant B. calyciflorus s.s. to identify SNPs and genes under selection that might reflect their adaptive history. These analyses did not reveal adaptive genetic variation related to heat, however, they show putatively adaptive genetic variation which may reflect local adaptation. Functional enrichment of putatively positively selected genes revealed signals of adaptation in genes related to "lipid metabolism", "xenobiotics biodegradation and metabolism" and "sensory system", comprising candidate genes which can be utilized in studies on local adaptation. An absence of genetically-based differences in thermal adaptation between the two mtDNA lineages, together with our knowledge that B. calyciflorus s.s. can withstand a broad range of temperatures, led to the idea to further investigate shared transcriptomic responses to long-term exposure to high and low temperatures regimes. With this, I identified candidate genes that are involved in the response to temperature imposed stress. Lastly, I used comparative transcriptomics to examine responses to imposed heat-stress in heat-tolerant and heat-sensitive Brachionus species. I found considerably different patterns of gene expression in the two species. Most striking are patterns of expression regarding the heat shock proteins (hsps) between the two species. In the heat-tolerant, B. calyciflorus s.s., significant up-regulation of hsps at low temperatures was indicative of a stress response at the cooler end of the temperature regimes tested here. In contrast, in the heat-sensitive B. fernandoi, hsps generally exhibited up-regulation of these genes along with rising temperatures. Overall, identification of differences in expression of genes suggests suppression of protein biosynthesis to be a mechanism to increase thermal tolerance. Observed patterns in population growth are correlated with the hsp gene expression differences, indicating that this physiological stress response is indeed related to phenotypic life history performance.}, language = {en} } @phdthesis{PerlazaJimenez2019, author = {Perlaza-Jimenez, Laura}, title = {Discerning functional associations and relationships between molecules in Arabidopsis thaliana using genome-wide correlated mutations}, school = {Universit{\"a}t Potsdam}, pages = {118}, year = {2019}, language = {en} } @phdthesis{Petrovic2019, author = {Petrovic, Nevena}, title = {Analysis of the role of Forgetter2 in thermotolerance responses in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {117}, year = {2019}, language = {en} } @phdthesis{Raatz2019, author = {Raatz, Michael}, title = {Strategies within predator-prey interactions - from individuals to ecosystems}, doi = {10.25932/publishup-42658}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426587}, school = {Universit{\"a}t Potsdam}, pages = {175}, year = {2019}, abstract = {Predator-prey interactions provide central links in food webs. These interaction are directly or indirectly impacted by a number of factors. These factors range from physiological characteristics of individual organisms, over specifics of their interaction to impacts of the environment. They may generate the potential for the application of different strategies by predators and prey. Within this thesis, I modelled predator-prey interactions and investigated a broad range of different factors driving the application of certain strategies, that affect the individuals or their populations. In doing so, I focused on phytoplankton-zooplankton systems as established model systems of predator-prey interactions. At the level of predator physiology I proposed, and partly confirmed, adaptations to fluctuating availability of co-limiting nutrients as beneficial strategies. These may allow to store ingested nutrients or to regulate the effort put into nutrient assimilation. We found that these two strategies are beneficial at different fluctuation frequencies of the nutrients, but may positively interact at intermediate frequencies. The corresponding experiments supported our model results. We found that the temporal structure of nutrient fluctuations indeed has strong effects on the juvenile somatic growth rate of {\itshape Daphnia}. Predator colimitation by energy and essential biochemical nutrients gave rise to another physiological strategy. High-quality prey species may render themselves indispensable in a scenario of predator-mediated coexistence by being the only source of essential biochemical nutrients, such as cholesterol. Thereby, the high-quality prey may even compensate for a lacking defense and ensure its persistence in competition with other more defended prey species. We found a similar effect in a model where algae and bacteria compete for nutrients. Now, being the only source of a compound that is required by the competitor (bacteria) prevented the competitive exclusion of the algae. In this case, the essential compounds were the organic carbon provided by the algae. Here again, being indispensable served as a prey strategy that ensured its coexistence. The latter scenario also gave rise to the application of the two metabolic strategies of autotrophy and heterotrophy by algae and bacteria, respectively. We found that their coexistence allowed the recycling of resources in a microbial loop that would otherwise be lost. Instead, these resources were made available to higher trophic levels, increasing the trophic transfer efficiency in food webs. The predation process comprises the next higher level of factors shaping the predator-prey interaction, besides these factors that originated from the functioning or composition of individuals. Here, I focused on defensive mechanisms and investigated multiple scenarios of static or adaptive combinations of prey defense and predator offense. I confirmed and extended earlier reports on the coexistence-promoting effects of partially lower palatability of the prey community. When bacteria and algae are coexisting, a higher palatability of bacteria may increase the average predator biomass, with the side effect of making the population dynamics more regular. This may facilitate experimental investigations and interpretations. If defense and offense are adaptive, this allows organisms to maximize their growth rate. Besides this fitness-enhancing effect, I found that co-adaptation may provide the predator-prey system with the flexibility to buffer external perturbations. On top of these rather internal factors, environmental drivers also affect predator-prey interactions. I showed that environmental nutrient fluctuations may create a spatio-temporal resource heterogeneity that selects for different predator strategies. I hypothesized that this might favour either storage or acclimation specialists, depending on the frequency of the environmental fluctuations. We found that many of these factors promote the coexistence of different strategies and may therefore support and sustain biodiversity. Thus, they might be relevant for the maintenance of crucial ecosystem functions that also affect us humans. Besides this, the richness of factors that impact predator-prey interactions might explain why so many species, especially in the planktonic regime, are able to coexist.}, language = {en} } @phdthesis{Ramming2019, author = {Ramming, Anna}, title = {Specific Roles of POLY(A) POLYMERASE1 in the male Gametophyte and Beyond}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2019}, language = {en} } @phdthesis{Reeg2019, author = {Reeg, Jette}, title = {Simulating the impact of herbicide drift exposure on non-target terrestrial plant communities}, doi = {10.25932/publishup-42907}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429073}, school = {Universit{\"a}t Potsdam}, pages = {178}, year = {2019}, abstract = {In Europe, almost half of the terrestrial landscape is used for agriculture. Thus, semi-natural habitats such as field margins are substantial for maintaining diversity in intensively managed farmlands. However, plants located at field margins are threatened by agricultural practices such as the application of pesticides within the fields. Pesticides are chemicals developed to control for undesired species within agricultural fields to enhance yields. The use of pesticides implies, however, effects on non-target organisms within and outside of the agricultural fields. Non-target organisms are organisms not intended to be sprayed or controlled for. For example, plants occurring in field margins are not intended to be sprayed, however, can be impaired due to herbicide drift exposure. The authorization of plant protection products such as herbicides requires risk assessments to ensure that the application of the product has no unacceptable effects on the environment. For non-target terrestrial plants (NTTPs), the risk assessment is based on standardized greenhouse studies on plant individual level. To account for the protection of plant populations and communities under realistic field conditions, i.e. extrapolating from greenhouse studies to field conditions and from individual-level to community-level, assessment factors are applied. However, recent studies question the current risk assessment scheme to meet the specific protection goals for non-target terrestrial plants as suggested by the European Food Safety Authority (EFSA). There is a need to clarify the gaps of the current risk assessment and to include suitable higher tier options in the upcoming guidance document for non-target terrestrial plants. In my thesis, I studied the impact of herbicide drift exposure on NTTP communities using a mechanistic modelling approach. I addressed main gaps and uncertainties of the current risk assessment and finally suggested this modelling approach as a novel higher tier option in future risk assessments. Specifically, I extended the plant community model IBC-grass (Individual-based community model for grasslands) to reflect herbicide impacts on plant individuals. In the first study, I compared model predictions of short-term herbicide impacts on artificial plant communities with empirical data. I demonstrated the capability of the model to realistically reflect herbicide impacts. In the second study, I addressed the research question whether or not reproductive endpoints need to be included in future risk assessments to protect plant populations and communities. I compared the consequences of theoretical herbicide impacts on different plant attributes for long-term plant population dynamics in the community context. I concluded that reproductive endpoints only need to be considered if the herbicide effect is assumed to be very high. The endpoints measured in the current vegetative vigour and seedling emergence studies had high impacts for the dynamic of plant populations and communities already at lower effect intensities. Finally, the third study analysed long-term impacts of herbicide application for three different plant communities. This study highlighted the suitability of the modelling approach to simulate different communities and thus detecting sensitive environmental conditions. Overall, my thesis demonstrates the suitability of mechanistic modelling approaches to be used as higher tier options for risk assessments. Specifically, IBC-grass can incorporate available individual-level effect data of standardized greenhouse experiments to extrapolate to community-level under various environmental conditions. Thus, future risk assessments can be improved by detecting sensitive scenarios and including worst-case impacts on non-target plant communities.}, language = {en} } @phdthesis{Riedel2019, author = {Riedel, Simona}, title = {Characterization of Mitochondrial ABC Transporter Homologues in Rhodobacter capsulatus}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2019}, abstract = {ABC-Transporter (ABC abgeleitet von ATP-Binding Cassette) geh{\"o}ren zur Klasse der Transmembran-Proteine und kommen in allen drei Dom{\"a}nen des Lebens vor. Ihr struktureller Aufbau ist dabei stets {\"a}hnlich, wohingegen konservierte Proteinsequenzen selten vorkommen. Die Transporter sind aus zwei lipophilen, membran-durchspannenden Dom{\"a}nen, welche auch TMDs (abgeleitet von Transmembrane spanning Domains) genannt werden, und zwei hydrophilen Dom{\"a}nen, die auch NBDs (abgeleitet von Nucleotide Binding Domains) genannt werden, aufgebaut. Die Vielzahl der durch ABC-Transporter bef{\"o}rderten Molek{\"u}le erkl{\"a}rt dabei die enorme Anzahl diverser TMDs. In den Mitochondrien des Menschen findet man vier ABC-Transporter (ABCB6, ABCB7, ABCB8 und ABCB10) mit funktionellen Homologen in Hefen und Pflanzen. In Bakterien hingegen k{\"o}nnen, mit Ausnahme von Rickettsiae und verwandten Bakterien, keine Homologen zu mitochondrialen ABC-Transportern identifiziert werden. Die transportierten Molek{\"u}le sowie die damit verbundenen Funktionen sind im Einzelnen bislang weitgehend unbekannt. ABCB7 und die entsprechenden Homologen in Hefen (Atm1) und in Pflanzen (ATM3) konnten mit der cytosolischen Eisen-Schwefel-Cluster-Biosynthese in Zusammenhang gebracht werden. Eine schwefelhaltige Verbindung der mitochondrialen Matrix wird mit Hilfe dieses Transporters der cytosolischen Eisen-Schwefel-Cluster-Assemblierung zur Verf{\"u}gung gestellt. Die 2014 publizierten Kristallstrukturen von Atm1 (Hefe) und Atm1 aus Novosphingobium aromaticivorans offenbarten dabei eine hoch konservierte Glutathion-Bindetasche innerhalb der TMDs f{\"u}r ABCB7 Homologe. In der Modellpflanze Arabidopsis thaliana konnte ATM3 zus{\"a}tzlich mit der Biosynthese des Molybd{\"a}n-Cofaktors in Verbindung gebracht werden. In der vorliegenden Arbeit wurde das α-Proteobacterium Rhodobacter capsulatus als Modellorganismus genutzt, um mitochondriale ABC-Transporter Homologe zu untersuchen. Das Bakterium enth{\"a}lt zwei ABC-Transporter-Gene, rcc03139 und rcc02305, die mit den humanen mitochondrialen Transportern große Sequenz{\"u}bereinstimmungen aufweisen (rcc03139: 41 \% respektive 38 \% Identit{\"a}t mit ABCB8 und ABCB10, rcc02305: 47 \% identisch mit ABCB7 und ABCB6). Mit Hilfe erzeugter Interposon-Mutanten (Δrcc02305I und Δrcc03139I) konnte erstmals gezeigt werden, dass bakterielle Transporter funktionell sehr {\"a}hnliche Aufgaben wie die mitochondrialen ABC-Transporter {\"u}bernehmen. Beispielsweise akkumulierten beide Interposon-Mutanten reaktive Sauerstoff-Spezies (ROS) ohne gleichzeitige Akkumulation von Glutathion oder Eisen. Weiterhin konnten wir zeigen, dass, {\"a}hnlich wie bereits f{\"u}r ATM3 postuliert, die Biosynthese des Molybd{\"a}n-Cofaktors in Δrcc02305I ver{\"a}ndert ist. Mit Hilfe einer lebensf{\"a}higen Doppelmutante, in der beide ABC-Transporter-Gene gleichzeitig deletiert wurden, konnten wir ausschließen, dass die beiden bakteriellen ABC-Transporter grunds{\"a}tzlich redundante Funktionen haben. Durch die Analyse des Proteoms von Δrcc03139I im Vergleich zu der des Wildtyps, konnte eine extreme Beeinflussung der Tetrapyrrol Biosynthese sowie entsprechender Zielproteine identifiziert werden. Dies konnte zus{\"a}tzlich durch die Quantifizierung einzelner Zwischenprodukte der Biosynthese best{\"a}tigt werden. Im Gegensatz dazu konnte anhand der Analyse des Proteoms in Verbindung mit analytischen Methoden in Δrcc02305I ein Ungleichgewicht in der Schwefelverteilung identifiziert werden. Zusammen mit der Entdeckung einer Pyridoxalphosphat (PLP) Bindestelle in Rcc02305 und anderen ABCB7-artigen Transportern, welche direkt mit dem Walker-A-Motiv der NBD {\"u}berlappt, erm{\"o}glichte dies eine v{\"o}llig neue Theorie, wie die schwefelhaltige Verbindung transportiert werden kann. Wir gehen davon aus, dass an PLP zun{\"a}chst ein Persulfid produziert wird, welches unmittelbar mit dem Glutathion der transmembranen Bindetasche zu einem gemischten Polysulfid reagiert. Im Anschluss daran wird die ATP-Bindestelle frei und die Hydrolyse des ATPs l{\"o}st eine Konformations{\"a}nderung aus, welche das gemischte Polysulfid ins Periplasma bzw. in den intermembranen Raum freigibt.}, language = {en} } @phdthesis{RomeroMujalli2019, author = {Romero Mujalli, Daniel}, title = {Ecological modeling of adaptive evolutionary responses to rapid climate change}, doi = {10.25932/publishup-43062}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430627}, school = {Universit{\"a}t Potsdam}, pages = {167}, year = {2019}, abstract = {A contemporary challenge in Ecology and Evolutionary Biology is to anticipate the fate of populations of organisms in the context of a changing world. Climate change and landscape changes due to anthropic activities have been of major concern in the contemporary history. Organisms facing these threats are expected to respond by local adaptation (i.e., genetic changes or phenotypic plasticity) or by shifting their distributional range (migration). However, there are limits to their responses. For example, isolated populations will have more difficulties in developing adaptive innovations by means of genetic changes than interconnected metapopulations. Similarly, the topography of the environment can limit dispersal opportunities for crawling organisms as compared to those that rely on wind. Thus, populations of species with different life history strategy may differ in their ability to cope with changing environmental conditions. However, depending on the taxon, empirical studies investigating organisms' responses to environmental change may become too complex, long and expensive; plus, complications arising from dealing with endangered species. In consequence, eco-evolutionary modeling offers an opportunity to overcome these limitations and complement empirical studies, understand the action and limitations of underlying mechanisms, and project into possible future scenarios. In this work I take a modeling approach and investigate the effect and relative importance of evolutionary mechanisms (including phenotypic plasticity) on the ability for local adaptation of populations with different life strategy experiencing climate change scenarios. For this, I performed a review on the state of the art of eco-evolutionary Individual-Based Models (IBMs) and identify gaps for future research. Then, I used the results from the review to develop an eco-evolutionary individual-based modeling tool to study the role of genetic and plastic mechanisms in promoting local adaption of populations of organisms with different life strategies experiencing scenarios of climate change and environmental stochasticity. The environment was simulated through a climate variable (e.g., temperature) defining a phenotypic optimum moving at a given rate of change. The rate of change was changed to simulate different scenarios of climate change (no change, slow, medium, rapid climate change). Several scenarios of stochastic noise color resembling different climatic conditions were explored. Results show that populations of sexual species will rely mainly on standing genetic variation and phenotypic plasticity for local adaptation. Population of species with relatively slow growth rate (e.g., large mammals) - especially those of small size - are the most vulnerable, particularly if their plasticity is limited (i.e., specialist species). In addition, whenever organisms from these populations are capable of adaptive plasticity, they can buffer fitness losses in reddish climatic conditions. Likewise, whenever they can adjust their plastic response (e.g., bed-hedging strategy) they will cope with bluish environmental conditions as well. In contrast, life strategies of high fecundity can rely on non-adaptive plasticity for their local adaptation to novel environmental conditions, unless the rate of change is too rapid. A recommended management measure is to guarantee interconnection of isolated populations into metapopulations, such that the supply of useful genetic variation can be increased, and, at the same time, provide them with movement opportunities to follow their preferred niche, when local adaptation becomes problematic. This is particularly important for bluish and reddish climatic conditions, when the rate of change is slow, or for any climatic condition when the level of stress (rate of change) is relatively high.}, language = {en} } @phdthesis{Scherer2019, author = {Scherer, Philipp C{\´e}dric}, title = {Infection on the move}, school = {Universit{\"a}t Potsdam}, pages = {x, 107, XXXVIII}, year = {2019}, abstract = {Movement plays a major role in shaping population densities and contact rates among individuals, two factors that are particularly relevant for disease outbreaks. Although any differences in movement behaviour due to individual characteristics of the host and heterogeneity in landscape structure are likely to have considerable consequences for disease dynamics, these mechanisms are neglected in most epidemiological studies. Therefore, developing a general understanding how the interaction of movement behaviour and spatial heterogeneity shapes host densities, contact rates and ultimately pathogen spread is a key question in ecological and epidemiological research. In my thesis, I address this gap using both theoretical and empirical modelling approaches. In the theoretical part of my thesis, I investigated bottom-up effects of individual movement behaviour and landscape structure on host density, contact rates, and ultimately disease dynamics. I extended an established agent-based model that simulates ecological and epidemiological key processes to incorporate explicit movement of host individuals and landscape complexity. Neutral landscape models are a powerful basis for spatially-explicit modelling studies to imitate the complex characteristics of natural landscapes. In chapter 2, the first study of my thesis, I introduce two complementary R packages, NLMR and landscapetools, that I have co-developed to simplify the workflow of simulation and customization of such landscapes. To demonstrate the use of the packages I present a case study using the spatially explicit eco-epidemiological model and show that landscape complexity per se increases the probability of disease persistence. By using simple rules to simulate explicit host movement, I highlight in chapter 3 how disease dynamics are affected by population-level properties emerging from different movement rules leading to differences in the realized movement distance, spatiotemporal host density, and heterogeneity in transmission rates. As a consequence, mechanistic movement decisions based on the underlying landscape or conspecific competition led to considerably higher probabilities than phenomenological random walk approaches due directed movement leading to spatiotemporal differences in host densities. The results of these two chapters highlight the need to explicitly consider spatial heterogeneity and host movement behaviour when theoretical approaches are used to assess control measures to prevent outbreaks or eradicate diseases. In the empirical part of my thesis (chapter 4), I focus on the spatiotemporal dynamics of Classical Swine Fever in a wild boar population by analysing epidemiological data that was collected during an outbreak in Northern Germany persisting for eight years. I show that infection risk exhibits different seasonal patterns on the individual and the regional level. These patterns on the one hand show a higher infection risk in autumn and winter that may arise due to onset of mating behaviour and hunting intensity, which result in increased movement ranges. On the other hand, the increased infection risk of piglets, especially during the birth season, indicates the importance of new susceptible host individuals for local pathogen spread. The findings of this chapter underline the importance of different spatial and temporal scales to understand different components of pathogen spread that can have important implications for disease management. Taken together, the complementary use of theoretical and empirical modelling in my thesis highlights that our inferences about disease dynamics depend heavily on the spatial and temporal resolution used and how the inclusion of explicit mechanisms underlying hosts movement are modelled. My findings are an important step towards the incorporation of spatial heterogeneity and a mechanism-based perspective in eco-epidemiological approaches. This will ultimately lead to an enhanced understanding of the feedbacks of contact rates on pathogen spread and disease persistence that are of paramount importance to improve predictive models at the interface of ecology and epidemiology.}, language = {en} } @phdthesis{Schirmer2019, author = {Schirmer, Annika}, title = {Consistent individual differences in movement-related behaviour as equalising and/or stabilising mechanisms for species coexistence}, school = {Universit{\"a}t Potsdam}, pages = {154}, year = {2019}, abstract = {The facilitation of species coexistence has been a central theme in ecological research for years, highlighting two key aspects: ecological niches and competition between species. According to the competitive exclusion principle, the overlap of species niches predicts the amount of shared resources and therefore competition between species, determining their ability to coexist. Only if niches of two species are sufficiently different, thus niche overlap is low, competition within species is higher than competition between species and stable coexistence is possible. Thereby, differences in species mean traits are focused on and conspecific individuals are assumed to be interchangeable. This approach might be outdated since behaviour, as a key aspect mediating niche differentiation between species, is individual based. Individuals from one species consistently differ across time and situations in their behavioural traits. Causes and consequences of consistent behavioural differences have been thoroughly investigated stimulating their recent incorporation into ecological interactions and niche theory. Spatial components have so far been largely overlooked, although animal movement is strongly connected to several aspects of ecological niches and interactions between individuals. Furthermore, numerous movement aspects haven been proven to be crucially influenced by consistent individual differences. Considering spatial parameters could therefore crucially broaden our understanding of how individual niches are formed and ecological interactions are shaped. Furthermore, extending established concepts on species interactions by an individual component could provide new insights into how species coexistence is facilitated and local biodiversity is maintained. The main aim of this thesis was to test whether consistent inter-individual differences can facilitate the coexistence of ecological similar species. Therefore, the effects of consistent inter-individual differences on the spatial behaviour of two rodent species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius), were investigated and put in the context of: (i) individual spatial niches, (ii) interactions between species, and (iii) the importance of different levels of behavioural variation within species for their interactions. Consistent differences of study animals in boldness and exploration were quantified with the same tests in all presented studies and always combined with observations of movement and space use via automated VHF radio telemetry. Consequently, results are comparable throughout the thesis and the methods provide a common denominator for all chapters. The first two chapters are based on observations of free-ranging rodents in natural populations, while chapter III represents an experimental approach under semi-natural conditions. Chapter I focusses on the effect of consistent differences in boldness and exploration on movement and space use of bank voles and their contribution to individual spatial niche separation. Results show boldness to be the dominating predictor for spatial parameters in bank voles. Irrespective of sex, bolder individuals had larger home ranges, moved longer distances, had less spatial interactions with conspecifics and occupied different microhabitats compared to shy individuals. The same boldness-dependent spatial patterns could be observed in striped field mice which is reported in chapter II. Therefore, both study species showed individual spatial niche occupation. Chapter II builds on findings from the first chapter, investigating the effect of boldness driven individual spatial niche occupation on the interactions between species. Irrespective of species and sex, bolder individuals had more interspecific spatial interactions, but less intraspecific interactions, compared to shy individuals. Due to individual niches occupation the competitive environment individuals experience is not random. Interactions are restricted to individuals of similar behavioural type with presumably similar competitive ability, which could balance differences on the species level and support coexistence. In chapter III the experimental populations were either comprised of only shy or only bold bank voles, while striped field mice varied, creating either a shy- or bold-biased competitive community. Irrespective of behavioural type, striped field mice had more intraspecific interactions in bold-biased competitive communities. Only in a shy-biased competitive community, bolder striped field mice had less interspecific interactions compared to shy individuals. Bank voles showed no difference in intra- or interspecific interactions between populations. Chapter III highlights, that not only consistent inter-individual differences per se are important for interactions within and between species, but also the amount of behavioural variation within coexisting species. Overall, this thesis highlights the importance of considering consistent inter-individual differences in a spatial context and their connection to individual spatial niche occupation, as well as the resulting effects on interactions within and between species. Individual differences are discussed in the context of similarity of individuals, individual and species niche width, and individual and species niche overlap. Thereby, this thesis makes one step further from the existing research on individual niches towards integrating consistent inter-individual differences into the larger framework of species coexistence.}, language = {en} } @phdthesis{Schiro2019, author = {Schiro, Gabriele}, title = {Spatial distribution of phyllosphere fungi in topographically heterogeneous wheat fields}, school = {Universit{\"a}t Potsdam}, pages = {105}, year = {2019}, language = {en} } @phdthesis{Schumacher2019, author = {Schumacher, Julia}, title = {Regulation and function of STERILE APETALA in Arabidopsis flower development}, school = {Universit{\"a}t Potsdam}, pages = {144}, year = {2019}, abstract = {STERILE APETALA (SAP) is known to be an essential regulator of flower development for over 20 years. Loss of SAP function in the model plant Arabidopsis thaliana is associated with a reduction of floral organ number, size and fertility. In accordance with the function of SAP during early flower development, its spatial expression in flowers is confined to meristematic stages and to developing ovules. However, to date, despite extensive research, the molecular function of SAP and the regulation of its spatio-temporal expression still remain elusive. In this work, amino acid sequence analysis and homology modeling revealed that SAP belongs to the rare class of plant F-box proteins with C-terminal WD40 repeats. In opisthokonts, this type of F-box proteins constitutes the substrate binding subunit of SCF complexes, which catalyze the ubiquitination of proteins to initiate their proteasomal degradation. With LC-MS/MS-based protein complex isolation, the interaction of SAP with major SCF complex subunits was confirmed. Additionally, candidate substrate proteins, such as the growth repressor PEAPOD 1 and 2 (PPD1/2), could be revealed during early stages of flower development. Also INDOLE-3-BUTYRIC ACID RESPONSE 5 (IBR5) was identified among putative interactors. Genetic analyses indicated that, different from substrate proteins, IBR5 is required for SAP function. Protein complex isolation together with transcriptome profiling emphasized that the SCFSAP complex integrates multiple biological processes, such as proliferative growth, vascular development, hormonal signaling and reproduction. Phenotypic analysis of sap mutant and SAP overexpressing plants positively correlated SAP function with plant growth during reproductive and vegetative development. Furthermore, to elaborate on the transcriptional regulation of SAP, publicly available ChIP-seq data of key floral homeotic proteins were reanalyzed. Here, it was shown that the MADS-domain transcription factors APETALA 1 (AP1), APETALA 3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA 3 (SEP3) bind to the SAP locus, which indicates that SAP is expressed in a floral organ-specific manner. Reporter gene analyses in combination with CRISPR/Cas9-mediated deletion of putative regulatory regions further demonstrated that the intron contains major regulatory elements of SAP in Arabidopsis thaliana. In conclusion, these data indicate that SAP is a pleiotropic developmental regulator that acts through tissue-specific destabilization of proteins. The presumed transcriptional regulation of SAP by the floral MADS-domain transcription factors could provide a missing link between the specification of floral organ identity and floral organ growth pathways.}, language = {en} } @phdthesis{Schwuchow2019, author = {Schwuchow, Viola}, title = {Charakterisierung der periplasmatischen Aldehyd-Oxidoreduktase (PaoABC) aus Escherichia coli}, school = {Universit{\"a}t Potsdam}, pages = {119}, year = {2019}, abstract = {Im Mittelpunkt dieser Arbeit standen Analysen zur Charakterisierung der periplasmatischen Aldehyd Oxidoreduktase aus E. coli. Kinetische Untersuchungen mit Ferricyanid als Elektronenakzeptor unter anaeroben Bedingungen zeigten f{\"u}r dieses Enzym eine h{\"o}here Aktivit{\"a}t als unter aeroben Bedingungen. Die getroffene Hypothese, dass PaoABC f{\"a}hig ist Elektronen an molekularen Sauerstoff weiter zu geben, konnte best{\"a}tigt werden. F{\"u}r den Umsatz aromatischer Aldehyde mit molekularem Sauerstoff wurde ein Optimum von pH 6,0 ermittelt. Dies steht im Gegensatz zur Reaktion mit Ferricyanid, mit welchem ein pH-Optimum von 4,0 gezeigt wurde. Die Reaktion von PaoABC mit molekularem Sauerstoff generiert zwar Wasserstoffperoxid, die Produktion von Superoxid konnte dagegen nicht beobachtet werden. Dass aerobe Bedingungen einen Einfluss auf das Ausl{\"o}sen der Expression von PaoABC haben, wurde in dieser Arbeit ebenfalls ermittelt. Im Zusammenhang mit der Produktion von ROS durch PaoABC wurde die Funktion eines k{\"u}rzlich in Elektronentransfer-Distanz zum FAD identifizierten [4Fe4S]-Clusters untersucht. Ein Austausch der f{\"u}r die Bindung des Clusters zust{\"a}ndigen Cysteine f{\"u}hrte zur Instabilit{\"a}t der Proteinvarianten, weswegen f{\"u}r diese keine weiteren Untersuchungen erfolgten. Daher wird zumindest ein struktur-stabilisierender Einfluss des [4Fe4S]-Clusters angenommen. Zur weiteren Untersuchung der Funktion dieses Clusters, wurde ein zwischen FAD und [4Fe4S]-Cluster lokalisiertes Arginin gegen ein Alanin ausgetauscht. Diese Proteinvariante zeigte eine reduzierte Geschwindigkeit der Reaktion gegen{\"u}ber dem Wildtyp. Die Bildung von Superoxid konnte auch hier nicht beobachtet werden. Die Vermutung, dass dieser Cluster einen elektronen-sammelnden Mechanismus unterst{\"u}tzt, welcher die Radikalbildung verhindert, kann trotz allem nicht ausgeschlossen werden. Da im Umkreis des Arginins weitere geladene und aromatische Aminos{\"a}uren lokalisiert sind, k{\"o}nnen diese den notwendigen Elektronentransfer {\"u}bernehmen. Neben der Ermittlung eines physiologischen Elektronenakzeptors und dessen Einfluss auf die Expression von PaoABC zeigt diese Arbeit auch, dass die Chaperone PaoD und MocA w{\"a}hrend der Reifung des MCD-Kofaktor eine gemeinsame Bindung an PaoABC realisieren. Es konnte im aktiven Zentrum von PaoABC ein Arginin beschrieben werden, welches auf Grund der engen Nachbarschaft zum MCD-Kofaktor und zum Glutamat (PaoABC-EC692) am Prozess der Substratbindung beteiligt ist. Im Zusammenhang mit dem Austausch dieses Arginins gegen ein Histidin oder ein Lysin wurden die Enzymspezifit{\"a}t und der Einfluss physiologischer Bedingungen, wie pH und Ionenst{\"a}rke, auf die Reaktion des Enzyms untersucht. Gegen{\"u}ber dem Wildtyp zeigten die Varianten mit molekularem Sauerstoff eine geringere Affinit{\"a}t zum Substrat aber auch eine h{\"o}here Geschwindigkeit der Reaktion. Vor allem f{\"u}r die Histidin-Variante konnte im gesamten pH-Bereich ein instabiles Verhalten bestimmt werden. Der Grund daf{\"u}r wurde durch das L{\"o}sen der Struktur der Histidin-Variante beschreiben. Durch den Austausch der Aminos{\"a}uren entf{\"a}llt die stabilisierende Wirkung der delokalisierten Elektronen des Arginins und es kommt zu einer Konformations{\"a}nderung im aktiven Zentrum. Neben der Reaktion von PaoABC mit einer Vielzahl aromatischer Aldehyde konnte auch der Umsatz von Salicylaldehyd zu Salicyls{\"a}ure durch PaoABC in einer Farbreaktion bestimmt werden. Durch Ausschluss von molekularem Sauerstoff als terminaler Elektronenakzeptor, in einer enzym-gekoppelten Reaktion, erfolgte ein Elektronentransport auf Ferrocencarboxyls{\"a}ure. Die Kombination aus beiden Methoden erm{\"o}glichte eine Verwendung von Ferrocen-Derivaten zur Generierung einer enzym-gekoppelten Reaktion mit PaoABC. Die Untersuchungen zu PaoABC zeigen, dass die Vielfalt der durch das Enzym katalysierten Rektionen weitere M{\"o}glichkeiten der enzymatischen Bestimmung biokatalytischer Prozesse bietet.}, language = {de} } @phdthesis{Schaefer2019, author = {Sch{\"a}fer, Merlin}, title = {Understanding and predicting global change impacts on migratory birds}, doi = {10.25932/publishup-43925}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439256}, school = {Universit{\"a}t Potsdam}, pages = {XIV, 153}, year = {2019}, abstract = {This is a publication-based dissertation comprising three original research stud-ies (one published, one submitted and one ready for submission; status March 2019). The dissertation introduces a generic computer model as a tool to investigate the behaviour and population dynamics of animals in cyclic environments. The model is further employed for analysing how migratory birds respond to various scenarios of altered food supply under global change. Here, ecological and evolutionary time-scales are considered, as well as the biological constraints and trade-offs the individual faces, which ultimately shape response dynamics at the population level. Further, the effect of fine-scale temporal patterns in re-source supply are studied, which is challenging to achieve experimentally. My findings predict population declines, altered behavioural timing and negative carry-over effects arising in migratory birds under global change. They thus stress the need for intensified research on how ecological mechanisms are affected by global change and for effective conservation measures for migratory birds. The open-source modelling software created for this dissertation can now be used for other taxa and related research questions. Overall, this thesis improves our mechanistic understanding of the impacts of global change on migratory birds as one prerequisite to comprehend ongoing global biodiversity loss. The research results are discussed in a broader ecological and scientific context in a concluding synthesis chapter.}, language = {en} } @phdthesis{Taube2019, author = {Taube, Robert}, title = {Characterisations of Fungal Communities in Temperate Lakes}, school = {Universit{\"a}t Potsdam}, pages = {139}, year = {2019}, language = {en} } @phdthesis{Teckentrup2019, author = {Teckentrup, Lisa}, title = {Understanding predator-prey interactions}, doi = {10.25932/publishup-43162}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431624}, school = {Universit{\"a}t Potsdam}, pages = {ix, 133}, year = {2019}, abstract = {Predators can have numerical and behavioral effects on prey animals. While numerical effects are well explored, the impact of behavioral effects is unclear. Furthermore, behavioral effects are generally either analyzed with a focus on single individuals or with a focus on consequences for other trophic levels. Thereby, the impact of fear on the level of prey communities is overlooked, despite potential consequences for conservation and nature management. In order to improve our understanding of predator-prey interactions, an assessment of the consequences of fear in shaping prey community structures is crucial. In this thesis, I evaluated how fear alters prey space use, community structure and composition, focusing on terrestrial mammals. By integrating landscapes of fear in an existing individual-based and spatially-explicit model, I simulated community assembly of prey animals via individual home range formation. The model comprises multiple hierarchical levels from individual home range behavior to patterns of prey community structure and composition. The mechanistic approach of the model allowed for the identification of underlying mechanism driving prey community responses under fear. My results show that fear modified prey space use and community patterns. Under fear, prey animals shifted their home ranges towards safer areas of the landscape. Furthermore, fear decreased the total biomass and the diversity of the prey community and reinforced shifts in community composition towards smaller animals. These effects could be mediated by an increasing availability of refuges in the landscape. Under landscape changes, such as habitat loss and fragmentation, fear intensified negative effects on prey communities. Prey communities in risky environments were subject to a non-proportional diversity loss of up to 30\% if fear was taken into account. Regarding habitat properties, I found that well-connected, large safe patches can reduce the negative consequences of habitat loss and fragmentation on prey communities. Including variation in risk perception between prey animals had consequences on prey space use. Animals with a high risk perception predominantly used safe areas of the landscape, while animals with a low risk perception preferred areas with a high food availability. On the community level, prey diversity was higher in heterogeneous landscapes of fear if individuals varied in their risk perception compared to scenarios in which all individuals had the same risk perception. Overall, my findings give a first, comprehensive assessment of the role of fear in shaping prey communities. The linkage between individual home range behavior and patterns at the community level allows for a mechanistic understanding of the underlying processes. My results underline the importance of the structure of the landscape of fear as a key driver of prey community responses, especially if the habitat is threatened by landscape changes. Furthermore, I show that individual landscapes of fear can improve our understanding of the consequences of trait variation on community structures. Regarding conservation and nature management, my results support calls for modern conservation approaches that go beyond single species and address the protection of biotic interactions.}, language = {en} } @phdthesis{Thirumalaikumar2019, author = {Thirumalaikumar, Venkatesh P.}, title = {Investigating drought and heat stress regulatory networks in Arabidopsis and tomato}, school = {Universit{\"a}t Potsdam}, pages = {154}, year = {2019}, language = {en} } @phdthesis{Tong2019, author = {Tong, Hao}, title = {Dissection of genetic architecture of intermediate phenotypes and predictions in plants}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2019}, abstract = {Determining the relationship between genotype and phenotype is the key to understand the plasticity and robustness of phenotypes in nature. While the directly observable plant phenotypes (e.g. agronomic, yield and stress resistance traits) have been well-investigated, there is still a lack in our knowledge about the genetic basis of intermediate phenotypes, such as metabolic phenotypes. Dissecting the links between genotype and phenotype depends on suitable statistical models. The state-of-the-art models are developed for directly observable phenotypes, regardless the characteristics of intermediate phenotypes. This thesis aims to fill the gaps in understanding genetic architecture of intermediate phenotypes, and how they tie to composite traits, namely plant growth. The metabolite levels and reaction fluxes, as two aspects of metabolic phenotypes, are shaped by the interrelated chemical reactions formed in genome-scale metabolic network. Here, I attempt to answer the question: Can the knowledge of underlying genome-scale metabolic network improve the model performance for prediction of metabolic phenotypes and associated plant growth? To this end, two projects are investigated in this thesis. Firstly, we propose an approach that couples genomic selection with genome-scale metabolic network and metabolic profiles in Arabidopsis thaliana to predict growth. This project is the first integration of genomic data with fluxes predicted based on constraint-based modeling framework and data on biomass composition. We demonstrate that our approach leads to a considerable increase of prediction accuracy in comparison to the state-of-the-art methods in both within and across environment predictions. Therefore, our work paves the way for combining knowledge on metabolic mechanisms in the statistical approach underlying genomic selection to increase the efficiency of future plant breeding approaches. Secondly, we investigate how reliable is genomic selection for metabolite levels, and which single nucleotide polymorphisms (SNPs), obtained from different neighborhoods of a given metabolic network, contribute most to the accuracy of prediction. The results show that the local structure of first and second neighborhoods are not sufficient for predicting the genetic basis of metabolite levels in Zea mays. Furthermore, we find that the enzymatic SNPs can capture most the genetic variance and the contribution of non-enzymatic SNPs is in fact small. To comprehensively understand the genetic architecture of metabolic phenotypes, I extend my study to a local Arabidopsis thaliana population and their hybrids. We analyze the genetic architecture in primary and secondary metabolism as well as in growth. In comparison to primary metabolites, compounds from secondary metabolism were more variable and show more non-additive inheritance patterns which could be attributed to epistasis. Therefore, our study demonstrates that heterozygosity in local Arabidopsis thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. The studies in this thesis improve the knowledge of genetic architecture of metabolic phenotypes in both inbreed and hybrid population. The approaches I proposed to integrate genome-scale metabolic network with genomic data provide the opportunity to obtain mechanistic insights about the determinants of agronomically important polygenic traits.}, language = {en} } @phdthesis{Vandrich2019, author = {Vandrich, Jasmina}, title = {Metabolic Engineering in Halomonas elongata}, school = {Universit{\"a}t Potsdam}, pages = {80}, year = {2019}, language = {en} } @phdthesis{Wozniak2019, author = {Wozniak, Natalia Joanna}, title = {Convergent evolution of the selfing syndrome in the genus Capsella}, school = {Universit{\"a}t Potsdam}, pages = {229}, year = {2019}, language = {en} } @phdthesis{Yishai2019, author = {Yishai, Oren}, title = {Engineering the reductive glycine pathway in Escherichia coli}, school = {Universit{\"a}t Potsdam}, pages = {86}, year = {2019}, language = {en} } @phdthesis{Zemella2019, author = {Zemella, Anne}, title = {Fluoreszenzmarkierung und Modifizierung von komplexen Proteinen in eukaryotischen zellfreien Systemen durch die Etablierung von orthogonalen tRNA/Aminoacyl-tRNA-Synthetase-Paaren}, doi = {10.25932/publishup-44236}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442361}, school = {Universit{\"a}t Potsdam}, pages = {XI, 141}, year = {2019}, abstract = {Die funktionelle Charakterisierung von therapeutisch relevanten Proteinen kann bereits durch die Bereitstellung des Zielproteins in ad{\"a}quaten Mengen limitierend sein. Dies trifft besonders auf Membranproteine zu, die aufgrund von zytotoxischen Effekten auf die Produktionszelllinie und der Tendenz Aggregate zu bilden, in niedrigen Ausbeuten an aktivem Protein resultieren k{\"o}nnen. Der lebende Organismus kann durch die Verwendung von translationsaktiven Zelllysaten umgangen werden- die Grundlage der zellfreien Proteinsynthese. Zu Beginn der Arbeit wurde die ATP-abh{\"a}ngige Translation eines Lysates auf der Basis von kultivierten Insektenzellen (Sf21) analysiert. F{\"u}r diesen Zweck wurde ein ATP-bindendes Aptamer eingesetzt, durch welches die Translation der Nanoluziferase reguliert werden konnte. Durch die dargestellte Applizierung von Aptameren, k{\"o}nnten diese zuk{\"u}nftig in zellfreien Systemen f{\"u}r die Visualisierung der Transkription und Translation eingesetzt werden, wodurch zum Beispiel komplexe Prozesse validiert werden k{\"o}nnen. Neben der reinen Proteinherstellung k{\"o}nnen Faktoren wie posttranslationale Modifikationen sowie eine Integration in eine lipidische Membran essentiell f{\"u}r die Funktionalit{\"a}t des Membranproteins sein. Im zweiten Abschnitt konnte, im zellfreien Sf21-System, f{\"u}r den G-Protein-gekoppelten Rezeptor Endothelin B sowohl eine Integration in die endogen vorhandenen Endoplasmatisch Retikulum-basierten Membranstrukturen als auch Glykosylierungen, identifiziert werden. Auf der Grundlage der erfolgreichen Synthese des ET-B-Rezeptors wurden verschiedene Methoden zur Fluoreszenzmarkierung des Adenosin-Rezeptors A2a (Adora2a) angewandt und optimiert. Im dritten Abschnitt wurde der Adora2a mit Hilfe einer vorbeladenen tRNA, welche an eine fluoreszierende Aminos{\"a}ure gekoppelt war, im zellfreien Chinesischen Zwerghamster Ovarien (CHO)-System markiert. Zus{\"a}tzlich konnte durch den Einsatz eines modifizierten tRNA/Aminoacyl-tRNA-Synthetase-Paares eine nicht-kanonische Aminos{\"a}ure an Position eines integrierten Amber-Stopcodon in die Polypeptidkette eingebaut und die funktionelle Gruppe im Anschluss an einen Fluoreszenzfarbstoff gekoppelt werden. Aufgrund des offenen Charakters eignen sich zellfreie Proteinsynthesesysteme besonders f{\"u}r eine Integration von exogenen Komponenten in den Translationsprozess. Mit Hilfe der Fluoreszenzmarkierung wurde eine ligandvermittelte Konformations{\"a}nderung im Adora2a {\"u}ber einen Biolumineszenz-Resonanzenergietransfer detektiert. Durch die Etablierung der Amber-Suppression wurde dar{\"u}ber hinaus das Hormon Erythropoetin pegyliert, wodurch Eigenschaften wie Stabilit{\"a}t und Halbwertszeit des Proteins ver{\"a}ndert wurden. Zu guter Letzt wurde ein neues tRNA/Aminoacyl-tRNA-Synthetase-Paar auf Basis der Methanosarcina mazei Pyrrolysin-Synthetase etabliert, um das Repertoire an nicht-kanonischen Aminos{\"a}uren und den damit verbundenen Kopplungsreaktionen zu erweitern. Zusammenfassend wurden die Potenziale zellfreier Systeme in Bezug auf der Herstellung von komplexen Membranproteinen und der Charakterisierung dieser durch die Einbringung einer positionsspezifischen Fluoreszenzmarkierung verdeutlicht, wodurch neue M{\"o}glichkeiten f{\"u}r die Analyse und Funktionalisierung von komplexen Proteinen geschaffen wurden.}, language = {de} } @phdthesis{Zhang2019, author = {Zhang, Xiaorong}, title = {Electrosynthesis and characterization of molecularly imprinted polymers for peptides and proteins}, school = {Universit{\"a}t Potsdam}, pages = {116}, year = {2019}, language = {en} }