@misc{ParaskevopoulouDennisWeithoffetal.2019, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Hartmann, Stefanie and Tiedemann, Ralph}, title = {Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {796}, issn = {1866-8372}, doi = {10.25932/publishup-44105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441050}, pages = {23}, year = {2019}, abstract = {Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).}, 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{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{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{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{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} } @misc{KettnerOberbeckmannLabrenzetal.2019, author = {Kettner, Marie Therese and Oberbeckmann, Sonja and Labrenz, Matthias and Grossart, Hans-Peter}, title = {The Eukaryotic Life on Microplastics in Brackish Ecosystems}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {741}, issn = {1866-8372}, doi = {10.25932/publishup-43499}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434996}, pages = {10}, year = {2019}, abstract = {Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.}, language = {en} } @misc{CeulemansGaedkeKlauschiesetal.2019, author = {Ceulemans, Ruben and Gaedke, Ursula and Klauschies, Toni and Guill, Christian}, title = {The effects of functional diversity on biomass production, variability, and resilience of ecosystem functions in a tritrophic system}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {744}, issn = {1866-8372}, doi = {10.25932/publishup-43543}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435439}, pages = {16}, year = {2019}, abstract = {Diverse communities can adjust their trait composition to altered environmental conditions, which may strongly influence their dynamics. Previous studies of trait-based models mainly considered only one or two trophic levels, whereas most natural system are at least tritrophic. Therefore, we investigated how the addition of trait variation to each trophic level influences population and community dynamics in a tritrophic model. Examining the phase relationships between species of adjacent trophic levels informs about the strength of top-down or bottom-up control in non-steadystate situations. Phase relationships within a trophic level highlight compensatory dynamical patterns between functionally different species, which are responsible for dampening the community temporal variability. Furthermore, even without trait variation, our tritrophic model always exhibits regions with two alternative states with either weak or strong nutrient exploitation, and correspondingly low or high biomass production at the top level. However, adding trait variation increased the basin of attraction of the high-production state, and decreased the likelihood of a critical transition from the high- to the lowproduction state with no apparent early warning signals. Hence, our study shows that trait variation enhances resource use efficiency, production, stability, and resilience of entire food webs.}, language = {en} } @misc{DeCahsanWestburyDrewsetal.2019, author = {De Cahsan, Binia and Westbury, Michael V. and Drews, Hauke and Tiedemann, Ralph}, title = {The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {532}, issn = {1866-8372}, doi = {10.25932/publishup-42322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423222}, pages = {3}, year = {2019}, abstract = {The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany.}, language = {en} } @misc{RiedelSiemiatkowskaWatanabeetal.2019, author = {Riedel, Simona and Siemiatkowska, Beata and Watanabe, Mutsumi and M{\"u}ller, Christina S. and Sch{\"u}nemann, Volker and Hoefgen, Rainer and Leimk{\"u}hler, Silke}, title = {The ABCB7-Like Transporter PexA in Rhodobacter capsulatus Is Involved in the Translocation of Reactive Sulfur Species}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {740}, issn = {1866-8372}, doi = {10.25932/publishup-43497}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434975}, pages = {10}, year = {2019}, abstract = {The mitochondrial ATP-binding cassette (ABC) transporters ABCB7 in humans, Atm1 in yeast and ATM3 in plants, are highly conserved in their overall architecture and particularly in their glutathione binding pocket located within the transmembrane spanning domains. These transporters have attracted interest in the last two decades based on their proposed role in connecting the mitochondrial iron sulfur (Fe-S) cluster assembly with its cytosolic Fe-S cluster assembly (CIA) counterpart. So far, the specific compound that is transported across the membrane remains unknown. In this report we characterized the ABCB7-like transporter Rcc02305 in Rhodobacter capsulatus, which shares 47\% amino acid sequence identity with its mitochondrial counterpart. The constructed interposon mutant strain in R. capsulatus displayed increased levels of intracellular reactive oxygen species without a simultaneous accumulation of the cellular iron levels. The inhibition of endogenous glutathione biosynthesis resulted in an increase of total glutathione levels in the mutant strain. Bioinformatic analysis of the amino acid sequence motifs revealed a potential aminotransferase class-V pyridoxal-50-phosphate (PLP) binding site that overlaps with the Walker A motif within the nucleotide binding domains of the transporter. PLP is a well characterized cofactor of L-cysteine desulfurases like IscS and NFS1 which has a role in the formation of a protein-bound persulfide group within these proteins. We therefore suggest renaming the ABCB7-like transporter Rcc02305 in R. capsulatus to PexA for PLP binding exporter. We further suggest that this ABC-transporter in R. capsulatus is involved in the formation and export of polysulfide species to the periplasm.}, language = {en} } @misc{SchieferdeckerWendler2019, author = {Schieferdecker, Anne and Wendler, Petra}, title = {Structural mapping of missense mutations in the Pex1/Pex6 complex}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1072}, issn = {1866-8372}, doi = {10.25932/publishup-47284}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472843}, pages = {27}, year = {2019}, abstract = {Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65\% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients.}, 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{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} } @misc{BreedveldFolkertsmaEccard2019, author = {Breedveld, Merel Cathelijne and Folkertsma, Remco and Eccard, Jana}, title = {Rodent mothers increase vigilance behaviour when facing infanticide risk}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch- Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch- Naturwissenschaftliche Reihe}, number = {766}, issn = {1866-8372}, doi = {10.25932/publishup-43807}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438074}, pages = {12}, year = {2019}, abstract = {Infanticide, the killing of unrelated young, is widespread and frequently driven by sexual conflict. especially in mammals with exclusive maternal care, infanticide by males is common and females suffer fitness costs. Recognizing infanticide risk and adjusting offspring protection accordingly should therefore be adaptive in female mammals. Using a small mammal (Myodes glareolus) in outdoor enclosures, we investigated whether lactating mothers adjust offspring protection, and potential mate search behaviour, in response to different infanticide risk levels. We presented the scent of the litter's sire or of a stranger male near the female's nest, and observed female nest presence and movement by radiotracking. While both scents simulated a mating opportunity, they represented lower (sire) and higher (stranger) infanticide risk. compared to the sire treatment, females in the stranger treatment left their nest more often, showed increased activity and stayed closer to the nest, suggesting offspring protection from outside the nest through elevated alertness and vigilance. females with larger litters spent more time investigating scents and used more space in the sire but not in the stranger treatment. Thus, current investment size affected odour inspection and resource acquisition under higher risk. Adjusting nest protection and resource acquisition to infanticide risk could allow mothers to elicit appropriate (fitness-saving) counterstrategies, and thus, may be widespread.}, language = {en} } @misc{GeisslerHeblackUuguluetal.2019, author = {Geißler, Katja and Heblack, Jessica and Uugulu, Shoopala and Wanke, Heike and Blaum, Niels}, title = {Partitioning of Water Between Differently Sized Shrubs and Potential Groundwater Recharge in a Semiarid Savanna in Namibia}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {798}, issn = {1866-8372}, doi = {10.25932/publishup-44111}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441110}, pages = {13}, year = {2019}, abstract = {Introduction: Many semiarid regions around the world are presently experiencing significant changes in both climatic conditions and vegetation. This includes a disturbed coexistence between grasses and bushes also known as bush encroachment, and altered precipitation patterns with larger rain events. Fewer, more intense precipitation events might promote groundwater recharge, but depending on the structure of the vegetation also encourage further woody encroachment. Materials and Methods: In this study, we investigated how patterns and sources of water uptake of Acacia mellifera (blackthorn), an important encroaching woody plant in southern African savannas, are associated with the intensity of rain events and the size of individual shrubs. The study was conducted at a commercial cattle farm in the semiarid Kalahari in Namibia (MAP 250 mm/a). We used soil moisture dynamics in different depths and natural stable isotopes as markers of water sources. Xylem water of fifteen differently sized individuals during eight rain events was extracted using a Scholander pressure bomb. Results and Discussion: Results suggest the main rooting activity zone of A. mellifera in 50 and 75 cm soil depth but a reasonable water uptake from 10 and 25 cm. Any apparent uptake pattern seems to be driven by water availability, not time in the season. Bushes prefer the deeper soil layers after heavier rain events, indicating some evidence for the classical Walter's two-layer hypothesis. However, rain events up to a threshold of 6 mm/day cause shallower depths of use and suggest several phases of intense competition with perennial grasses. The temporal uptake pattern does not depend on shrub size, suggesting a fast upwards water flow inside. d2H and d18O values in xylem water indicate that larger shrubs rely less on upper and very deep soil water than smaller shrubs. It supports the hypothesis that in environments where soil moisture is highly variable in the upper soil layers, the early investment in a deep tap-root to exploit deeper, more reliable water sources could reduce the probability of mortality during the establishment phase. Nevertheless, independent of size and time in the season, bushes do not compete with potential groundwater recharge. In a savanna encroached by A. mellifera, groundwater will most likely be affected indirectly.}, 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{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{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} } @misc{HoffmannSchirmerEccard2019, author = {Hoffmann, Julia and Schirmer, Annika and Eccard, Jana}, title = {Light pollution affects space use and interaction of two small mammal species irrespective of personality}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {749}, issn = {1866-8372}, doi = {10.25932/publishup-43630}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436307}, pages = {11}, year = {2019}, abstract = {Background: Artificial light at night (ALAN) is one form of human-induced rapid environmental changes (HIREC) and is strongly interfering with natural dark-light cycles. Some personality types within a species might be better suited to cope with environmental change and therefore might be selected upon under ongoing urbanization. Results: We used LED street lamps in a large outdoor enclosure to experimentally investigate the effects of ALAN on activity patterns, movement and interaction of individuals of two species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius). We analyzed effects combined with individual boldness score. Both species reduced their activity budget during daylight hours. While under natural light conditions home ranges were larger during daylight than during nighttime, this difference vanished under ALAN. Conspecifics showed reduced home range overlap, proximity and activity synchrony when subjected to nighttime illumination. Changes in movement patterns in reaction to ALAN were not associated with differences in boldness score of individuals. Conclusions: Our results suggest that light pollution can lead to changes in movement patterns and individual interactions in small mammals. This could lead to fitness consequences on the population level.}, language = {en} } @misc{DahmaniLudwigChiantia2019, author = {Dahmani, Ismail and Ludwig, Kai and Chiantia, Salvatore}, title = {Influenza A matrix protein M1 induces lipid membrane deformation via protein multimerization}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {768}, issn = {1866-8372}, doi = {10.25932/publishup-43868}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438689}, pages = {16}, year = {2019}, abstract = {The matrix protein M1 of the Influenza A virus (IAV) is supposed to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle toward the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In the present study, we use a combination of fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), cryo-electron tomography (cryo-ET) and scanning fluorescence correlation spectroscopy (sFCS) to investigate M1-induced membrane deformation in biophysical models of the PM. Our results indicate that M1 is indeed able to cause membrane curvature in lipid bilayers containing negatively charged lipids, in the absence of other viral components. Furthermore, we prove that protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1-M1 interactions and multimer formation are required in order to alter the bilayer three-dimensional structure, through the formation of a protein scaffold. Finally, our results suggest that, in a physiological context,M1-induced membrane deformation might be modulated by the initial bilayer curvature and the lateral organization of membrane components (i.e. the presence of lipid domains).}, language = {en} }