@article{GomulaNowakSzczepanskaHermanussenetal.2020, author = {Gomula, Aleksandra and Nowak-Szczepanska, Natalia and Hermanussen, Michael and Scheffler, Christiane and Koziel, Slawomir}, title = {Trends in growth and developmental tempo in boys aged 7 to 18 years between 1966 and 2012 in Poland}, series = {American journal of human biology : the official journal of the Human Biology Council}, volume = {33}, journal = {American journal of human biology : the official journal of the Human Biology Council}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1042-0533}, doi = {10.1002/ajhb.23548}, pages = {7}, year = {2020}, abstract = {Objectives: To assess trends in growth in different developmental periods and trends in developmental tempo in Polish boys between 1966 and 2012. Methods: Data on 34 828 boys aged 7 to 18 years were collected during Polish Anthropological Surveys conducted in 1966, 1978, 1988, and 2012. Biological parameters, related to onset of adolescent growth spurt (OGS) and peak height velocity (PHV), were derived from a Preece-Baines 1 model (PB1). Childhood (height at 7 years of age), pre-adolescent (height at OGS) and adolescent growth (adult height minus height at OGS) were identified. Results: Positive secular trend between 1966 and 2012 in adult height accounted for, on average, 1.5 cm/decade, with varying intensity between the Surveys. Decline in both age at OGS and APHV between 1966 and 2012 (1.5 and 1.4 years, respectively) indicated an acceleration in developmental tempo, on average, by 0.3 year/decade. Increases in the contribution to the trend in adult height gained during growth in particular developmental periods between 1966 and 2012 were as followed-childhood: 0.6\%, pre-adolescent growth: -3.1\%, adolescent growth: 3.1\%. Conclusions: Secular trend in developmental tempo and growth among boys reflects changes in living conditions and socio-political aspirations in Poland during nearly 50 years. Acceleration in tempo is already visible at age at OGS, whereas the trend in adult height occurs largely during adolescence, pointing to different regulation of developmental tempo and growth in body height. This finding emphasizes the importance of extending public health intervention into children's growth up until adolescence.}, language = {en} } @article{MitrovaTadjoungWaffoKaufmannetal.2018, author = {Mitrova, Biljana and Tadjoung Waffo, Armel Franklin and Kaufmann, Paul and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke and Wollenberger, Ulla}, title = {Trimethylamine N-Oxide Electrochemical Biosensor with a Chimeric Enzyme}, series = {ChemElectroChem}, volume = {6}, journal = {ChemElectroChem}, number = {6}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2196-0216}, doi = {10.1002/celc.201801422}, pages = {1732 -- 1737}, year = {2018}, abstract = {For the first time, an enzyme-based electrochemical biosensor system for determination of trimethylamine N-oxide (TMAO) is described. It employs an active chimeric variant of TorA in combination with an enzymatically deoxygenating system and a low-potential mediator for effective regeneration of the enzyme and cathodic current generation. TMAO reductase (TorA) is a molybdoenzyme found in marine and most enterobacteria that specifically catalyzes the reduction of TMAO to trimethylamine (TMA). The chimeric TorA, named TorA-FDH, corresponds to the apoform of TorA from Escherichia coli reconstituted with the molybdenum cofactor from formate dehydrogenase (FDH). Each enzyme, TorA and TorA-FDH, was immobilized on the surface of a carbon electrode and protected with a dialysis membrane. The biosensor operates at an applied potential of -0.8V [vs. Ag/AgCl (1M KCl)] under ambient air conditions thanks to an additional enzymatic O-2-scavenger system. A comparison between the two enzymatic sensors revealed a much higher sensitivity for the biosensor with immobilized TorA-FDH. This biosensor exhibits a sensitivity of 14.16nA/M TMAO in a useful measuring range of 2-110M with a detection limit of LOD=2.96nM (S/N=3), and was similar for TMAO in buffer and in spiked serum samples. With a response time of 16 +/- 2 s, the biosensor is stable over prolonged daily measurements (n=20). This electrochemical biosensor provides suitable applications in detecting TMAO levels in human serum.}, language = {en} } @article{KaechDennisVorburger2021, author = {Kaech, Heidi and Dennis, Alice B. and Vorburger, Christoph}, title = {Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa}, series = {BMC genomics}, volume = {22}, journal = {BMC genomics}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-021-07742-8}, pages = {21}, year = {2021}, abstract = {Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.}, language = {en} } @misc{DammhahnGoodman2014, author = {Dammhahn, Melanie and Goodman, Steven M.}, title = {Trophic niche differentiation and microhabitat utilization revealed by stable isotope analyses in a dry-forest bat assemblage at Ankarana, northern Madagascar}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-41515}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415157}, pages = {97 -- 109}, year = {2014}, abstract = {Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measuredstable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4\% in delta N-15 and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3\% enriched over plants) and different insectivorous bats as secondary consumers (c. 4\% enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of delta C-13-delta N-15 bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.}, language = {en} } @article{MehnerAttermeyerBraunsetal.2022, author = {Mehner, Thomas and Attermeyer, Katrin and Brauns, Mario and Brothers, Soren and Hilt, Sabine and Scharnweber, Inga Kristin and Dorst, Renee Minavan and Vanni, Michael J. and Gaedke, Ursula}, title = {Trophic transfer efficiency in lakes}, series = {Ecosystems}, volume = {25}, journal = {Ecosystems}, number = {8}, publisher = {Springer}, address = {New York}, issn = {1432-9840}, doi = {10.1007/s10021-022-00776-3}, pages = {1628 -- 1652}, year = {2022}, abstract = {Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate. We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE. Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes. Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment. We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups. This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms. An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production. We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes.}, language = {en} } @article{KehlmaierBarlowHastingsetal.2017, author = {Kehlmaier, Christian and Barlow, Axel and Hastings, Alexander K. and Vamberger, Melita and Paijmans, Johanna L. A. and Steadman, David W. and Albury, Nancy A. and Franz, Richard and Hofreiter, Michael and Fritz, Uwe}, title = {Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum}, series = {Proceedings of the Royal Society of London : Series B, Biological sciences}, volume = {284}, journal = {Proceedings of the Royal Society of London : Series B, Biological sciences}, publisher = {The Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2016.2235}, pages = {8}, year = {2017}, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, language = {en} } @article{FrancoObregonCambriaGreutertetal.2018, author = {Franco-Obregon, Alfredo and Cambria, Elena and Greutert, Helen and Wernas, Timon and Hitzl, Wolfgang and Egli, Marcel and Sekiguchi, Miho and Boos, Norbert and Hausmann, Oliver and Ferguson, Stephen J. and Kobayashi, Hiroshi and W{\"u}rtz-Kozak, Karin}, title = {TRPC6 in simulated microgravity of intervertebral disc cells}, series = {European Spine Journal}, volume = {27}, journal = {European Spine Journal}, number = {10}, publisher = {Springer}, address = {New York}, issn = {0940-6719}, doi = {10.1007/s00586-018-5688-8}, pages = {2621 -- 2630}, year = {2018}, abstract = {Purpose Prolonged bed rest and microgravity in space cause intervertebral disc (IVD) degeneration. However, the underlying molecular mechanisms are not completely understood. Transient receptor potential canonical (TRPC) channels are implicated in mechanosensing of several tissues, but are poorly explored in IVDs. Methods Primary human IVD cells from surgical biopsies composed of both annulus fibrosus and nucleus pulposus (passage 1-2) were exposed to simulated microgravity and to the TRPC channel inhibitor SKF-96365 (SKF) for up to 5days. Proliferative capacity, cell cycle distribution, senescence and TRPC channel expression were analyzed. Results Both simulated microgravity and TRPC channel antagonism reduced the proliferative capacity of IVD cells and induced senescence. While significant changes in cell cycle distributions (reduction in G1 and accumulation in G2/M) were observed upon SKF treatment, the effect was small upon 3days of simulated microgravity. Finally, downregulation of TRPC6 was shown under simulated microgravity. Conclusions Simulated microgravity and TRPC channel inhibition both led to reduced proliferation and increased senescence. Furthermore, simulated microgravity reduced TRPC6 expression. IVD cell senescence and mechanotransduction may hence potentially be regulated by TRPC6 expression. This study thus reveals promising targets for future studies.}, language = {en} } @misc{LaraNitzeGrosseetal.2018, author = {Lara, Mark J. and Nitze, Ingmar and Große, Guido and McGuire, David}, title = {Tundra landform and vegetation productivity trend maps for the Arctic Coastal Plain of northern Alaska}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1035}, issn = {1866-8372}, doi = {10.25932/publishup-45987}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459875}, pages = {12}, year = {2018}, abstract = {Arctic tundra landscapes are composed of a complex mosaic of patterned ground features, varying in soil moisture, vegetation composition, and surface hydrology over small spatial scales (10-100 m). The importance of microtopography and associated geomorphic landforms in influencing ecosystem structure and function is well founded, however, spatial data products describing local to regional scale distribution of patterned ground or polygonal tundra geomorphology are largely unavailable. Thus, our understanding of local impacts on regional scale processes (e.g., carbon dynamics) may be limited. We produced two key spatiotemporal datasets spanning the Arctic Coastal Plain of northern Alaska (similar to 60,000 km(2)) to evaluate climate-geomorphological controls on arctic tundra productivity change, using (1) a novel 30m classification of polygonal tundra geomorphology and (2) decadal-trends in surface greenness using the Landsat archive (1999-2014). These datasets can be easily integrated and adapted in an array of local to regional applications such as (1) upscaling plot-level measurements (e.g., carbon/energy fluxes), (2) mapping of soils, vegetation, or permafrost, and/or (3) initializing ecosystem biogeochemistry, hydrology, and/or habitat modeling.}, language = {en} } @phdthesis{Sarlet2023, author = {Sarlet, Adrien}, title = {Tuning the viscoelasticity of Escherichia coli biofilms}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2023}, abstract = {Biofilms are heterogeneous structures made of microorganisms embedded in a self-secreted extracellular matrix. Recently, biofilms have been studied as sustainable living materials with a focus on the tuning of their mechanical properties. One way of doing so is to use metal ions. In particular biofilms have been shown to stiffen in presence of some metal cations and to soften in presence of others. However, the specificity and the determinants of those interactions vary between species. While Escherichia coli is a widely studied model organism, little is known concerning the response of its biofilms to metal ions. In this work, we aimed at tuning the mechanics of E. coli biofilms by acting on the interplay between matrix composition and metal cations. To do so, we worked with E. coli strains producing a matrix composed of curli amyloid fibres or phosphoethanolamine-cellulose (pEtN-cellulose) fibres or both. The viscoelastic behaviour of the resulting biofilms was investigated with rheology after incubation with one of the following metal ion solutions: FeCl3, AlCl3, ZnCl2 and CaCl2 or ultrapure water. We observed that the strain producing both fibres stiffen by a factor of two when exposed to the trivalent metal cations Al(III) and Fe(III) while no such response is observed for the bivalent cations Zn(II) and Ca(II). Strains producing only one matrix component did not show any stiffening in response to either cation, but even a small softening. In order to investigate further the contribution of each matrix component to the mechanical properties, we introduced additional bacterial strains producing curli fibres in combination with non-modified cellulose, non-modified cellulose only or neither component. We measured biofilms produced by those different strains with rheology and without any solution. Since rheology does not preserve the architecture of the matrix, we compared those results to the mechanical properties of biofilms probed with the non-destructive microindentation. The microindentation results showed that biofilm stiffness is mainly determined by the presence of curli amyloid fibres in the matrix. However, this clear distinction between biofilm matrices containing or not containing curli is absent from the rheology results, i.e. following partial destruction of the matrix architecture. In addition, rheology also indicated a negative impact of curli on biofilm yield stress and flow stress. This suggests that curli fibres are more brittle and therefore more affected by the mechanical treatments. Finally, to examine the molecular interactions between the biofilms and the metal cations, we used Attenuated total reflectance - Fourier transform infrared spectroscopy (ATR-FTIR) to study the three E.coli strains producing a matrix composed of curli amyloid fibres, pEtN-cellulose fibres or both. We measured biofilms produced by those strains in presence of each of the aforementioned metal cation solutions or ultrapure water. We showed that the three strains cannot be distinguished based on their FTIR spectra and that metal cations seem to have a non-specific effect on bacterial membranes in absence of pEtN-cellulose. We subsequently conducted similar experiments on purified curli or pEtN-cellulose fibres. The spectra of the pEtN-cellulose fibres revealed a non-valence-specific interaction between metal cations and the phosphate of the pEtN-modification. Altogether, these results demonstrate that the mechanical properties of E. coli biofilms can be tuned via incubation with metal ions. While the mechanism involving curli fibres remains to be determined, metal cations seem to adsorb onto pEtN-cellulose and this is not valence-specific. This work also underlines the importance of matrix architecture to biofilm mechanics and emphasises the specificity of each matrix composition.}, language = {en} } @article{YildizLeimkuehler2021, author = {Yildiz, Tugba and Leimk{\"u}hler, Silke}, title = {TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli}, series = {Journal of bacteriology}, volume = {203}, journal = {Journal of bacteriology}, number = {7}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {1098-5530}, doi = {10.1128/JB.00659-20}, pages = {20}, year = {2021}, abstract = {To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.
IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.}, language = {en} } @article{KamaliLoriteWebberetal.2022, author = {Kamali, Bahareh and Lorite, Ignacio J. and Webber, Heidi A. and Rezaei, Ehsan Eyshi and Gabaldon-Leal, Clara and Nendel, Claas and Siebert, Stefan and Ramirez-Cuesta, Juan Miguel and Ewert, Frank and Ojeda, Jonathan J.}, title = {Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Macmillan Publishers Limited,}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-022-08056-9}, pages = {13}, year = {2022}, abstract = {This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability. Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields. The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017). By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29\% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66\%). However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses. Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale.}, language = {en} } @phdthesis{Ogden2022, author = {Ogden, Michael}, title = {Uncovering the interplay between nutrient availability and cellulose biosynthesis inhibitor activity}, school = {Universit{\"a}t Potsdam}, pages = {XI, 124}, year = {2022}, abstract = {All plant cells are surrounded by a dynamic, carbohydrate-rich extracellular matrix known as the cell wall. Nutrient availability affects cell wall composition via uncharacterized regulatory mechanisms, and cellulose deficient mutants develop a hypersensitive root response to growth on high concentrations of nitrate. Since cell walls account for the bulk of plant biomass, it is important to understand how nutrients regulate cell walls. This could provide important knowledge for directing fertilizer treatments and engineering plants with higher nutrient use efficiency. The direct effect of nitrate on cell wall synthesis was investigated through growth assays on varying concentrations of nitrate, measuring cellulose content of roots and shoots, and assessing cellulose synthase activity (CESA) using live cell imaging with spinning disk confocal microscopy. A forward genetic screen was developed to isolate mutants impaired in nutrient-mediated cell wall regulation, revealing that cellulose biosynthesis inhibitor (CBI) activity is modulated by nutrient availability. Various non-CESA mutants were isolated that displayed CBI resistance, with the majority of mutations causing perturbation of mitochondria-localized proteins. To investigate mitochondrial involvement, the CBI mechanism of action was investigated using a reverse genetic screen, a targeted pharmacological screen, and -omics approaches. The results generated suggest that CBI-induced cellulose inhibition is due to off-target effects. This provides the groundwork to investigate uncharacterized processes of CESA regulation and adds valuable knowledge to the understanding of CBI activity, which could be harnessed to develop new and improved herbicides.}, language = {en} } @article{LehmannEccardScheffleretal.2018, author = {Lehmann, Andreas and Eccard, Jana and Scheffler, Christiane and Kurvers, Ralf H. J. M. and Dammhahn, Melanie}, title = {Under pressure: human adolescents express a pace-of-life syndrome}, series = {Behavioral ecology and sociobiology}, volume = {72}, journal = {Behavioral ecology and sociobiology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0340-5443}, doi = {10.1007/s00265-018-2465-y}, pages = {15}, year = {2018}, abstract = {The pace-of-life syndrome (POLS) hypothesis posits that life-history characteristics, among individual differences in behavior, and physiological traits have coevolved in response to environmental conditions. This hypothesis has generated much research interest because it provides testable predictions concerning the association between the slow-fast life-history continuum and behavioral and physiological traits. Although humans are among the most well-studied species and similar concepts exist in the human literature, the POLS hypothesis has not yet been directly applied to humans. Therefore, we aimed to (i) test predicted relationships between life history, physiology, and behavior in a human population and (ii) better integrate the POLS hypothesis with other similar concepts. Using data of a representative sample of German adolescents, we extracted maturation status for girls (menarche, n = 791) and boys (voice break, n = 486), and a set of health-related risk-taking behaviors and cardiovascular parameters. Maturation status and health-related risk behavior as well as maturation status and cardiovascular physiology covaried in boys and girls. Fast maturing boys and girls had higher blood pressure and expressed more risk-taking behavior than same-aged slow maturing boys and girls, supporting general predictions of the POLS hypothesis. Only some physiological and behavioral traits were positively correlated, suggesting that behavioral and physiological traits might mediate life-history trade-offs differently. Moreover, some aspects of POLS were sex-specific. Overall, the POLS hypothesis shares many similarities with other conceptual frameworks from the human literature and these concepts should be united more thoroughly to stimulate the study of POLS in humans and other animals. Significance statement The pace-of-life syndrome (POLS) hypothesis suggests that life history, behavioral and physiological traits have coevolved in response to environmental conditions. Here, we tested this link in a representative sample of German adolescents, using data from a large health survey (the KIGGs study) containing information on individual age and state of maturity for girls and boys, and a set of health-related risk-taking behaviors and cardiovascular parameters. We found that fast maturing girls and boys had overall higher blood pressure and expressed more risk-taking behavior than same-aged slow maturing girls and boys. Only some behavioral and physiological traits were positively correlated, suggesting that behavioral and physiological traits might mediate life-history trade-offs differently and not necessarily form a syndrome. Our results demonstrate a general link between life history, physiological and behavioral traits in humans, while simultaneously highlighting a more complex and rich set of relationships, since not all relationships followed predictions by the POLS hypothesis.}, 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{Ullmann2018, author = {Ullmann, Wiebke}, title = {Understanding animal movement behaviour in dynamic agricultural landscapes}, doi = {10.25932/publishup-42715}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427153}, school = {Universit{\"a}t Potsdam}, pages = {vii, 183}, year = {2018}, abstract = {The movement of organisms has formed our planet like few other processes. Movements shape populations, communities, entire ecosystems, and guarantee fundamental ecosystem functions and services, like seed dispersal and pollination. Global, regional and local anthropogenic impacts influence animal movements across ecosystems all around the world. In particular, land-use modification, like habitat loss and fragmentation disrupt movements between habitats with profound consequences, from increased disease transmissions to reduced species richness and abundance. However, neither the influence of anthropogenic change on animal movement processes nor the resulting effects on ecosystems are well understood. Therefore, we need a coherent understanding of organismal movement processes and their underlying mechanisms to predict and prevent altered animal movements and their consequences for ecosystem functions. In this thesis I aim at understanding the influence of anthropogenically caused land-use change on animal movement processes and their underlying mechanisms. In particular, I am interested in the synergistic influence of large-scale landscape structure and fine-scale habitat features on basic-level movement behaviours (e.g. the daily amount of time spend running, foraging, and resting) and their emerging higher-level movements (home range formation). Based on my findings, I identify the likely consequences of altered animal movements that lead to the loss of species richness and abundances. The study system of my thesis are hares in agricultural landscapes. European brown hares (Lepus europaeus) are perfectly suited to study animal movements in agricultural landscapes, as hares are hermerophiles and prefer open habitats. They have historically thrived in agricultural landscapes, but their numbers are in decline. Agricultural areas are undergoing strong land-use changes due to increasing food demand and fast developing agricultural technologies. They are already the largest land-use class, covering 38\% of the world's terrestrial surface. To consider the relevance of a given landscape structure for animal movement behaviour I selected two differently structured agricultural landscapes - a simple landscape in Northern Germany with large fields and few landscape elements (e.g. hedges and tree stands), and a complex landscape in Southern Germany with small fields and many landscape elements. I applied GPS devices (hourly fixes) with internal high-resolution accelerometers (4 min samples) to track hares, receiving an almost continuous observation of the animals' behaviours via acceleration analyses. I used the spatial and behavioural information in combination with remote sensing data (normalized difference vegetation index, or NDVI, a proxy for resource availability), generating an almost complete idea of what the animal was doing when, why and where. Apart from landscape structure (represented by the two differently structured study areas), I specifically tested whether the following fine-scale habitat features influence animal movements: resource, agricultural management events, habitat diversity, and habitat structure. My results show that, irrespective of the movement process or mechanism and the type of fine-scale habitat features, landscape structure was the overarching variable influencing hare movement behaviour. High resource variability forces hares to enlarge their home ranges, but only in the simple and not in the complex landscape. Agricultural management events result in home range shifts in both landscapes, but force hares to increase their home ranges only in the simple landscape. Also the preference of habitat patches with low vegetation and the avoidance of high vegetation, was stronger in the simple landscape. High and dense crop fields restricted hare movements temporarily to very local and small habitat patch remnants. Such insuperable barriers can separate habitat patches that were previously connected by mobile links. Hence, the transport of nutrients and genetic material is temporarily disrupted. This mechanism is also working on a global scale, as human induced changes from habitat loss and fragmentation to expanding monocultures cause a reduction in animal movements worldwide. The mechanisms behind those findings show that higher-level movements, like increasing home ranges, emerge from underlying basic-level movements, like the behavioural modes. An increasing landscape simplicity first acts on the behavioural modes, i.e. hares run and forage more, but have less time to rest. Hence, the emergence of increased home range sizes in simple landscapes is based on an increased proportion of time running and foraging, largely due to longer travelling times between distant habitats and scarce resource items in the landscape. This relationship was especially strong during the reproductive phase, demonstrating the importance of high-quality habitat for reproduction and the need to keep up self-maintenance first, in low quality areas. These changes in movement behaviour may release a cascade of processes that start with more time being allocated to running and foraging, resulting into an increased energy expenditure and may lead to a decline in individual fitness. A decrease in individual fitness and reproductive output will ultimately affect population viability leading to local extinctions. In conclusion, I show that landscape structure has one of the most important effects on hare movement behaviour. Synergistic effects of landscape structure, and fine-scale habitat features, first affect and modify basic-level movement behaviours, that can scales up to altered higher-level movements and may even lead to the decline of species richness and abundances, and the disruption of ecosystem functions. Understanding the connection between movement mechanisms and processes can help to predict and prevent anthropogenically induced changes in movement behaviour. With regard to the paramount importance of landscape structure, I strongly recommend to decrease the size of agricultural fields and increase crop diversity. On the small-scale, conservation policies should assure the year round provision of areas with low vegetation height and high quality forage. This could be done by generating wildflower strips and additional (semi-) natural habitat patches. This will not only help to increase the populations of European brown hares and other farmland species, but also ensure and protects the continuity of mobile links and their intrinsic value for sustaining important ecosystem functions and services.}, 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} } @article{GhoddousiVanCayzeeleNegahdaretal.2022, author = {Ghoddousi, Arash and Van Cayzeele, Corinna and Negahdar, Pegah and Soofi, Mahmood and Kh. Hamidi, Amirhossein and Bleyhl, Benjamin and Fandos, Guillermo and Khorozyan, Igor and Waltert, Matthias and Kuemmerle, Tobias}, title = {Understanding spatial patterns of poaching pressure using ranger logbook data to optimize future patrolling strategies}, series = {Ecological applications : a publication of the Ecological Society of America}, volume = {32}, journal = {Ecological applications : a publication of the Ecological Society of America}, number = {5}, publisher = {Wiley}, address = {Hoboken}, issn = {1051-0761}, doi = {10.1002/eap.2601}, pages = {13}, year = {2022}, abstract = {Poaching is driving many species toward extinction, and as a result, lowering poaching pressure is a conservation priority. This requires understanding where poaching pressure is high and which factors determine these spatial patterns. However, the cryptic and illegal nature of poaching makes this difficult. Ranger patrol data, typically recorded in protected area logbooks, contain information on patrolling efforts and poaching detection and should thus provide opportunities for a better understanding of poaching pressure. However, these data are seldom analyzed and rarely used to inform adaptive management strategies. We developed a novel approach to making use of analog logbook records to map poaching pressure and to test environmental criminology and predator-prey relationship hypotheses explaining poaching patterns. We showcase this approach for Golestan National Park in Iran, where poaching has substantially depleted ungulate populations. We digitized data from >4800 ranger patrols from 2014 to 2016 and used an occupancy modeling framework to relate poaching to (1) accessibility, (2) law enforcement, and (3) prey availability factors. Based on predicted poaching pressure and patrolling intensity, we provide suggestions for future patrol allocation strategies. Our results revealed a low probability (12\%) of poacher detection during patrols. Poaching distribution was best explained by prey availability, indicating that poachers target areas with high concentrations of ungulates. Poaching pressure was estimated to be high (>0.49) in 39\% of our study area. To alleviate poaching pressure, we recommend ramping up patrolling intensity in 12\% of the national park, which could be achievable by reducing excess patrols in about 20\% of the park. However, our results suggest that for 27\% of the park, it is necessary to improve patrolling quality to increase detection probability of poaching, for example, by closing temporal patrolling gaps or expanding informant networks. Our approach illustrates that analog ranger logbooks are an untapped resource for evidence-based and adaptive planning of protected area management. Using this wealth of data can open up new avenues to better understand poaching and its determinants, to expand effectiveness assessments to the past, and, more generally, to allow for strategic conservation planning in protected areas.}, language = {en} } @article{StoneNicenboimVasishthetal.2023, author = {Stone, Kate and Nicenboim, Bruno and Vasishth, Shravan and R{\"o}sler, Frank}, title = {Understanding the effects of constraint and predictability in ERP}, series = {Neurobiology of language}, volume = {4}, journal = {Neurobiology of language}, number = {2}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, issn = {2641-4368}, doi = {10.1162/nol_a_00094}, pages = {221 -- 256}, year = {2023}, abstract = {Intuitively, strongly constraining contexts should lead to stronger probabilistic representations of sentences in memory. Encountering unexpected words could therefore be expected to trigger costlier shifts in these representations than expected words. However, psycholinguistic measures commonly used to study probabilistic processing, such as the N400 event-related potential (ERP) component, are sensitive to word predictability but not to contextual constraint. Some research suggests that constraint-related processing cost may be measurable via an ERP positivity following the N400, known as the anterior post-N400 positivity (PNP). The PNP is argued to reflect update of a sentence representation and to be distinct from the posterior P600, which reflects conflict detection and reanalysis. However, constraint-related PNP findings are inconsistent. We sought to conceptually replicate Federmeier et al. (2007) and Kuperberg et al. (2020), who observed that the PNP, but not the N400 or the P600, was affected by constraint at unexpected but plausible words. Using a pre-registered design and statistical approach maximising power, we demonstrated a dissociated effect of predictability and constraint: strong evidence for predictability but not constraint in the N400 window, and strong evidence for constraint but not predictability in the later window. However, the constraint effect was consistent with a P600 and not a PNP, suggesting increased conflict between a strong representation and unexpected input rather than greater update of the representation. We conclude that either a simple strong/weak constraint design is not always sufficient to elicit the PNP, or that previous PNP constraint findings could be an artifact of smaller sample size.}, language = {en} } @phdthesis{Weiss2017, author = {Weiß, Lina}, title = {Understanding the emergence and maintenance of biodiversity in grasslands}, school = {Universit{\"a}t Potsdam}, pages = {153}, year = {2017}, language = {en} } @phdthesis{Zhang2018, author = {Zhang, Yunming}, title = {Understanding the functional specialization of poly(A) polymerases in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {131}, year = {2018}, language = {de} } @phdthesis{RodriguezCubillos2018, author = {Rodriguez Cubillos, Andres Eduardo}, title = {Understanding the impact of heterozygosity on metabolism, growth and hybrid necrosis within a local Arabidopsis thaliana collection site}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416758}, school = {Universit{\"a}t Potsdam}, pages = {106}, year = {2018}, abstract = {Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization's impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around T{\"u}bingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size. In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed. This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation.}, language = {en} } @phdthesis{Aleksandrova2020, author = {Aleksandrova, Krasimira}, title = {Understanding the link between obesity and colorectal cancer}, school = {Universit{\"a}t Potsdam}, year = {2020}, language = {de} } @article{KnebelNeebZahnetal.2018, author = {Knebel, Constanze and Neeb, Jannika and Zahn, Elisabeth and Schmidt, Flavia and Carazo, Alejandro and Holas, Ondej and Pavek, Petr and P{\"u}schel, Gerhard Paul and Zanger, Ulrich M. and S{\"u}ssmuth, Roderich and Lampen, Alfonso and Marx-Stoelting, Philip and Braeuning, Albert}, title = {Unexpected Effects of Propiconazole, Tebuconazole, and Their Mixture on the Receptors CAR and PXR in Human Liver Cells}, series = {Toxicological sciences}, volume = {163}, journal = {Toxicological sciences}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1096-6080}, doi = {10.1093/toxsci/kfy026}, pages = {170 -- 181}, year = {2018}, abstract = {Analyzing mixture toxicity requires an in-depth understanding of the mechanisms of action of its individual components. Substances with the same target organ, same toxic effect and same mode of action (MoA) are believed to cause additive effects, whereas substances with different MoAs are assumed to act independently. Here, we tested 2 triazole fungicides, propiconazole, and tebuconazole (Te), for individual and combined effects on liver toxicity-related endpoints. Both triazoles are proposed to belong to the same cumulative assessment group and are therefore thought to display similar and additive behavior. Our data show that Te is an antagonist of the constitutive androstane receptor (CAR) in rats and humans, while propiconazole is an agonist of this receptor. Both substances activate the pregnane X-receptor (PXR) and further induce mRNA expression of CYP3A4. CYP3A4 enzyme activity, however, is inhibited by propiconazole. For common targets of PXR and CAR, the activation of PXR by Te overrides CAR inhibition. In summary, propiconazole and Te affect different hepatotoxicity-relevant cellular targets and, depending on the individual endpoint analyzed, act via similar or dissimilar mechanisms. The use of molecular data based on research in human cell systems extends the picture to refine cumulative assessment group grouping and substantially contributes to the understanding of mixture effects of chemicals in biological systems.}, language = {en} } @article{PancraceIshidaBriandetal.2018, author = {Pancrace, Claire and Ishida, Keishi and Briand, Enora and Pichi, Douglas Gatte and Weiz, Annika R. and Guljarmow, Arthur and Scalvenzi, Thibault and Sassoon, Nathalie and Hertweck, Christian and Dittmann, Elke and Gugger, Muriel}, title = {Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines}, series = {ACS chemical biology}, volume = {14}, journal = {ACS chemical biology}, number = {1}, publisher = {American Chemical Society}, address = {Washington}, issn = {1554-8929}, doi = {10.1021/acschembio.8b00918}, pages = {67 -- 75}, year = {2018}, abstract = {The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.}, language = {en} } @article{DehmKrumbholzBaunachetal.2019, author = {Dehm, Daniel and Krumbholz, Julia and Baunach, Martin and Wiebach, Vincent and Hinrichs, Katrin and Guljamow, Arthur and Tabuchi, Takeshi and Jenke-Kodama, Holger and S{\"u}ssmuth, Roderich D. and Dittmann-Th{\"u}nemann, Elke}, title = {Unlocking the spatial control of secondary metabolism uncovers hidden natural product diversity in nostoc punctiforme}, series = {ACS chemical biology}, volume = {14}, journal = {ACS chemical biology}, number = {6}, publisher = {American Chemical Society}, address = {Washington}, issn = {1554-8929}, doi = {10.1021/acschembio.9b00240}, pages = {1271 -- 1279}, year = {2019}, abstract = {Filamentous cyanobacteria belong to the most prolific producers of structurally unique and biologically active natural products, yet the majority of biosynthetic gene clusters predicted for these multicellular collectives are currently orphan. Here, we present a systems analysis of secondary metabolite gene expression in the model strain Nostoc punctiforme PCC73102 using RNA-seq and fluorescence reporter analysis. Our data demonstrate that the majority of the cryptic gene clusters are not silent but are expressed with regular or sporadic pattern. Cultivation of N. punctiforme using high-density fermentation overrules the spatial control and leads to a pronounced upregulation of more than 50\% of biosynthetic gene clusters. Our data suggest that a combination of autocrine factors, a high CO2 level, and high light account for the upregulation of individual pathways. Our overarching study not only sheds light on the strategies of filamentous cyanobacteria to share the enormous metabolic burden connected with the production of specialized molecules but provides an avenue for the genome-based discovery of natural products in multicellular cyanobacteria as exemplified by the discovery of highly unusual variants of the tricyclic peptide microviridin.}, language = {en} } @phdthesis{Westbury2018, author = {Westbury, Michael V.}, title = {Unraveling evolution through Next Generation Sequencing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409981}, school = {Universit{\"a}t Potsdam}, pages = {129}, year = {2018}, abstract = {The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the biological sciences, one of which being the field of evolutionary biology. Researchers have begun to move away from the study of laboratory model organisms to wild, natural populations and species which has greatly expanded our knowledge of evolution. NGS boasts a number of benefits over more traditional sequencing approaches. The main benefit comes from the capability to generate information for drastically more loci for a fraction of the cost. This is hugely beneficial to the study of wild animals as, even when large numbers of individuals are unobtainable, the amount of data produced still allows for accurate, reliable population and species level results from a small selection of individuals. The use of NGS to study species for which little to no previous research has been carried out on and the production of novel evolutionary information and reference datasets for the greater scientific community were the focuses of this thesis. Two studies in this thesis focused on producing novel mitochondrial genomes from shotgun sequencing data through iterative mapping, bypassing the need for a close relative to serve as a reference sequence. These mitochondrial genomes were then used to infer species level relationships through phylogenetic analyses. The first of these studies involved reconstructing a complete mitochondrial genome of the bat eared fox (Otocyon megalotis). Phylogenetic analyses of the mitochondrial genome confidently placed the bat eared fox as sister to the clade consisting of the raccoon dog and true foxes within the canidae family. The next study also involved reconstructing a mitochondrial genome but in this case from the extinct Macrauchenia of South America. As this study utilised ancient DNA, it involved a lot of parameter testing, quality controls and strict thresholds to obtain a near complete mitochondrial genome devoid of contamination known to plague ancient DNA studies. Phylogenetic analyses confidently placed Macrauchenia as sister to all living representatives of Perissodactyla with a divergence time of ~66 million years ago. The third and final study of this thesis involved de novo assemblies of both nuclear and mitochondrial genomes from brown and striped hyena and focussed on demographic, genetic diversity and population genomic analyses within the brown hyena. Previous studies of the brown hyena hinted at very low levels of genomic diversity and, perhaps due to this, were unable to find any notable population structure across its range. By incorporating a large number of genetic loci, in the form of complete nuclear genomes, population structure within the brown hyena was uncovered. On top of this, genomic diversity levels were compared to a number of other species. Results showed the brown hyena to have the lowest genomic diversity out of all species included in the study which was perhaps caused by a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. The studies within this thesis show the power NGS sequencing has and its utility within evolutionary biology. The most notable capabilities outlined in this thesis involve the study of species for which no reference data is available and in the production of large amounts of data, providing evolutionary answers at the species and population level that data produced using more traditional techniques simply could not.}, language = {en} } @misc{HempelKoseskaNikoloskietal.2017, author = {Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Kurths, J{\"u}rgen}, title = {Unraveling gene regulatory networks from time-resolved gene expression data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400924}, pages = {26}, year = {2017}, abstract = {Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.}, language = {en} } @article{deAbreueLimaLiWenetal.2018, author = {de Abreu e Lima, Francisco Anastacio and Li, Kun and Wen, Weiwei and Yan, Jianbing and Nikoloski, Zoran and Willmitzer, Lothar and Brotman, Yariv}, title = {Unraveling lipid metabolism in maize with time-resolved multi-omics data}, series = {The plant journal}, volume = {93}, journal = {The plant journal}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13833}, pages = {1102 -- 1115}, year = {2018}, abstract = {Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high-oil line By804 in two distinct time-series experiments. The integrative analysis based on high-dimensional regularized regression yielded lipid-transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co-localization of lipid-transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 x By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl-lipid classes. Therefore, the proposed approach provides high-confidence candidates for experimental testing in maize and model plant species.}, language = {en} } @article{TarazonaMachatschekLendlein2019, author = {Tarazona, Natalia A. and Machatschek, Rainhard Gabriel and Lendlein, Andreas}, title = {Unraveling the interplay between abiotic hydrolytic degradation and crystallization of bacterial polyesters comprising short and medium side-chain-length Polyhydroxyalkanoates}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {21}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {2}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/acs.biomac.9b01458}, pages = {761 -- 771}, year = {2019}, abstract = {Polyhydroxyalkanoates (PHAs) have attracted attention as degradable (co)polyesters which can be produced by microorganisms with variations in the side chain. This structural variation influences not only the thermomechanical properties of the material but also its degradation behavior. Here, we used Langmuir monolayers at the air-water (A-W) interface as suitable models for evaluating the abiotic degradation of two PHAs with different side-chain lengths and crystallinity. By controlling the polymer state (semi crystalline, amorphous), the packing density, the pH, and the degradation mechanism, we could draw several significant conclusions. (i) The maximum degree of crystallinity for a PHA film to be efficiently degraded up to pH = 12.3 is 40\%. (ii) PHA made of repeating units with shorter side-chain length are more easily hydrolyzed under alkaline conditions. The efficiency of alkaline hydrolysis decreased by about 65\% when the polymer was 40\% crystalline. (iii) In PHA films with a relatively high initial crystallinity, abiotic degradation initiated a chemicrystallization phenomenon, detected as an increase in the storage modulus (E'). This could translate into an increase in brittleness and reduction in the material degradability. Finally, we demonstrate the stability of the measurement system for long-term experiments, which allows degradation conditions for polymers that could closely simulate real-time degradation.}, language = {en} } @phdthesis{MatallanaRamirez2012, author = {Matallana-Ram{\´i}rez, Lilian Paola}, title = {Unraveling the ORE1 regulon in Arabidopsis thaliana : molecular and functional characterization of up- and down-stream components}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62646}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {Leaf senescence is an active process required for plant survival, and it is flexibly controlled, allowing plant adaptation to environmental conditions. Although senescence is largely an age-dependent process, it can be triggered by environmental signals and stresses. Leaf senescence coordinates the breakdown and turnover of many cellular components, allowing a massive remobilization and recycling of nutrients from senescing tissues to other organs (e.g., young leaves, roots, and seeds), thus enhancing the fitness of the plant. Such metabolic coordination requires a tight regulation of gene expression. One important mechanism for the regulation of gene expression is at the transcriptional level via transcription factors (TFs). The NAC TF family (NAM, ATAF, CUC) includes various members that show elevated expression during senescence, including ORE1 (ANAC092/AtNAC2) among others. ORE1 was first reported in a screen for mutants with delayed senescence (oresara1, 2, 3, and 11). It was named after the Korean word "oresara," meaning "long-living," and abbreviated to ORE1, 2, 3, and 11, respectively. Although the pivotal role of ORE1 in controlling leaf senescence has recently been demonstrated, the underlying molecular mechanisms and the pathways it regulates are still poorly understood. To unravel the signaling cascade through which ORE1 exerts its function, we analyzed particular features of regulatory pathways up-stream and down-stream of ORE1. We identified characteristic spatial and temporal expression patterns of ORE1 that are conserved in Arabidopsis thaliana and Nicotiana tabacum and that link ORE1 expression to senescence as well as to salt stress. We proved that ORE1 positively regulates natural and dark-induced senescence. Molecular characterization of the ORE1 promoter in silico and experimentally suggested a role of the 5'UTR in mediating ORE1 expression. ORE1 is a putative substrate of a calcium-dependent protein kinase named CKOR (unpublished data). Promising data revealed a positive regulation of putative ORE1 targets by CKOR, suggesting the phosphorylation of ORE1 as a requirement for its regulation. Additionally, as part of the ORE1 up-stream regulatory pathway, we identified the NAC TF ATAF1 which was able to transactivate the ORE1 promoter in vivo. Expression studies using chemically inducible ORE1 overexpression lines and transactivation assays employing leaf mesophyll cell protoplasts provided information on target genes whose expression was rapidly induced upon ORE1 induction. First, a set of target genes was established and referred to as early responding in the ORE1 regulatory network. The consensus binding site (BS) of ORE1 was characterized. Analysis of some putative targets revealed the presence of ORE1 BSs in their promoters and the in vitro and in vivo binding of ORE1 to their promoters. Among these putative target genes, BIFUNCTIONAL NUCLEASE I (BFN1) and VND-Interacting2 (VNI2) were further characterized. The expression of BFN1 was found to be dependent on the presence of ORE1. Our results provide convincing data which support a role for BFN1 as a direct target of ORE1. Characterization of VNI2 in age-dependent and stress-induced senescence revealed ORE1 as a key up-stream regulator since it can bind and activate VNI2 expression in vivo and in vitro. Furthermore, VNI2 was able to promote or delay senescence depending on the presence of an activation domain located in its C-terminal region. The plasticity of this gene might include alternative splicing (AS) to regulate its function in different organs and at different developmental stages, particularly during senescence. A model is proposed on the molecular mechanism governing the dual role of VNI2 during senescence.}, language = {en} } @phdthesis{Sedaghatmehr2017, author = {Sedaghatmehr, Mastoureh}, title = {Unraveling the regulatory mechanisms of heat stress memory in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {176}, year = {2017}, language = {en} } @phdthesis{Nguyen2022, author = {Nguyen, Van Thanh}, title = {Unravelling the mysteries of the Annamites}, school = {Universit{\"a}t Potsdam}, pages = {116}, year = {2022}, abstract = {The Annamites mountain range of Southeast Asia which runs along the border of Viet Nam and Laos is an important biodiversity hotspot with high levels of endemism. However, that biodiversity is threatened by unsustainable hunting, and many protected areas across the region have been emptied of their wildlife. To better protect the unique species in the Annamites, it is crucial to have a better understanding of their ecology and distribution. Additionally, basic genetic information is needed to provide conservation stakeholders with essential information to facilitate conservation breeding and counteract the illegal wildlife trade. To date, this baseline information is lacking for many Annamites species. This thesis aims to assess the effectiveness of using non-invasive collection methods, i.e. camera-trap surveys and leech-derived wildlife host DNA, in order to improve and enhance our understanding of ecology, distribution, and genetic diversity of the Annamites terrestrial mammals. In chapter 1, we analysed data from a systematic landscape camera-trap survey using single-species occupancy models to assess the ecology and distribution of two little-known Annamite endemics, the Annamite dark muntjac (Muntiacus rooseveltorum / truongsonensis) and Annamite striped rabbit (Nesolagus timminsi), in multiple protected areas across the Annamites. This chapter provided the first in-depth information on their ecology, as well as distribution patterns at large spatial scales. Most notably, we found that the Annamite dark muntjac was predominantly found at higher elevations, while responses to elevation varied among study areas for the Annamite striped rabbit. We estimated occupancy probabilities for both endemics by using their responses to environmental and anthropogenic influences and used this information to make recommendations for targeted conservation actions. We discuss how the approach we used for these two Annamites endemics can be expanded for other little-known and threatened species in other tropical regions. As is the case with ecology and distribution, very little is known about the genetic diversity of the Annamite striped rabbit and other mammals of the Annamites. This poor understanding is mainly attributed to the lack of a comprehensive DNA sample collection that covers the species' entire distribution range, which is believed to be a consequence of the low density of mammals or the remoteness of species' habitat. In order to overcome the difficulties when trying to collect DNA samples from elusive mammals, we applied invertebrate-derived DNA (iDNA) sampling via hematophagous leeches to indirectly obtain genetic materials of their terrestrial host mammals. In chapter 2, leech-derived DNA was used to study the genetic diversity of the Annamite striped rabbit population. By analysing the DNA extracted from leech samples collected at multiple study areas of the central Annamites, we found a genetic variation with five haplotypes among nine obtained sequences. Despite this diversity, we found no clear phylogeographic pattern among the lagomorph's populations in central Annamites. The findings have direct conservation implications for the species, as local stakeholders are currently establishing a conservation rescue and breeding facility for Annamite endemic species. Thus our results suggested that Annamite striped rabbits from multiple protected areas in central Annamites can be used as founders for the breeding program. In chapter 3, the genetic material of six mammals, which are frequently found in Indochina's illegal wildlife trade, was extracted from leeches collected at six study sites across the Anamites. Species-specific genetic markers were used to obtain DNA fragments that were analysed together with Genbank reference sequences from other parts of the species' distribution range. Our results showed that invertebrate-derived DNA can be used to fill the sampling gaps and provide genetic reference data that is needed for conservation breeding programmes or to counteract the illegal wildlife trade. Overal, this dissertation provides the first insights in the ecology, distribution, and genetics of rare and threatened species of the Annamites by utilising camera traps and leech-derived DNA as two non-invasive collection methods. This information is essential for improving conservation efforts of local stakeholders and managers, especially for the Annamite endemics. Results in this dissertation also show the effectiveness of both non-invasive methods for studying terrestrial mammals at a landscape level. By expanding the application of these methods to other protected areas across the Annamites, we will further our understanding of ecology, distribution, and genetics of Annamite endemics. With such landscape-scale surveys, we are able to provide stakeholders with an overview of the current status of wildlife in the Annamites which supports efforts to protect these secretive species from illegal hunting and thus their extinction.}, language = {en} } @phdthesis{ShahnejatBushehri2016, author = {Shahnejat-Bushehri, Sara}, title = {Unravelling the role of the Arabidopsis NAC transcription factor JUNGBRUNNEN1 (JUB1) for the regulation of growth and stress responses}, school = {Universit{\"a}t Potsdam}, pages = {155}, year = {2016}, language = {en} } @phdthesis{Schmidt2009, author = {Schmidt, Antje}, title = {Untersuchung des Recyclings Kaede-fusionierter Corticotropin-Releasing-Factor Rezeptoren Typ 1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-34902}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Aktivierte G-Protein-gekoppelte Rezeptoren (GPCR) werden schnell desensitisiert, internalisiert und anschließend entweder lysosomal degradiert oder zur Plasmamembran (PM) recycelt. Zur Resensitisierung der Zellen tragen neben recycelten auch neusynthetisierte Rezeptoren bei. Die {\"U}berlagerung beider Prozesse erschwert die Untersuchung des Rezeptorrecyclings. In dieser Arbeit sollte mit Hilfe des photokonvertierbaren Fluoreszenzproteins Kaede eine Technik entwickelt werden, mit der es m{\"o}glich ist Recycling- von Neusyntheseprozessen zu trennen und das Recycling von GPCR mikroskopisch in Echtzeit zu beobachten. Als Modellproteine wurden der Vasopressin-1a-Rezeptor V1aR (recycelnder Rezeptor), der Vasopressin-2-Rezeptor V2R (degradierter Rezeptor) und der Corticotropin-Releasing Factor-Rezeptor Typ 1 (CRF1R) verwendet, wobei bei Letzterem untersucht werden sollte, ob er nach Stimulation zur PM zur{\"u}cktransportiert wird. Da Kaede als fluoreszierendes Protein mit den GPCR fusioniert wird, wurde zun{\"a}chst {\"u}berpr{\"u}ft, ob es die Eigenschaften der Rezeptoren ver{\"a}ndert und generell f{\"u}r Transportstudien geeignet ist. Eventuell k{\"o}nnte die bereits publizierte Tetramerisierung von Kaede seine Anwendung verhindern oder erschweren. Mittels Fluoreszenz-Korrelationsspektroskopie konnte gezeigt werden, dass Kaede nicht tetramerisiert, wenn es an ein Membranprotein fusioniert ist. Außerdem konnte in in vitro- und Zellkulturexperimenten belegt werden, dass die native und die photokonvertierte Form von Kaede gleichermaßen stabil sind. Dar{\"u}ber hinaus zeigten Kaede-fusionierte GPCR sowohl in Kolokalisationsstudien als auch in Agonistbindungs- und Rezeptoraktivierungsexperimenten die gleichen Eigenschaften wie CFP- bzw. die unfusionierte Rezeptoren. Lediglich die Expression der Kaede-fusionierten Rezeptoren war geringer. Parallel wurde anhand der bereits publizierten Kaede-Struktur versucht, die Tetramerisierung des Proteins durch den Austausch interagierender Aminos{\"a}uren zu unterbinden. Die eingef{\"u}hrten Mutationen bewirkten aber eine Fehlfaltung des Proteins und damit den Verlust der Fluoreszenz. Da zuvor gezeigt werden konnte, dass Kaede-fusionierte Membranproteine nicht tetramerisieren und nicht die Eigenschaften der fusionierten Proteine ver{\"a}ndern, war monomerisiertes Kaede zur Untersuchung des Rezeptorrecyclings nicht notwendig. Im zweiten Teil der Arbeit wurde mit Hilfe von Kaede-Fusionsproteinen und mikroskopischer Testsysteme das noch unbekannte Recyclingverhalten des CRF1R untersucht. Hierf{\"u}r wurden die Kaede-fusionierten Rezeptoren in eukaryotischen Zellen exprimiert und mit Agonisten internalisiert. Die internalisierten Rezeptoren wurden in Endosomen selektiv mit UV-Strahlung photokonvertiert. Anschließend wurde der Transport der photokonvertierten Form verfolgt. Sowohl beim CRF1R als auch beim V1aR wurden Signale in der PM detektiert, beim V2R hingegen nicht. Dies zeigt, dass es sich beim CRF1R um einen recycelnden Rezeptor handelt. Die als Kontrolle eingesetzten Rezeptoren verhielten sich in diesem Experiment wie erwartet: Der V1aR wurde zur PM zur{\"u}cktransportiert, der V2R nicht. Diese Ergebnisse konnten mit Hilfe biochemischer und durchflusscytometrischer Experimente best{\"a}tigt werden. Die Internalisierung des CRF1R verl{\"a}uft Clathrin-vermittelt in Anwesenheit von β-Arrestin. Je nach Stabilit{\"a}t der β Arrestin-Interaktion unterscheidet man zwei Klassen von Rezeptoren: Klasse A-Rezeptoren interagieren transient mit β Arrestin und k{\"o}nnen recyceln. Im Gegensatz dazu gehen Klasse B-Rezeptoren eine stabile Interaktion mit β Arrestin ein und werden nach Internalisierung degradiert. In mikroskopischen Untersuchungen konnte f{\"u}r die aktivierten CRF1R und V1aR eine Rekrutierung von β Arrestin zur PM und eine transiente Interaktion mit β Arrestin gezeigt werden (Klasse A-Rezeptoren). F{\"u}r den V2R wurde dagegen eine stabile Interaktion mit β Arrestin beobachtet (Klasse B-Rezeptor). Diese Daten st{\"u}tzen die Ergebnisse des Kaede-basierten Recyclingversuchs und zeigen, dass der CRF1R ein recycelnder Rezeptor ist. Ferner wurde untersucht, ob der CRF1R zu den schnell oder langsam recycelnden Rezeptoren z{\"a}hlt. Schnell recycelnde Rezeptoren werden direkt aus fr{\"u}hen Endosomen, langsam recycelnde hingegen {\"u}ber das Trans-Golgi-Netzwerk (TGN) bzw. {\"u}ber Recycling-Endosomen zur PM transportiert. Als Marker f{\"u}r das TGN oder die Recycling-Endosomen wurde Rab11 verwendet. In Kolokalisationsstudien konnte gezeigt werden, dass der CRF1R den langsam recycelnden Rezeptoren zugeordnet werden kann. Zusammenfassend konnte in dieser Arbeit belegt werden, dass Kaede als Fusionspartner f{\"u}r Membranproteine genutzt werden kann um deren Transport in Echtzeit zu studieren. Damit wurde erstmals eine mikroskopische Methode etabliert, die es erlaubt recycelnde von neusynthetisierten Rezeptoren zu unterscheiden. Mit Hilfe dieser Methode war es m{\"o}glich zu zeigen, dass der CRF1R ein recycelnder Rezeptor ist.}, language = {de} } @phdthesis{Machowetz2006, author = {Machowetz, Anja}, title = {Untersuchung kardioprotektiver Wirkungen des Oliven{\"o}les und seiner phenolischen Komponenten in einer Gruppe gesunder deutscher M{\"a}nner}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10432}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {"Untersuchung kardioprotektiver Wirkungen des Oliven{\"o}les und seiner phenolischen Komponenten in einer Gruppe gesunder deutscher M{\"a}nner" EINLEITUNG: Epidemiologische Daten belegen, dass die mediterrane Ern{\"a}hrung mit einer niedrigen Inzidenz an mit oxidativen Stress assoziierten kardiovaskul{\"a}ren Erkrankungen einhergeht. Dabei wird vor allem dem Oliven{\"o}l, als Hauptfettlieferant in der mediterranen Ern{\"a}hrung, eine kardioprotektive Wirkung zugesprochen. Oliven{\"o}l zeichnet sich neben dem hohen Gehalt an einfach unges{\"a}ttigten Fetts{\"a}uren (MUFA) durch ein reichhaltiges Spektrum an phenolischen Verbindungen aus, deren antioxidative Wirkung bereits zahlreichen in in vitro Studien beschrieben wurde. Demnach k{\"o}nnte der Verzehr von phenolreichem Oliven{\"o}l auch in vivo vor oxidativen Sch{\"a}digungen sch{\"u}tzen und somit das Risiko f{\"u}r kardiovaskul{\"a}re Erkrankungen senken. ZIELSTELLUNG: Untersuchung der kardioprotektiven Wirkung von Oliven{\"o}l und seiner phenolischen Komponenten in einer Gruppe gesunder deutscher M{\"a}nner. METHODE: Dazu wurde eine randomisierte cross-over doppelt-verblindete Interventionsstudie an 70 gesunden M{\"a}nnern zwischen 20 - 60 Jahren im Raum Berlin-Brandenburg durchgef{\"u}hrt. In jeweils drei dreiw{\"o}chigen Interventionsphasen konsumierten die Probanden t{\"a}glich 25 ml natives (phenolreich), gemischtes (mittlerer Phenolgehalt) und raffiniertes (ann{\"a}hernd phenolfrei) Oliven{\"o}l, was sich ausschließlich im Gehalt an phenolischen Verbindungen unterschied. Das Oliven{\"o}l sollte dabei die gew{\"o}hnlich verzehrten Fette ersetzen. Die Interventionsphasen waren durch zweiw{\"o}chige Wash out-Phasen unterbrochen. Die Erhebung der Blutlipide, Biomarker der Lipidperoxidation und endogene Antioxidantien erfolgte zu Studienbeginn sowie zu Beginn und Ende jeder Verzehrsperiode.ERGEBNISSE: Bei den Blutlipiden sowie den Biomarkern der Lipidperoxidation und den endogenen Antioxidantien konnte keine signifikante Ver{\"a}nderung in Abh{\"a}ngigkeit vom Phenolgehalt der applizierten Oliven{\"o}le nachgewiesen werden. Einzig die Glutathion-Reduktase-Aktivit{\"a}t stieg mit zunehmendem Gehalt an phenolischen Verbindungen (pTrend = 0,041). Unabh{\"a}ngig von der Konzentration der Phenole im Oliven{\"o}l wurde bei den Probanden durch den Oliven{\"o}lverzehr eine Senkung von Gesamtcholesterol (p = 0,007) und Triglyzeride (p = 0,013) im Serum erzielt. Diese Wirkung geht einher mit einem gestiegenen MUFA-Anteil in der Ern{\"a}hrung aufgrund des Oliven{\"o}lkonsums (p < 0,001). SCHLUSSFOLGERUNG: Die Hypothese, dass die Phenole im Oliven{\"o}l aufgrund ihrer in in vitro und Tierstudien beschriebenen antioxidativen Wirkung dem Oliven{\"o}l neben dem einzigartigen Fetts{\"a}ureprofil eine zus{\"a}tzliche kardioprotektive Wirkung bescheren, konnte in der vorliegenden Studie nicht gezeigt werden. Dennoch konnte durch den Oliven{\"o}lverzehr und der damit einhergehenden Erh{\"o}hung des MUFA-Anteils in der Ern{\"a}hrung eine vorteilhafte Beeinflussung der Blutlipide erzielt werden. Obgleich Oliven{\"o}l nicht das vorwiegend verzehrte Fett in Deutschland darstellt, zeigten die befragten Probanden eine hohe Akzeptanz. Folglich k{\"o}nnte die Integration von Oliven{\"o}l in die habituelle Ern{\"a}hrung einen Beitrag zur Senkung des kardiovaskul{\"a}ren Erkrankungsrisikos leisten.}, subject = {Oliven{\"o}l}, language = {de} } @phdthesis{Uhlig2010, author = {Uhlig, Katja}, title = {Untersuchungen PEG-basierter thermo-responsiver Polymeroberfl{\"a}chen zur Steuerung der Zelladh{\"a}sion}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-47784}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Moderne Methoden f{\"u}r die Einzelzellanalyse werden dank der fortschreitenden Weiterentwicklung immer sensitiver. Dabei steigen jedoch auch die Anforderungen an das Probenmaterial. Viele Aufbereitungsprotokolle adh{\"a}renter Zellen beinhalten eine enzymatische Spaltung der Oberfl{\"a}chenproteine, um die Abl{\"o}sung vom Zellkultursubstrat zu erm{\"o}glichen. Verschiedene Methoden, wie die Patch-Clamp-Technik oder eine auf der Markierung extrazellul{\"a}rer Dom{\"a}nen von Membranproteinen basierende Durchflusszytometrie k{\"o}nnen dann nur noch eingeschr{\"a}nkt eingesetzt werden. Daher ist die Etablierung neuer Zellabl{\"o}semethoden dringend notwendig. In der vorliegenden Arbeit werden erstmals PEG-basierte thermo-responsive Oberfl{\"a}chen erfolgreich f{\"u}r die Zellkultur eingesetzt. Dabei wird das zerst{\"o}rungsfreie Abl{\"o}sen verschiedener Zelllinien von den Oberfl{\"a}chen durch Temperatursenkung realisiert. Die Funktionalit{\"a}t der Oberfl{\"a}chen wird durch Variation der Polymerstruktur, sowie der Konzentration der Beschichtungsl{\"o}sung, durch Beschichtung der Oberfl{\"a}chen mit einem zelladh{\"a}sionsf{\"o}rdernden Protein (Fibronektin) und durch Adsorption zelladh{\"a}sionsvermittelnder Peptide (RGD) optimiert. Um den Zellabl{\"o}sungsprozess detaillierter zu untersuchen, wird hier zum ersten Mal der direkte Zellkontakt mit thermo-responsiven Oberfl{\"a}chen mittels oberfl{\"a}chensensitiver Mikroskopie (TIRAF) sichtbar gemacht. Mit dieser Technik sind die exakte Quantifizierung und die Analyse der Reduktion der Zelladh{\"a}sionsfl{\"a}che w{\"a}hrend des Abk{\"u}hlens m{\"o}glich. Hierbei werden in Abh{\"a}ngigkeit von der Zelllinie Unterschiede im Zellverhalten w{\"a}hrend des Abl{\"o}sens festgestellt: Zellen, wie eine Brustkrebszelllinie und eine Ovarzelllinie, die bekanntermaßen st{\"a}rker mit ihrer Umgebung in Kontakt treten, vergr{\"o}ßern im Verlauf des Beobachtungszeitraumes den Abstand zwischen Zellmembran und Oberfl{\"a}che, reduzieren jedoch ihre Zell-Substratkontaktfl{\"a}che kaum. Mausfibroblasten hingegen verkleinern drastisch die Zelladh{\"a}sionsfl{\"a}che. Der Abl{\"o}sungsprozess wird vermutlich aktiv von den Zellen gesteuert. Diese Annahme wird durch zwei Beobachtungen gest{\"u}tzt: Erstens verl{\"a}uft die Reduktion der Zelladh{\"a}sionsfl{\"a}che bei Einschr{\"a}nkung des Zellmetabolismus durch eine Temperatursenkung auf 4 °C verz{\"o}gert. Zweitens hinterlassen die Zellen Spuren, die nach dem Abl{\"o}sen der Zellen auf den Oberfl{\"a}chen zur{\"u}ckbleiben. Mittels Kombination von TIRAF- und TIRF-Mikroskopie werden die Zelladh{\"a}sionsfl{\"a}che und die Aktinstruktur gleichzeitig beobachtet. Die Verkn{\"u}pfung beider Methoden stellt eine neue M{\"o}glichkeit dar, intrazellul{\"a}re Prozesse mit der Zellabl{\"o}sung von thermo-responsiven Oberfl{\"a}chen zu korrelieren.}, language = {de} } @phdthesis{Drechsel2008, author = {Drechsel, Oliver}, title = {Untersuchungen zu Struktur und Expression des Plastidengenoms h{\"o}herer Pflanzen}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-31056}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Auf dem Weg der genetischen Information stellt die Translation der RNA in eine Aminos{\"a}uresequenz den letzten Schritt dar. In Chloroplasten, den gr{\"u}nen Organellen der Pflanzenzellen, findet ein Großteil der Regulation der Genexpression auf Ebene der Initiation dieses Schrittes statt. Eine Vielzahl von Eigenschaften der RNA und von Faktoren, die an die RNA binden, entfalten einen Einfluss auf diesen Schritt. Bisher unvollst{\"a}ndig aufgekl{\"a}rt ist die Rolle einer konservierten Nukleotidsequenz in der untranslatierten Region der RNA -- der Shine-Dalgarno-Sequenz. Diese stellt in Bakterien, wie z.B. E. coli als Ribosomenbindestelle sicher, dass Ribosomen den Anfang der zu translatierenden Sequenz zuverl{\"a}ssig erkennen. Im Rahmen dieser Arbeit wurden diverse DNA-Konstrukte in Plastiden von Tabak eingebracht. Hierzu z{\"a}hlten Konstrukte, die sowohl eine erh{\"o}hte Anzahl von Ribosomenbindestellen enthielten als auch vermehrte Startpunkte der Translation. Zus{\"a}tzlich wurden Konstrukte hergestellt, die die Situation von mehreren zu translatierenden Regionen in der RNA nachstellten. Es konnte festgestellt werden, dass plastid{\"a}re Ribosomen die strangaufw{\"a}rts gelegenen Translationsstartpunkte bevorzugen -- im Gegensatz zu E. coli, wo alle Startpunkte gleichm{\"a}ßig genutzt wurden. Hierdurch zeigten die prokaryotischen Ribosomen aus Chloroplasten, die sich aus bakteriellen Systemen ableiten, Eigenschaften von eukaryotischen Ribosomen. Ein zweites Teilprojekt dieser Arbeit besch{\"a}ftigte sich mit der Inkompatibilit{\"a}t von Chloroplasten mit dem Kerngenom. In Kreuzungen von Arten der Gattung Pelargonium fielen Kombinationen auf, bei denen die Tochterpflanzen bleiche Blattbereiche bis hin zu vollst{\"a}ndig weißen Pflanzen zeigten. Dieses Ph{\"a}nomen wird als Bastardbleichheit bezeichnet. In der Gattung Pelargonium werden Chloroplasten von beiden Elternteilen an die Tochterpflanzen vererbt. Da das Ph{\"a}nomen der Bastardbleichheit nur in einem der Plastiden vorkommt, nicht jedoch im anderen in der gleichen Pflanze, muss von einem Effekt ausgegangen werden, der von Plastiden ausgeht. Die Interaktionen zwischen Zellkern und Chloroplasten sind offensichtlich stark gest{\"o}rt. Zur detaillierten Untersuchung dieses Effekts wurde die Nukleotidsequenz von drei Chloroplastengenomen aufgekl{\"a}rt. Es konnte eine Reihe von Sequenzunterschieden der Genome ermittelt werden. Aus diesen wurde eine Reihe von Unterschieden beobachtet, die einen solchen Effekt zur Folge haben k{\"o}nnen. Aus diesen Unterschieden wurde eine Reihe von potentiellen Kandidatengenen zusammengestellt, die in weiteren Arbeiten auf ihre Rolle in der Entstehung der Bastardbleichheit untersucht werden.}, language = {de} } @phdthesis{Lehmann2003, author = {Lehmann, Cathleen}, title = {Untersuchungen zum Aufnahmemechanismus und intrazellul{\"a}rem Transport von fusogenen und kationischen Liposomen-DNA-Komplexen f{\"u}r den Gentransfer}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001196}, school = {Universit{\"a}t Potsdam}, year = {2003}, abstract = {Mit der vorliegenden Arbeit sollten mit Hilfe elektronenmikroskopischer Methoden verschiedene Liposomen-DNA-Komplexe zum Gentransfer charakterisiert sowie die Aufnahme und Verteilung in der Zellkultur untersucht werden. Dabei waren vor allem solche Pr{\"a}parationen von besonderem Interesse, die in unserer Arbeitsgruppe 'Drug Targeting' getestet oder entwickelt und verwendet wurden, wie Sendai-Virus Liposomen (HVJ-Liposomen), Virosomen sowie DAC-Chol und DOCSPER-Liposomen als Vertreter der kationischen Lipide. Im ersten Teil der Arbeit wurden fusogene Liposomen und Virosomen charakterisiert. Bei diesen Untersuchungen wurden folgende Ergebnisse erzielt: ·Sendai-Viren fusionieren mit Liposomen unterschiedlicher Lipidzusammensetzung. ·Die daraus resultierenden HVJ-Liposomen sind mit elektronenmikroskopischen Methoden identifizierbar. ·Die Spikes auf den HVJ-Liposomen besitzen fusogene Eigenschaften. ·HVJ-Liposomen eignen sich auf Grund der geringen Ausbeute sowie der geringen Transfektionseffizienz nicht zum in vitro Gentransfer. ·Virosomen stellen einen weiteren Typ fusogener Gentransfervesikel dar. ·Ihre Gr{\"o}ße und fusogenen Eigenschaften sind abh{\"a}ngig von der externen Zugabe einer optimierten Lipidmischung. ·Im Innenraum der Virosomen kann mit Poly-L-Lysin vorkomplexierte DNA verkapselt werden. ·Die fusogenen Eigenschaften der Virosomen wurden mit Hilfe immunelektronenmikroskopischer Techniken und monoklonaler Antik{\"o}rper gegen H{\"a}magglutinin/Neuraminidase und das Fusionsprotein sowie mit polyklonalen Antiseren gezeigt. ·An Hand goldmarkierter DNA sind Virosomen nach der Transfektion in der Zelle nachweisbar. Da in unserer Arbeitsgruppe bevorzugt kationische Liposomen zum Gentransfer verwendet werden, wurde auch die Struktur der Liposomen untersucht und folgende Ergebnisse dokumentiert: ·Die Struktur und die Gr{\"o}ße kationischer Liposomen werden haupts{\"a}chlich durch die Lipidzusammensetzung bestimmt. ·Die Bildung von Liposomen-DNA-Komplexen ist mit einer Gr{\"o}ßenzunahme der Komplexe gekoppelt. ·Die Anzahl gebundener Plasmide steigt mit der Gr{\"o}ße der Lipoplexe. ·Gentransferaktive Lipopolyplexe (mit Protaminsulfat komplexierte DNA und DAC-Chol- Liposomen) sind kleiner als Lipoplexe. Ihre Struktur wird von der Zusammensetzung bestimmt. Eine weitere wichtige Frage betrifft den Weg der Gencarrier in der Zelle. Kenntnisse {\"u}ber diese Vorg{\"a}nge sind vorteilhaft, um die einzelnen Schritte zu verstehen und m{\"o}glichst gezielt zu verbessern. Bei der Untersuchung der Partikel im Hinblick auf zellul{\"a}re Barrieren beim Gentransfer konnten folgende Ergebnisse erzielt werden: ·Die Bindung der Partikel an die Zellmembran und Aufnahme sind abh{\"a}ngig von den eingesetzten Zellen und Komplexen sowie derInkubationszeit. ·Die Aufnahme erfolgt {\"u}ber endozytotische Mechanismen, wobei Lipopolyplexe schneller als Lipoplexe in die Zellen gelangen. Nicht alle gebundenen Komplexe werden aufgenommen. ·Die aufgenommenen Partikel befinden sich in Endosomen und werden ins Innere der Zelle transportiert. ·Freisetzung der DNA und Eintritt in den Zellkern {\"u}ber Kernporen konnte nicht beobachtet werden. ·DNA-haltige Vesikel in Kernn{\"a}he deuten auf einen weiteren Mechanismus hin (Vesikeltransfer zum Zellkern).}, language = {de} } @phdthesis{Usadel2004, author = {Usadel, Bj{\"o}rn}, title = {Untersuchungen zur Biosynthese der pflanzlichen Zellwand = [Identification and characterization of genes involved in plant cell wall synthesis]}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-2947}, school = {Universit{\"a}t Potsdam}, year = {2004}, abstract = {Even though the structure of the plant cell wall is by and large quite well characterized, its synthesis and regulation remains largely obscure. However, it is accepted that the building blocks of the polysaccharidic part of the plant cell wall are nucleotide sugars. Thus to gain more insight into the cell wall biosynthesis, in the first part of this thesis, plant genes possibly involved in the nucleotide sugar interconversion pathway were identified using a bioinformatics approach and characterized in plants, mainly in Arabidopsis. For the computational identification profile hidden markov models were extracted from the Pfam and TIGR databases. Mainly with these, plant genes were identified facilitating the "hmmer" program. Several gene families were identified and three were further characterized, the UDP-rhamnose synthase (RHM), UDP-glucuronic acid epimerase (GAE) and the myo-inositol oxygenase (MIOX) families. For the three-membered RHM family relative ubiquitous expression was shown using variuos methods. For one of these genes, RHM2, T-DNA lines could be obtained. Moreover, the transcription of the whole family was downregulated facilitating an RNAi approach. In both cases a alteration of cell wall typic polysaccharides and developmental changes could be shown. In the case of the rhm2 mutant these were restricted to the seed or the seed mucilage, whereas the RNAi plants showed profound changes in the whole plant. In the case of the six-membered GAE family, the gene expressed to the highest level (GAE6) was cloned, expressed heterologously and its function was characterized. Thus, it could be shown that GAE6 encodes for an enzyme responsible for the conversion of UDP-glucuronic acid to UDP-galacturonic acid. However, a change in transcript level of variuos GAE family members achieved by T-DNA insertions (gae2, gae5, gae6), overexpression (GAE6) or an RNAi approach, targeting the whole family, did not reveal any robust changes in the cell wall. Contrary to the other two families the MIOX gene family had to be identified using a BLAST based approach due to the lack of enough suitable candidate genes for building a hidden markov model. An initial bioinformatic characterization was performed which will lead to further insights into this pathway. In total it was possible to identify the two gene families which are involved in the synthesis of the two pectin backbone sugars galacturonic acid and rhamnose. Moreover with the identification of the MIOX genes a genefamily, important for the supply of nucleotide sugar precursors was identified. In a second part of this thesis publicly available microarray datasets were analyzed with respect to co-responsive behavior of transcripts on a global basis using nearly 10,000 genes. The data has been made available to the community in form of a database providing additional statistical and visualization tools (http://csbdb.mpimp-golm.mpg.de). Using the framework of the database to identify nucleotide sugar converting genes indicated that co-response might be used for identification of novel genes involved in cell wall synthesis based on already known genes.}, subject = {Zellwand}, language = {en} } @phdthesis{Schaefer2024, author = {Sch{\"a}fer, Marj{\"a}nn Helena}, title = {Untersuchungen zur Evolution der 15-Lipoxygenase (ALOX15) bei S{\"a}ugetieren und funktionelle Charakterisierung von Knock-in-M{\"a}usen mit humanisierter Reaktionsspezifit{\"a}t der 15-Lipoxygenase-2 (Alox15b)}, doi = {10.25932/publishup-62034}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-620340}, school = {Universit{\"a}t Potsdam}, pages = {XVII, 280}, year = {2024}, abstract = {Arachidons{\"a}urelipoxygenasen (ALOX-Isoformen) sind Lipid-peroxidierenden Enzyme, die bei der Zelldifferenzierung und bei der Pathogenese verschiedener Erkrankungen bedeutsam sind. Im menschlichen Genom gibt es sechs funktionelle ALOX-Gene, die als Einzelkopiegene vorliegen. F{\"u}r jedes humane ALOX-Gen gibt es ein orthologes Mausgen. Obwohl sich die sechs humanen ALOX-Isoformen strukturell sehr {\"a}hnlich sind, unterscheiden sich ihre funktionellen Eigenschaften deutlich voneinander. In der vorliegenden Arbeit wurden vier unterschiedliche Fragestellungen zum Vorkommen, zur biologischen Rolle und zur Evolutionsabh{\"a}ngigkeit der enzymatischen Eigenschaften von S{\"a}ugetier-ALOX-Isoformen untersucht: 1) Spitzh{\"o}rnchen (Tupaiidae) sind evolution{\"a}r n{\"a}her mit dem Menschen verwandt als Nagetiere und wurden deshalb als Alternativmodelle f{\"u}r die Untersuchung menschlicher Erkrankungen vorgeschlagen. In dieser Arbeit wurde erstmals der Arachidons{\"a}urestoffwechsel von Spitzh{\"o}rnchen untersucht. Dabei wurde festgestellt, dass im Genom von Tupaia belangeri vier unterschiedliche ALOX15-Gene vorkommen und die Enzyme sich hinsichtlich ihrer katalytischen Eigenschaften {\"a}hneln. Diese genomische Vielfalt, die weder beim Menschen noch bei M{\"a}usen vorhanden ist, erschwert die funktionellen Untersuchungen zur biologischen Rolle des ALOX15-Weges. Damit scheint Tupaia belangeri kein geeigneteres Tiermodel f{\"u}r die Untersuchung des ALOX15-Weges des Menschen zu sein. 2) Entsprechend der Evolutionshypothese k{\"o}nnen S{\"a}ugetier-ALOX15-Orthologe in Arachidons{\"a}ure-12-lipoxygenierende- und Arachidons{\"a}ure-15-lipoxygenierende Enzyme eingeteilt werden. Dabei exprimieren S{\"a}ugetierspezies, die einen h{\"o}heren Evolutionsgrad als Gibbons aufweisen, Arachidons{\"a}ure-15-lipoxygenierende ALOX15-Orthologe, w{\"a}hrend evolution{\"a}r weniger weit entwickelte S{\"a}ugetiere Arachidons{\"a}ure-12 lipoxygenierende Enzyme besitzen. In dieser Arbeit wurden elf neue ALOX15-Orthologe als rekombinante Proteine exprimiert und funktionell charakterisiert. Die erhaltenen Ergebnisse f{\"u}gen sich widerspruchsfrei in die Evolutionshypothese ein und verbreitern deren experimentelle Basis. Die experimentellen Daten best{\"a}tigen auch das Triadenkonzept. 3) Da humane und murine ALOX15B-Orthologe unterschiedliche funktionelle Eigenschaften aufweisen, k{\"o}nnen Ergebnisse aus murinen Krankheitsmodellen zur biologischen Rolle der ALOX15B nicht direkt auf den Menschen {\"u}bertragen werden. Um die ALOX15B-Orthologen von Maus und Mensch funktionell einander anzugleichen, wurden im Rahmen der vorliegenden Arbeit Knock-in M{\"a}use durch die In vivo Mutagenese mittels CRISPR/Cas9-Technik hergestellt. Diese exprimieren eine humanisierte Mutante (Doppelmutation von Tyrosin603Asparagins{\"a}ure+Histidin604Valin) der murinen Alox15b. Diese M{\"a}use waren lebens- und fortpflanzungsf{\"a}hig, zeigten aber geschlechtsspezifische Unterschiede zu ausgekreuzten Wildtyp-Kontrolltieren im Rahmen ihre Individualentwicklung. 4) In vorhergehenden Untersuchungen zur Rolle der ALOX15B in Rahmen der Entz{\"u}ndungsreaktion wurde eine antiinflammatorische Wirkung des Enzyms postuliert. In der vorliegenden Arbeit wurde untersucht, ob eine Humanisierung der murinen Alox15b die Entz{\"u}ndungsreaktion in zwei verschiedenen murinen Entz{\"u}ndungsmodellen beeinflusst. Eine Humanisierung der murinen Alox15b f{\"u}hrte zu einer verst{\"a}rkten Ausbildung von Entz{\"u}ndungssymptomen im induzierten Dextran-Natrium-Sulfat-Kolitismodell. Im Gegensatz dazu bewirkte die Humanisierung der Alox15b eine Abschw{\"a}chung der Entz{\"u}ndungssymptome im Freund'schen Adjuvans Pfoten{\"o}demmodell. Diese Daten deuten darauf hin, dass sich die Rolle der ALOX15B in verschiedenen Entz{\"u}ndungsmodellen unterscheidet.}, language = {de} } @phdthesis{Senger2007, author = {Senger, Toralf}, title = {Untersuchungen zur Metallhom{\"o}ostase in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13234}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Alle Organismen sind f{\"u}r ihr {\"U}berleben auf Metalle angewiesen. Hierbei gibt es f{\"u}r jedes Metall einen Konzentrationsbereich, der das Optimum zwischen Metallmangel, -bedarf und -toxizit{\"a}t darstellt. Es gilt mittlerweile als erwiesen, dass alle Organismen zur Aufrechterhaltung des Metallgleichgewichts ein komplexes Netzwerk von Proteinen und niedermolekularen Verbindungen entwickelt haben. Die molekularen Komponenten dieses Netzwerks sind nur zu einem Teil bekannt und charakterisiert: In den letzten Jahren wurden einige Proteinfamilien identifiziert, deren Mitglieder Metalle durch Lipidmembranen transportieren. Eine dieser Metalltransporterfamilien ist die Cation Diffusion Facilitator (CDF)-Familie: Alle charakterisierten Mitglieder exportieren Metalle aus dem Zytoplasma - entweder in zellul{\"a}re Kompartimente oder aus der Zelle heraus. Von den zw{\"o}lf Mitgliedern dieser Familie in Arabidopsis thaliana (A. thaliana) - Metall Toleranz Protein (MTP)-1 bis -12 - wurden bisher AtMTP1 und AtMTP3 charakterisiert. In dieser Arbeit wird die Charakterisierung von AtMTP2 beschrieben. Wie die homologen Proteine AtMTP1 und AtMTP3 f{\"u}hrt AtMTP2 zu Zn-Toleranz, wenn es heterolog in Zn-sensitiven Hefemutanten exprimiert wird. Mit AtMTP2 transformierte Hefemutanten zeigten dar{\"u}ber hinaus erh{\"o}hte Co-Toleranz. Expression von chim{\"a}ren AtMTP2/GFP Fusionsproteinen in Hefe, A.thaliana protoplasten und in stabil transformierten A.thalinana Planzenlinien deutet auf Lokalisation of AtMTP2 in Membranen des Endoplasmatischen Retikulums (ER) hin, wenn GFP an den C-Terminus von MTP2 fusioniert wird. Fusion of GFP an den N-Terminus von AtMTP2 f{\"u}hrte zu Lokalisation in der vakuol{\"a}ren Membran, was wahrscheinlichsten auf Fehllokalisierung durch Maskierung eines ER-Retentionsmotivs (XXRR) am N-Terminus von AtMTP2 zur{\"u}ckgeht. Dies legt nahe, dass AtMTP2 die erw{\"a}hnten Metalle in das Endomembransystem der Zelle transportieren kann. Eine gewebespezifische Lokalisierung wurde mit Pflanzen durchgef{\"u}hrt, die das β-Glucuronidase (GUS)-Reporterprotein bzw. chim{\"a}re Fusionsproteine aus EGFP und AtMTP2 unter Kontrolle des nativen pMTP2-Promotors exprimierten. Diese Experimente best{\"a}tigten zum einen, dass der pMTP2-Promotor nur unter Zn-Defizienz aktiv ist. GUS-Aktivit{\"a}t wurde unter diesen Bedingungen in zwei Zonen der Wurzelspitze beobachtet: in den isodiametrischen Zellen der meristematischen Zone und in der beginnenden Wurzelhaarzone. Dar{\"u}ber hinaus konnte gezeigt werden, dass die EGFP-Fusionsproteine unter Kontrolle des nativen pMTP2-Promotors nur in epidermalen Zellen exprimiert werden. F{\"u}r eine homozygote Knockout- Linie, mtp2-S3, konnte bisher kein eindeutiger Ph{\"a}notyp identifiziert werden. Auf Grundlage der bisher durchgef{\"u}hrten Charakterisierung von AtMTP2 erscheinen zwei Modelle der Funktion von AtMTP2 in der Pflanze m{\"o}glich: AtMTP2 k{\"o}nnte essentiell f{\"u}r die Versorgung des ER mit Zn unter Zn-Mangelbedingungen sein. Hierf{\"u}r spricht, dass AtMTP2 in jungen, teilungsaktiven und damit Zn-ben{\"o}tigenden Wurzelzonen exprimiert wird. Die auf die Epidermis beschr{\"a}nkte Lokalisation k{\"o}nnte bei diesem Modell auf die M{\"o}glichkeit der zwischenzellul{\"a}ren Zn-Verteilung innerhalb des ER {\"u}ber Desmotubules hindeuten. Alternativ k{\"o}nnte AtMTP2 eine Funktion bei der Detoxifizierung von Zn unter Zn-Schock Bedingungen haben: Es ist bekannt, dass unter Zn- Mangelbedingungen die Expression der zellul{\"a}ren Zn-Aufnahmesysteme hochreguliert wird. Wenn nun die Zn-Verf{\"u}gbarkeit im Boden z. B durch eine pH-{\"A}nderung innerhalb kurzer Zeit stark ansteigt, besteht die Notwendigkeit der Entgiftung von Zn innerhalb der Zelle, bis der starke Einstrom von Zn ins Zytoplasma durch die Deaktivierung der Zn-Aufnahmesysteme und einer geringeren Expression in der Pflanze gedrosselt ist. Ein {\"a}hnlicher Mechanismus wurde in der B{\"a}ckerhefe S. cerevisae beschrieben, in der dar{\"u}ber hinaus ein Zn-Transporter verst{\"a}rkt exprimiert wird, der Zn durch Transport in die Vakuole entgiften kann. Es ist durchaus m{\"o}glich, dass in Arabidopsis AtMTP2 die Zn-Detoxifizierung unter diesen speziellen Bedingungen durch Zn-Transport in das ER oder die Vakuole vermittelt. Zur Identifikation weiterer Komponenten des Metallhom{\"o}ostasenetzwerks sind verschiedene Ans{\"a}tze denkbar. In dieser Arbeit wurde in Hefe ein heterologer Screen durchgef{\"u}hrt, um Interaktoren f{\"u}r vier Mitglieder der Arabidopsis-CDF-Familie zu identifizieren. Unter den 11 im Hefesystem best{\"a}tigten Kandidaten befindet sich mit AtSPL1 ein AtMTP1-Interaktionskandidat, der m{\"o}glicherweise eine Rolle bei der Cu-,Zn-Hom{\"o}ostase spielt. Als wahrscheinliche AtMTP3-Interaktionskandidaten wurde die c"-Untereinheit der vakuol{\"a}ren H+-ATPase AtVHA identifiziert sowie mit AtNPSN13 ein Protein, das vermutlich eine Rolle bei Fusionen von Vesikeln mit Zielmembranen spielt. Ein anderer Ansatz zur Identifikation neuer Metallhom{\"o}ostasegene ist die vergleichende Elementanalyse von nat{\"u}rlichen oder mutagenisierten Pflanzenpopulationen. Voraussetzung f{\"u}r diesen Ansatz ist die schnelle und genaue Analyse des Elementgehalts von Pflanzen. Eine etablierte Methode zur simultanen Bestimmung von bis zu 65 Elementen in einer Probe ist die Inductively Coupled Plasma Optical Emission Spectrometry (ICP OES). Der limitierende Faktor f{\"u}r einen hohen Probendurchsatz ist die Notwendigkeit, Proben f{\"u}r die Analyse zu verfl{\"u}ssigen. Eine alternative Methode der Probenzuf{\"u}hrung zum Analyseger{\"a}t ist die elektrothermale Verdampfung (ETV) der Probe. Zur weitgehend automatisierten Analyse von Pflanzenmaterial mit minimiertem Arbeitsaufwand wurde eine Methode entwickelt, die auf der Kopplung der ETV mit der ICP OES basiert.}, language = {de} } @phdthesis{Andres2008, author = {Andres, Janin}, title = {Untersuchungen {\"u}ber Regulationsmechanismen der 11beta-Hydroxysteroid Dehydrogenase Typ 1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33033}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Die 11beta-HSD1 reguliert intrazellul{\"a}r die Cortisolkonzentration durch Regeneration von Cortison z.B. aus dem Blutkreislauf, zu Cortisol. Daher stellt diese ein wichtiges Element in der Glucocorticoid-vermittelten Genregulation dar. Die 11beta-HSD1 wird ubiquit{\"a}r exprimiert, auf hohem Niveau besonders in Leber, Fettgewebe und glatten Muskelzellen. Insbesondere die Bedeutung der 11beta-HSD1 in Leber und Fettgewebe konnte mehrfach nachgewiesen werden. In der Leber f{\"u}hrte eine erh{\"o}hte Aktivit{\"a}t aufgrund einer {\"U}berexpression in M{\"a}usen zu einer verst{\"a}rkten Gluconeogeneserate. Des Weiteren konnte gezeigt werden, dass eine erh{\"o}hte Expression und erh{\"o}hte Enzymaktivit{\"a}t der 11beta-HSD1 im subkutanen und viszeralen Fettgewebe assoziiert ist mit Fettleibigkeit, Insulinresistenz und Dyslipid{\"a}mie. {\"U}ber die Regulation ist jedoch noch wenig bekannt. Zur Untersuchung der Promotoraktivit{\"a}t wurde der Promotorbereich von -3034 bis +188, vor und nach dem Translations- und Transkriptionsstart, der 11beta-HSD1 kloniert. 8 Promotorfragmente wurden mittels Dual-Luciferase-Assay in humanen HepG2-Zellen sowie undifferenzierten und differenzierten murinen 3T3-L1-Zellen untersucht. Anschließend wurde mittels nicht-radioaktiven EMSA die Bindung des TATA-Binding Proteins (TBP) sowie von CCAAT/Enhancer-Binding-Proteinen (C/EBP) an ausgew{\"a}hlte Promotorregionen analysiert. Nach der Charakterisierung des Promotors wurden spezifische endogene und exogene Regulatoren untersucht. Fetts{\"a}uren modifizieren die Entstehung von Adipositas und Insulinresistenz. Ihre Wirkung wird u.a. PPARgamma-abh{\"a}ngig vermittelt und kann durch das Inkretin (Glucose-dependent insulinotropic Peptide) GIP modifiziert werden. So wurden die Effekte von unterschiedlichen Fetts{\"a}uren, vom PPARgamma Agonisten Rosiglitazon sowie dem Inkretin GIP auf die Expression und Enzymaktivit{\"a}t der 11beta-HSD1 untersucht. Dies wurde in-vitro-, tierexperimentell und in humanen in-vivo-Studien realisiert. Zuletzt wurden 2 Single Nucleotide Polymorphismen (SNP) im Promotorbereich der 11beta-HSD1 in der Zellkultur im Hinblick auf potentielle Funktionalit{\"a}t analysiert sowie die Assoziation mit Diabetes mellitus Typ 2 und K{\"o}rpergewicht in der MeSyBePo-Kohorte bei rund 1.800 Personen untersucht. Die Luciferase-Assays zeigten basal eine zell-spezifische Regulation der 11beta-HSD1, wobei in allen 3 untersuchten Zelltypen die Bindung eines Repressors nachgewiesen werden konnte. Zudem konnte eine m{\"o}gliche Bindung des TBPs sowie von C/EBP-Proteinen an verschiedene Positionen gezeigt werden. Die Transaktivierungsassays mit den C/EBP-Proteinen -alpha, -beta und -delta zeigten eben-falls eine zellspezifische Regulation des 11beta-HSD1-Promotors. Die Aktivit{\"a}t und Expression der 11beta-HSD1 wurde durch die hier untersuchten endogenen und exogenen Faktoren spezifisch modifiziert, was sowohl in-vitro als auch in-vivo in unterschiedlichen Modellsystemen dargestellt werden konnte. Die Charakterisierung der MeSyBePo-Kohorte ergab keine direkten Assoziationen zwischen Polymorphismus und klinischem Ph{\"a}notyp, jedoch Tendenzen f{\"u}r eine erh{\"o}htes K{\"o}rper-gewicht und Typ 2 Diabetes mellitus in Abh{\"a}ngigkeit des Genotyps. Der Promotor der 11beta-HSD1 konnte aufgrund der Daten aus den Luciferaseassays sowie den Daten aus den EMSA-Analysen n{\"a}her charakterisiert werden. Dieser zeigt eine variable und zell-spezifische Regulation. Ein wichtiger Regulator stellen insbesondere in den HepG2-Zellen die C/EBP-Proteine -alpha, -beta und -delta dar. Aus den in-vivo-Studien ergab sich eine Regulation der 11beta-HSD1 durch endogene, exogene und pharmakologische Substanzen, die durch die Zellkulturversuche best{\"a}tigt und n{\"a}her charakterisiert werden konnten.}, language = {de} } @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} } @article{NumbergerZoccaratoWoodhouseetal.2022, author = {Numberger, Daniela and Zoccarato, Luca and Woodhouse, Jason Nicholas and Ganzert, Lars and Sauer, Sascha and Garc{\´i}a M{\´a}rquez, Jaime Ricardo and Domisch, Sami and Grossart, Hans-Peter and Greenwood, Alex}, title = {Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {845}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.157321}, pages = {13}, year = {2022}, abstract = {Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.}, language = {en} } @phdthesis{Wieneke2008, author = {Wieneke, Nadine}, title = {Ursachen und Folgen vermehrter Expression des nukle{\"a}ren Rezeptors Constitutiver-Androstan-Rezeptor (NR1I3) durch Agonisten des nukle{\"a}ren Rezeptors Peroxisomenproliferator-aktivierter-Rezeptor-alpha (NR1C1)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19167}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Der Fetts{\"a}urestoffwechsel unterliegt vielf{\"a}ltigen Kontrollmechanismen. So wird der Fetts{\"a}ureabbau {\"u}ber die Induktion und Aktivit{\"a}t spezifischer Enzyme reguliert. Ein zentraler Regulator ist dabei der nukle{\"a}re Rezeptor Peroxisomenproliferator-aktivierter-Rezeptor-α (PPARα). PPARα wird durch freie Fetts{\"a}uren in der Zelle aktiviert und f{\"o}rdert {\"u}ber die Induktion von Zielgenen den Fetts{\"a}uretransport und -abbau sowie die Gluconeogenese und Ketogenese. Der Anstieg an freien Fetts{\"a}uren beim Fasten, aber auch im Diabetes aktiviert PPARα. Unabh{\"a}ngig davon wurde in beiden Stoffwechsellagen auch eine erh{\"o}hte Expression des nukle{\"a}ren Rezeptors Constitutiver-Androstan-Rezeptor (CAR) und einiger CAR-Zielgene, vorrangig Enzyme des Fremdstoffmetabolismus wie Cytochrom P450 2B (CYP2B), festgestellt. Bei der Adaption an eine Fastensituation scheinen PPARα- und CAR-Signalwege {\"u}ber einen bisher unbekannten Mechanismus miteinander verschaltet zu sein. In der vorliegenden Arbeit sollte der der Verschaltung zugrunde liegende Mechanismus anhand eines Modelsystems, der PPARα-Agonisten-vermittelten Verst{\"a}rkung der Phenobarbital (PB)-abh{\"a}ngigen Induktion des CAR-Zielgens CYP2B, in vitro untersucht werden. Zudem sollte die physiologische Relevanz einer durch PPARα-Agonisten vermittelten Modulierung der CYP2B-Aktivit{\"a}t in einer Ganztierstudie in vivo belegt werden. Die verwendeten synthetischen PPARα-Agonisten steigerten in prim{\"a}ren Hepatozyten der Ratte signifikant die Phenobarbital (PB)-abh{\"a}ngige mRNA- und Protein-Expression sowie die Aktivit{\"a}t von CYP2B. Ohne vorherige PB-Behandlung induzierten PPARα-Agonisten CYP2B nicht. In Gegenwart von PB war die Steigerung der CYP2B-Aktivit{\"a}t durch PPARα-Agonisten dosisabh{\"a}ngig. In einem Luciferase-Reportergenassay wurde gezeigt, dass die Induktion durch PB unter der Kontrolle des CYP2B1-Promotors von einem distalen PBREM (PB-responsive-enhancer-module), an welches CAR binden kann, abh{\"a}ngig war. PPARα-Agonisten steigerten diese PB- und PBREM-abh{\"a}ngige Reportergentranskription und induzierten die CAR-mRNA und CAR-Proteinexpression. Sie aktivierten die Transkription eines Reportergens unter der Kontrolle eines Promotorfragments von bis zu 4,4 kb oberhalb des mutmaßlichen CAR-Transkriptionsstarts. Mit Hilfe von Deletionskonstrukten konnte ein potentielles Peroxisomenproliferator-aktivierter-Rezeptor-responsives Element (PPRE) im CAR-Promotorbereich von -942 bp bis -930 bp identifiziert werden, welches essentiell f{\"u}r die Initiation der Transkription durch PPARα-Agonisten ist. In band shift Experimenten akkumulierte verst{\"a}rkt Kernprotein mit diesem PPRE. Ein {\"U}berschuss an unmarkiertem Wildtyp-CAR-Reportergenvektor, nicht aber an CAR-Reportergenvektor mit PPRE-Deletion, konnte mit dem markierten PPRE um die Bindung von Kernprotein konkurrieren. Nach Chromatin-Immunpr{\"a}zipitation mit einem PPARα-Antik{\"o}rper wiederum wurde das betreffende PPRE amplifiziert. Bei in vivo Experimenten an m{\"a}nnlichen Ratten resultierte die Behandlung mit PPARα-Agonisten in einer signifikanten Induktion der CAR-mRNA-Expression und signifikant erh{\"o}hter PB-abh{\"a}ngiger CYP2B-Aktivit{\"a}t. Die physiologisch Relevanz wurde durch weiterf{\"u}hrenden Experimente unterstrichen, in denen gezeigt wurde, dass die Fasten-abh{\"a}ngige Induktion von CAR in PPARα-defizienten M{\"a}usen unterdr{\"u}ckt war. Diese Experimente legen nahe, dass durch PPARα-Agonisten aktiviertes PPARα an das PPRE im CAR-Promotorbereich von -942 bp bis -930 bp bindet und dadurch die CAR-Transkription induziert. Somit kann CAR als PPARα-Zielgen betrachtet werden, was die Schlussfolgerung zul{\"a}sst, dass die PPARα- und CAR-Signalwege {\"u}ber die direkte Bindung von PPARα an den CAR-Promotor unmittelbar miteinander verkn{\"u}pft sind. Allerdings ist davon unabh{\"a}ngig eine Aktivierung von CAR, etwa durch PB, f{\"u}r die vermehrte Induktion von CAR-Zielgenen notwendig . Die physiologische Relevanz der PPARα-abh{\"a}ngige CAR-Expression zeigt sich in den Ganztierexperimenten, bei denen die Wirksamkeit der PPARα-Agonisten best{\"a}tigt werden konnte. CAR-abh{\"a}ngig induzierte Enzyme sind nicht nur in großem Umfang am Fremdstoffmetabolismus beteiligt, sondern auch am Abbau von Schilddr{\"u}senhormonen und Glucocorticoiden. Sie k{\"o}nnen damit direkt Einfluss auf den Kohlenhydrat- und Energiestoffwechsel sowie die Regulation der Nahrungsaufnahme nehmen. {\"U}ber eine PPARα-abh{\"a}ngige Induktion von CAR im Rahmen der Fastenadaption k{\"o}nnten die CAR-Zielgene UDP-Glucuronyltransferase 1A1 und Sulfotransferase N beispielsweise verst{\"a}rkt Schilddr{\"u}senhormone abbauen und in der Folge den Grundumsatz senken. Der in dieser Arbeit erstmals beschriebene Mechanismus ist daf{\"u}r von zentraler Bedeutung.}, language = {de} } @misc{HartmannVision2008, author = {Hartmann, Stefanie and Vision, Todd J.}, title = {Using ESTs for phylogenomics}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {889}, issn = {1866-8372}, doi = {10.25932/publishup-43667}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436670}, pages = {15}, year = {2008}, abstract = {Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25\% to 40\% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83\% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.}, language = {en} } @phdthesis{Crawford2020, author = {Crawford, Michael Scott}, title = {Using individual-based modeling to understand grassland diversity and resilience in the Anthropocene}, doi = {10.25932/publishup-47941}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-479414}, school = {Universit{\"a}t Potsdam}, pages = {174}, year = {2020}, abstract = {The world's grassland systems are increasingly threatened by anthropogenic change. Susceptible to a variety of different stressors, from land-use intensification to climate change, understanding the mechanisms driving the maintenance of these systems' biodiversity and stability, and how these mechanisms may shift under human-mediated disturbance, is thus critical for successfully navigating the next century. Within this dissertation, I use an individual-based and spatially-explicit model of grassland community assembly (IBC-grass) to examine several processes, thought key to understanding their biodiversity and stability and how it changes under stress. In the first chapter of my thesis, I examine the conditions under which intraspecific trait variation influences the diversity of simulated grassland communities. In the second and third chapters of my thesis, I shift focus towards understanding how belowground herbivores influence the stability of these grassland systems to either a disturbance that results in increased, stochastic, plant mortality, or eutrophication. Intraspecific trait variation (ITV), or variation in trait values between individuals of the same species, is fundamental to the structure of ecological communities. However, because it has historically been difficult to incorporate into theoretical and statistical models, it has remained largely overlooked in community-level analyses. This reality is quickly shifting, however, as a consensus of research suggests that it may compose a sizeable proportion of the total variation within an ecological community and that it may play a critical role in determining if species coexist. Despite this increasing awareness that ITV matters, there is little consensus of the magnitude and direction of its influence. Therefore, to better understand how ITV changes the assembly of grassland communities, in the first chapter of my thesis, I incorporate it into an established, individual-based grassland community model, simulating both pairwise invasion experiments as well as the assembly of communities with varying initial diversities. By varying the amount of ITV in these species' functional traits, I examine the magnitude and direction of ITV's influence on pairwise invasibility and community coexistence. During pairwise invasion, ITV enables the weakest species to more frequently invade the competitively superior species, however, this influence does not generally scale to the community level. Indeed, unless the community has low alpha- and beta- diversity, there will be little effect of ITV in bolstering diversity. In these situations, since the trait axis is sparsely filled, the competitively inferior may suffer less competition and therefore ITV may buffer the persistence and abundance of these species for some time. In the second and third chapters of my thesis, I model how one of the most ubiquitous trophic interactions within grasslands, herbivory belowground, influences their diversity and stability. Until recently, the fundamental difficulty in studying a process within the soil has left belowground herbivory "out of sight, out of mind." This dilemma presents an opportunity for simulation models to explore how this understudied process may alter community dynamics. In the second chapter of my thesis, I implement belowground herbivory - represented by the weekly removal of plant biomass - into IBC-grass. Then, by introducing a pulse disturbance, modelled as the stochastic mortality of some percentage of the plant community, I observe how the presence of belowground herbivores influences the resistance and recovery of Shannon diversity in these communities. I find that high resource, low diversity, communities are significantly more destabilized by the presence of belowground herbivores after disturbance. Depending on the timing of the disturbance and whether the grassland's seed bank persists for more than one season, the impact of the disturbance - and subsequently the influence of the herbivores - can be greatly reduced. However, because human-mediated eutrophication increases the amount of resources in the soil, thus pressuring grassland systems, our results suggest that the influence of these herbivores may become more important over time. In the third chapter of my thesis, I delve further into understanding the mechanistic underpinnings of belowground herbivores on the diversity of grasslands by replicating an empirical mesocosm experiment that crosses the presence of herbivores above- and below-ground with eutrophication. I show that while aboveground herbivory, as predicted by theory and frequently observed in experiments, mitigates the impact of eutrophication on species diversity, belowground herbivores counterintuitively reduce biodiversity. Indeed, this influence positively interacts with the eutrophication process, amplifying its negative impact on diversity. I discovered the mechanism underlying this surprising pattern to be that, as the herbivores consume roots, they increase the proportion of root resources to root biomass. Because root competition is often symmetric, herbivory fails to mitigate any asymmetries in the plants' competitive dynamics. However, since the remaining roots have more abundant access to resources, the plants' competition shifts aboveground, towards asymmetric competition for light. This leads the community towards a low-diversity state, composed of mostly high-performance, large plant species. We further argue that this pattern will emerge unless the plants' root competition is asymmetric, in which case, like its counterpart aboveground, belowground herbivory may buffer diversity by reducing this asymmetry between the competitively superior and inferior plants. I conclude my dissertation by discussing the implications of my research on the state of the art in intraspecific trait variation and belowground herbivory, with emphasis on the necessity of more diverse theory development in the study of these fundamental interactions. My results suggest that the influence of these processes on the biodiversity and stability of grassland systems is underappreciated and multidimensional, and must be thoroughly explored if researchers wish to predict how the world's grasslands will respond to anthropogenic change. Further, should researchers myopically focus on understanding central ecological interactions through only mathematically tractable analyses, they may miss entire suites of potential coexistence mechanisms that can increase the coviability of species, potentially leading to coexistence over ecologically-significant timespans. Individual-based modelling, therefore, with its focus on individual interactions, will prove a critical tool in the coming decades for understanding how local interactions scale to larger contexts, and how these interactions shape ecological communities and further predicting how these systems will change under human-mediated stress.}, language = {en} } @misc{VossBlenauWalzetal.2009, author = {Voss, Martin and Blenau, Wolfgang and Walz, Bernd and Baumann, Otto}, title = {V-ATPase deactivation in blowfly salivary glands is mediated by protein phosphatase 2C}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44360}, year = {2009}, abstract = {The activity of vacuolar H+-ATPase (V-ATPase) in the apical membrane of blowfly (Calliphora vicina) salivary glands is regulated by the neurohormone serotonin (5-HT). 5-HT induces, via protein kinase A, the phosphorylation of V-ATPase subunit C and the assembly of V-ATPase holoenzymes. The protein phosphatase responsible for the dephosphorylation of subunit C and V-ATPase inactivation is not as yet known. We show here that inhibitors of protein phosphatases PP1 and PP2A (tautomycin, ocadaic acid) and PP2B (cyclosporin A, FK-506) do not prevent V-ATPase deactivation and dephosphorylation of subunit C. A decrease in the intracellular Mg2+ level caused by loading secretory cells with EDTA-AM leads to the activation of proton pumping in the absence of 5-HT, prolongs the 5-HT-induced response in proton pumping, and inhibits the dephosphorylation of subunit C. Thus, the deactivation of V-ATPase is most probably mediated by a protein phosphatase that is insensitive to okadaic acid and that requires Mg2+, namely, a member of the PP2C protein family. By molecular biological techniques, we demonstrate the expression of at least two PP2C protein family members in blowfly salivary glands. © 2009 Wiley Periodicals, Inc.}, language = {en} } @article{LiuVainViottietal.2018, author = {Liu, Qinsong and Vain, Thomas and Viotti, Corrado and Doyle, Siamsa M. and Tarkowska, Danuse and Novak, Ondrej and Zipfel, Cyril and Sitbon, Folke and Robert, Stephanie and Hofius, Daniel}, title = {Vacuole integrity maintained by DUF300 proteins is required for brassinosteroid signaling regulation}, series = {Molecular plant}, volume = {11}, journal = {Molecular plant}, number = {4}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2017.12.015}, pages = {553 -- 567}, year = {2018}, abstract = {Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.}, language = {en} } @article{SchjeideSchenkeSeegeretal.2022, author = {Schjeide, Brit-Maren and Schenke, Maren and Seeger, Bettina and P{\"u}schel, Gerhard}, title = {Validation of a novel double control quantitative copy number PCR method to quantify off-target transgene integration after CRISPR-induced DNA modification}, series = {Methods and protocols : M\&Ps}, volume = {5}, journal = {Methods and protocols : M\&Ps}, number = {3}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2409-9279}, doi = {10.3390/mps5030043}, pages = {1 -- 14}, year = {2022}, abstract = {In order to improve a recently established cell-based assay to assess the potency of botulinum neurotoxin, neuroblastoma-derived SiMa cells and induced pluripotent stem-cells (iPSC) were modified to incorporate the coding sequence of a reporter luciferase into a genetic safe harbor utilizing CRISPR/Cas9. A novel method, the double-control quantitative copy number PCR (dc-qcnPCR), was developed to detect off-target integrations of donor DNA. The donor DNA insertion success rate and targeted insertion success rate were analyzed in clones of each cell type. The dc-qcnPCR reliably quantified the copy number in both cell lines. The probability of incorrect donor DNA integration was significantly increased in SiMa cells in comparison to the iPSCs. This can possibly be explained by the lower bundled relative gene expression of a number of double-strand repair genes (BRCA1, DNA2, EXO1, MCPH1, MRE11, and RAD51) in SiMa clones than in iPSC clones. The dc-qcnPCR offers an efficient and cost-effective method to detect off-target CRISPR/Cas9-induced donor DNA integrations.}, language = {en} }