TY - JOUR A1 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions JF - Toxins N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 degrees C, 25 degrees C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 degrees C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions. KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2016 U6 - https://doi.org/10.3390/toxins8110344 SN - 2072-6651 VL - 8 SP - 570 EP - 583 PB - MDPI CY - Basel ER - TY - GEN A1 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the underdogs BT - an analysis of underrepresented alternaria mycotoxins formed depending on varying substrate, time and temperature conditions N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 353 KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400438 ER - TY - GEN A1 - Zwaag, Jelle A1 - Horst, Rob ter A1 - Blaženović, Ivana A1 - Stößel, Daniel A1 - Ratter, Jacqueline A1 - Worseck, Josephine M. A1 - Schauer, Nicolas A1 - Stienstra, Rinke A1 - Netea, Mihai G. A1 - Jahn, Dieter A1 - Pickkers, Peter A1 - Kox, Matthijs T1 - Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1413 KW - metabolomics KW - LPS KW - endotoxin KW - pyruvate KW - lactate KW - cytokines KW - inflammation KW - human endotoxemia KW - cori cycle KW - warburg effect Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-517784 SN - 1866-8372 IS - 4 ER - TY - JOUR A1 - Zwaag, Jelle A1 - Horst, Rob ter A1 - Blaženović, Ivana A1 - Stößel, Daniel A1 - Ratter, Jacqueline A1 - Worseck, Josephine M. A1 - Schauer, Nicolas A1 - Stienstra, Rinke A1 - Netea, Mihai G. A1 - Jahn, Dieter A1 - Pickkers, Peter A1 - Kox, Matthijs T1 - Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system JF - Metabolites N2 - We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects. KW - metabolomics KW - LPS KW - endotoxin KW - pyruvate KW - lactate KW - cytokines KW - inflammation KW - human endotoxemia KW - cori cycle KW - warburg effect Y1 - 2020 U6 - https://doi.org/10.3390/metabo10040148 SN - 2218-1989 VL - 10 IS - 4 SP - 1 EP - 18 PB - MDPI CY - Basel ER - TY - JOUR A1 - Zurell, Damaris A1 - von Wehrden, Henrik A1 - Rotics, Shay A1 - Kaatz, Michael A1 - Gross, Helge A1 - Schlag, Lena A1 - Schäfer, Merlin A1 - Sapir, Nir A1 - Turjeman, Sondra A1 - Wikelski, Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - Home range size and resource use of breeding and non-breeding white storks along a land use gradient JF - Frontiers in Ecology and Evolution N2 - Biotelemetry is increasingly used to study animal movement at high spatial and temporal resolution and guide conservation and resource management. Yet, limited sample sizes and variation in space and habitat use across regions and life stages may compromise robustness of behavioral analyses and subsequent conservation plans. Here, we assessed variation in (i) home range sizes, (ii) home range selection, and (iii) fine-scale resource selection of white storks across breeding status and regions and test model transferability. Three study areas were chosen within the Central German breeding grounds ranging from agricultural to fluvial and marshland. We monitored GPS-locations of 62 adult white storks equipped with solar-charged GPS/3D-acceleration (ACC) transmitters in 2013-2014. Home range sizes were estimated using minimum convex polygons. Generalized linear mixed models were used to assess home range selection and fine-scale resource selection by relating the home ranges and foraging sites to Corine habitat variables and normalized difference vegetation index in a presence/pseudo-absence design. We found strong variation in home range sizes across breeding stages with significantly larger home ranges in non-breeding compared to breeding white storks, but no variation between regions. Home range selection models had high explanatory power and well predicted overall density of Central German white stork breeding pairs. Also, they showed good transferability across regions and breeding status although variable importance varied considerably. Fine-scale resource selection models showed low explanatory power. Resource preferences differed both across breeding status and across regions, and model transferability was poor. Our results indicate that habitat selection of wild animals may vary considerably within and between populations, and is highly scale dependent. Thereby, home range scale analyses show higher robustness whereas fine-scale resource selection is not easily predictable and not transferable across life stages and regions. Such variation may compromise management decisions when based on data of limited sample size or limited regional coverage. We thus recommend home range scale analyses and sampling designs that cover diverse regional landscapes and ensure robust estimates of habitat suitability to conserve wild animal populations. KW - 3D-acceleration sensor KW - biotelemetry KW - Ciconia ciconia KW - home range selection KW - resource selection Y1 - 2018 U6 - https://doi.org/10.3389/fevo.2018.00079 SN - 2296-701X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Zurell, Damaris A1 - König, Christian A1 - Malchow, Anne-Kathleen A1 - Kapitza, Simon A1 - Bocedi, Greta A1 - Travis, Justin M. J. A1 - Fandos, Guillermo T1 - Spatially explicit models for decision-making in animal conservation and restoration JF - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos N2 - Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79%), towards the species and population level (80%) and towards conservation (rather than restoration) applications (71%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes. KW - adaptive management KW - biodiversity conservation KW - cost optimisation KW - ecosystem restoration KW - global change KW - predictive models Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05787 SN - 1600-0587 IS - 4 SP - 1 EP - 16 PB - Wiley-Blackwell CY - Oxford ER - TY - GEN A1 - Zurell, Damaris A1 - König, Christian A1 - Malchow, Anne-Kathleen A1 - Kapitza, Simon A1 - Bocedi, Greta A1 - Travis, Justin M. J. A1 - Fandos, Guillermo T1 - Spatially explicit models for decision-making in animal conservation and restoration T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79%), towards the species and population level (80%) and towards conservation (rather than restoration) applications (71%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1243 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549915 SN - 1866-8372 VL - 2022 SP - 1 EP - 16 PB - Universitätsverlag Potsdam CY - Potsdam ET - 4 ER - TY - JOUR A1 - Zurell, Damaris A1 - Jeltsch, Florian A1 - Dormann, Carsten F. A1 - Schröder-Esselbach, Boris T1 - Static species distribution models in dynamically changing systems : how good can predictions really be? N2 - SDM performance varied for different range dynamics. Prediction accuracies decreased when abrupt range shifts occurred as species were outpaced by the rate of climate change, and increased again when a new equilibrium situation was realised. When ranges contracted, prediction accuracies increased as the absences were predicted well. Far- dispersing species were faster in tracking climate change, and were predicted more accurately by SDMs than short- dispersing species. BRTs mostly outperformed GLMs. The presence of a predator, and the inclusion of its incidence as an environmental predictor, made BRTs and GLMs perform similarly. Results are discussed in light of other studies dealing with effects of ecological traits and processes on SDM performance. Perspectives are given on further advancements of SDMs and for possible interfaces with more mechanistic approaches in order to improve predictions under environmental change. Y1 - 2009 UR - http://www3.interscience.wiley.com/journal/117966123/home?CRETRY=1&SRETRY=0 U6 - https://doi.org/10.1111/j.1600-0587.2009.05810.x SN - 0906-7590 ER - TY - GEN A1 - Zurell, Damaris A1 - Elith, Jane A1 - Schröder-Esselbach, Boris T1 - Predicting to new environments tools for visualizing model behaviour and impacts on mapped distributions T2 - Diversity & distributions : a journal of biological invasions and biodiversity N2 - Data limitations can lead to unrealistic fits of predictive species distribution models (SDMs) and spurious extrapolation to novel environments. Here, we want to draw attention to novel combinations of environmental predictors that are within the sampled range of individual predictors but are nevertheless outside the sample space. These tend to be overlooked when visualizing model behaviour. They may be a cause of differing model transferability and environmental change predictions between methods, a problem described in some studies but generally not well understood. We here use a simple simulated data example to illustrate the problem and provide new and complementary visualization techniques to explore model behaviour and predictions to novel environments. We then apply these in a more complex real-world example. Our results underscore the necessity of scrutinizing model fits, ecological theory and environmental novelty. KW - Environmental niche KW - extrapolation KW - inflated response curves KW - novel environment KW - sampling space KW - species distribution models Y1 - 2012 U6 - https://doi.org/10.1111/j.1472-4642.2012.00887.x SN - 1366-9516 VL - 18 IS - 6 SP - 628 EP - 634 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Zurell, Damaris A1 - Eggers, Ute A1 - Kaatz, Michael A1 - Rotics, Shay A1 - Sapir, Nir A1 - Wikelski, Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - Individual-based modelling of resource competition to predict density-dependent population dynamics: a case study with white storks JF - Oikos N2 - Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual-based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine-scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density-dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions. Y1 - 2015 U6 - https://doi.org/10.1111/oik.01294 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 3 SP - 319 EP - 330 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Zuppinger-Dingley, D. A1 - Schmid, Bernhard A1 - Chen, Y. A1 - Brandl, H. A1 - van der Heijden, M. G. A. A1 - Joshi, Jasmin Radha T1 - In their native range, invasive plants are held in check by negative soil-feedbacks JF - Ecosphere : the magazine of the International Ecology University N2 - The ability of some plant species to dominate communities in new biogeographical ranges has been attributed to an innate higher competitive ability and release from co-evolved specialist enemies. Specifically, invasive success in the new range might be explained by release from biotic negative soil-feedbacks, which control potentially dominant species in their native range. To test this hypothesis, we grew individuals from sixteen phylogenetically paired European grassland species that became either invasive or naturalized in new ranges, in either sterilized soil or in sterilized soil with unsterilized soil inoculum from their native home range. We found that although the native members of invasive species generally performed better than those of naturalized species, these native members of invasive species also responded more negatively to native soil inoculum than did the native members of naturalized species. This supports our hypothesis that potentially invasive species in their native range are held in check by negative soil-feedbacks. However, contrary to expectation, negative soil-feedbacks in potentially invasive species were not much increased by interspecific competition. There was no significant variation among families between invasive and naturalized species regarding their feedback response (negative vs. neutral). Therefore, we conclude that the observed negative soil feedbacks in potentially invasive species may be quite widespread in European families of typical grassland species. KW - biotic interactions KW - enemy release KW - invasive species KW - native range KW - naturalized species KW - plant invasions KW - plant-soil feedbacks KW - soil inoculation KW - soil sterilization Y1 - 2011 U6 - https://doi.org/10.1890/ES11-00061.1 SN - 2150-8925 VL - 2 IS - 5 PB - Wiley CY - Washington ER - TY - JOUR A1 - Zupok, Arkadiusz A1 - Iobbi-Nivol, Chantal A1 - Mejean, Vincent A1 - Leimkühler, Silke T1 - The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria JF - Metallomics : integrated biometal science N2 - Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis. Y1 - 2019 U6 - https://doi.org/10.1039/c9mt00186g SN - 1756-5901 SN - 1756-591X VL - 11 IS - 10 SP - 1602 EP - 1624 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Zupok, Arkadiusz A1 - Górka, Michał Jakub A1 - Siemiatkowska, Beata A1 - Skirycz, Aleksandra A1 - Leimkühler, Silke T1 - Iron-Dependent Regulation of Molybdenum Cofactor Biosynthesis Genes in Escherichia coli JF - Journal of bacteriology N2 - Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two (4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional NFe-4S) cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the L-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production. IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes. KW - Escherichia coli KW - FNR KW - iron regulation KW - iron-sulfur cluster KW - anaerobic respiration KW - molybdenum cofactor Y1 - 2019 U6 - https://doi.org/10.1128/JB.00382-19 SN - 0021-9193 SN - 1098-5530 VL - 201 IS - 17 PB - American Society for Microbiology CY - Washington ER - TY - THES A1 - Zupok, Arkadiusz T1 - The psbB-operon is a major locus for plastome-genome incompatibility in Oenothera Y1 - 2015 ER - TY - JOUR A1 - Zuo, Zhili A1 - Gandhi, Neha S. A1 - Arndt, Katja Maren A1 - Mancera, Ricardo L. T1 - Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein JF - Biopolymers N2 - The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions. KW - free energy of binding KW - coiled-coil KW - molecular dynamics KW - MM KW - GBSA KW - leucine zipper Y1 - 2012 U6 - https://doi.org/10.1002/bip.22099 SN - 0006-3525 VL - 97 IS - 11 SP - 899 EP - 909 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Zulawski, Monika A1 - Schulze, Gunnar A1 - Braginets, Rostyslav A1 - Hartmann, Stefanie A1 - Schulze, Waltraud X. T1 - The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification JF - BMC genomics N2 - Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome. Y1 - 2014 U6 - https://doi.org/10.1186/1471-2164-15-548 SN - 1471-2164 VL - 15 PB - BioMed Central CY - London ER - TY - JOUR A1 - Zude, Manuela A1 - Pflanz, Michael A1 - Spinelli, Lorenzo A1 - Dosche, Carsten A1 - Torricelli, Alessandro T1 - Non-destructive analysis of anthocyanins in cherries by means of Lambert-Beer and multivariate regression based on spectroscopy and scatter correction using time-resolved analysis JF - Journal of food engineering N2 - In high-value sweet cherry (Prunus avium), the red coloration - determined by the anthocyanins content - is correlated with the fruit ripeness stage and market value. Non-destructive spectroscopy has been introduced in practice and may be utilized as a tool to assess the fruit pigments in the supply chain processes. From the fruit spectrum in the visible (Vis) wavelength range, the pigment contents are analyzed separately at their specific absorbance wavelengths. A drawback of the method is the need for re-calibration due to varying optical properties of the fruit tissue. In order to correct for the scattering differences, most often the spectral intensity in the visible spectrum is normalized by wavelengths in the near infrared (NIR) range, or pre-processing methods are applied in multivariate calibrations. In the present study, the influence of the fruit scattering properties on the Vis/NIR fruit spectrum were corrected by the effective pathlength in the fruit tissue obtained from time-resolved readings of the distribution of time-of-flight (DTOF). Pigment analysis was carried out according to Lambert-Beer law, considering fruit spectral intensities, effective pathlength, and refractive index. Results were compared to commonly applied linear color and multivariate partial least squares (PLS) regression analysis. The approaches were validated on fruits at different ripeness stages, providing variation in the scattering coefficient and refractive index exceeding the calibration sample set. In the validation, the measuring uncertainty of non-destructively analyzing fruits with Vis/NIR spectra by means of PLS or Lambert-Beer in comparison with combined application of Vis/NIR spectroscopy and DTOF measurements showed a dramatic bias reduction as well as enhanced coefficients of determination when using both, the spectral intensities and apparent information on the scattering influence by means of DTOF readings. Corrections for the refractive index did not render improved results. KW - Cherry KW - DTOF KW - Effective pathlength KW - Fruit maturity KW - Lambert-Beer KW - NIR KW - Non-invasive KW - Pigments KW - PLS KW - Ripeness KW - Sensor fusion KW - Spectroscopy KW - Time-resolved spectroscopy KW - TIRF KW - Vis KW - Scattering Y1 - 2011 U6 - https://doi.org/10.1016/j.jfoodeng.2010.09.021 SN - 0260-8774 VL - 103 IS - 1 SP - 68 EP - 75 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Zouhar, Jan A1 - Sauer, Michael T1 - Helping hands for budding prospects: ENTH/ANTH/VHS accessory proteins in endocytosis, vacuolar transport, and secretion JF - The plant cell N2 - Coated vesicles provide a major mechanism for the transport of proteins through the endomembrane system of plants. Transport between the endoplasmic reticulum and the Golgi involves vesicles with COPI and COPII coats, whereas clathrin is the predominant coat in endocytosis and post-Golgi trafficking. Sorting of cargo, coat assembly, budding, and fission are all complex and tightly regulated processes that involve many proteins. The mechanisms and responsible factors are largely conserved in eukaryotes, and increasing organismal complexity tends to be associated with a greater numbers of individual family members. Among the key factors is the class of ENTH/ANTH/VHS domain-containing proteins, which link membrane subdomains, clathrin, and other adapter proteins involved in early steps of clathrin coated vesicle formation. More than 30 Arabidopsis thaliana proteins contain this domain, but their generally low sequence conservation has made functional classification difficult. Reports from the last two years have greatly expanded our knowledge of these proteins and suggest that ENTH/ANTH/VHS domain proteins are involved in various instances of clathrin-related endomembrane trafficking in plants. This review aims to summarize these new findings and discuss the broader context of clathrin-dependent plant vesicular transport. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.131680 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 11 SP - 4232 EP - 4244 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Zou, Jie A1 - Wang, Weiwei A1 - Neffe, Axel T. A1 - Xu, Xun A1 - Li, Zhengdong A1 - Deng, Zijun A1 - Sun, Xianlei A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Adipogenic differentiation of human adipose derived mesenchymal stem cells in 3D architectured gelatin based hydrogels (ArcGel) JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Polymeric matrices mimicking multiple functions of the ECM are expected to enable a material induced regeneration of tissues. Here, we investigated the adipogenic differentiation of human adipose derived mesenchymal stem cells (hADSCs) in a 3D architectured gelatin based hydrogel (ArcGel) prepared from gelatin and L-lysine diisocyanate ethyl ester (LDI) in an one-step process, in which the formation of an open porous morphology and the chemical network formation were integrated. The ArcGel was designed to support adipose tissue regeneration with its 3D porous structure, high cell biocompatibility, and mechanical properties compatible with human subcutaneous adipose tissue. The ArcGel could support initial cell adhesion and survival of hADSCs. Under static culture condition, the cells could migrate into the inner part of the scaffold with a depth of 840 +/- 120 mu m after 4 days, and distributed in the whole scaffold (2mm in thickness) within 14 days. The cells proliferated in the scaffold and the fold increase of cell number after 7 days of culture was 2.55 +/- 0.08. The apoptotic rate of hADSCs in the scaffold was similar to that of cells maintained on tissue culture plates. When cultured in adipogenic induction medium, the hADSCs in the scaffold differentiated into adipocytes with a high efficiency (93 +/- 1%). Conclusively, this gelatin based 3D scaffold presented high cell compatibility for hADSC cultivation and differentiation, which could serve as a potential implant material in clinical applications for adipose tissue reparation and regeneration. KW - Mesenchymal stem cells KW - gelatin based scaffold KW - adipose tissue regeneration KW - adipogenic differentiation Y1 - 2017 U6 - https://doi.org/10.3233/CH-179210 SN - 1386-0291 SN - 1875-8622 VL - 67 IS - 3-4 SP - 297 EP - 307 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Zor, K. A1 - Heiskanen, A. A1 - Caviglia, Claudia A1 - Vergani, M. A1 - Landini, E. A1 - Shah, F. A1 - Carminati, Marco A1 - Martinez-Serrano, A. A1 - Ramos Moreno, T. A1 - Kokaia, M. A1 - Benayahu, Dafna A1 - Keresztes, Zs. A1 - Papkovsky, D. A1 - Wollenberger, Ursula A1 - Svendsen, W. E. A1 - Dimaki, M. A1 - Ferrari, G. A1 - Raiteri, R. A1 - Sampietro, M. A1 - Dufva, M. A1 - Emneus, Jenny T1 - A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection JF - RSC Advances N2 - Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring. Y1 - 2014 U6 - https://doi.org/10.1039/c4ra12632g SN - 2046-2069 VL - 4 IS - 109 SP - 63761 EP - 63771 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Zoccarato, Luca A1 - Sher, Daniel A1 - Miki, Takeshi A1 - Segre, Daniel A1 - Grossart, Hans-Peter T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions JF - Communications biology N2 - Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03184-4 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - Berlin ER - TY - THES A1 - Zinck, Richard T1 - Diversity, criticality and disturbance in wildfire ecosystems Y1 - 2009 CY - Potsdam ER - TY - JOUR A1 - Zimmermann, Wolfgang A1 - Breter, Holger A1 - Rudolph, Michael A1 - Ludwig, Hanns T1 - Borna disease virus : immunoelectron microscopic characterization of cell-free virus and further information about the genome Y1 - 1994 UR - http://jvi.asm.org/ SN - 0022-538X ER - TY - JOUR A1 - Zimmermann, P. A1 - Regierer, Babette A1 - Kossmann, Jens A1 - Frossard, Emmanuel A1 - Amrhein, Nikolaus A1 - Bucher, Matthias T1 - Differential expression of three purple acid phosphatases from potato N2 - Three cDNAs encoding purple acid phosphatase (PAP) were cloned from potato (Solanum tuberosum L. cv. Desiree) and expression of the corresponding genes was characterised. StPAP1 encodes a low-molecular weight PAP clustering with mammalian, cyanobacterial, and other plant PAPs. It was highly expressed in stem and root and its expression did not change in response to phosphorus (P) deprivation. StIPAP2 and StPAP3 code for high-molecular weight PAPs typical for plants. Corresponding gene expression was shown to be responsive to the level of P supply, with transcripts of StPAP2 and StPAP3 being most abundant in P-deprived roots or both stem and roots, respectively. Root colonisation by arbuscular mycorrhizal fungi had no effect on the expression of any of the three PAP genes. StIPAP1 mRNA is easily detectable along the root axis, including root hairs, but is barely detectable in root tips. In contrast, both StPAP2 and StPAP3 transcripts are abundant along the root axis, but absent in root hairs, and are most abundant in the root tip. All three PAPs described contain a predicted N-terminal secretion signal and could play a role in extracellular P scavenging, P mobilisation from the rhizosphere, or cell wall regeneration Y1 - 2004 SN - 1435-8603 ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Kruse, Stefan A1 - Müller, Juliane A1 - Stein, Ruediger A1 - Tiedemann, Ralf A1 - Herzschuh, Ulrike T1 - Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years JF - Ocean science N2 - The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7% of our sequences being assigned to diatoms across 18 different families, with 38.6% of them being resolved to species and 25.8% to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations - after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2% of the assemblage point towards past sea-ice presence. Y1 - 2020 U6 - https://doi.org/10.5194/os-16-1017-2020 SN - 1812-0784 VL - 16 IS - 5 SP - 1017 EP - 1032 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Raschke, Elena A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Schirrmeister, Lutz A1 - Schwamborn, Georg A1 - Herzschuh, Ulrike T1 - The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data JF - Genes N2 - Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns. KW - sedaDNA KW - metabarcoding KW - trnL KW - single-nucleotide polymorphism (SNP) KW - treeline KW - MIS 5 to 1 KW - permafrost deposits KW - radiocarbon ages KW - palaeoenvironment KW - Larix Y1 - 2017 U6 - https://doi.org/10.3390/genes8100273 SN - 2073-4425 VL - 8 IS - 10 SP - 273 PB - MDPI CY - Basel ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Harms, Lars A1 - Epp, Laura Saskia A1 - Mewes, Nick A1 - Bernhardt, Nadine A1 - Kruse, Stefan A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Wieczorek, Mareike A1 - Trense, Daronja A1 - Herzschuh, Ulrike T1 - Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly JF - PLoS one N2 - Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/ L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216966 SN - 1932-6203 VL - 14 IS - 7 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Zimmermann, Heike Hildegard T1 - Vegetation changes and treeline dynamics in northern Siberia since the last interglacial revealed by sedimentary ancient DNA metabarcoding and organelle genome assembly of modern larches Y1 - 2017 ER - TY - JOUR A1 - Zimmermann, Bernhard A1 - Walz, Bernd T1 - Serotonin-induced intercellular calcium waves in salivary glands of the blowfley Calliphora erythrocephala Y1 - 1997 ER - TY - JOUR A1 - Zimmermann, Bernhard A1 - Walz, Bernd T1 - The mechanism mediating regenerative intercellular Ca2+ waves in the blowfly salivary gland Y1 - 1999 ER - TY - JOUR A1 - Zimmermann, Bernhard A1 - Dames, Petra A1 - Walz, Bernd A1 - Baumann, Otto T1 - Distribution and serotonin-induced activation of vacuolar-type H+-ATPase in the salivary glands of the blowfly Calliphora vicina Y1 - 2003 ER - TY - JOUR A1 - Zimmermann, Bernhard T1 - Calcium store depletion activates two distinct calcium entry pathways in secretory cells of the blowfly salivary gland Y1 - 1998 ER - TY - JOUR A1 - Zimmermann, Bernhard T1 - Control of insP(3)-induced Ca2+ oscillations in permeabilized blowfly salivary gland cells : contribution of mitochondria Y1 - 2000 SN - 0022-3751 ER - TY - JOUR A1 - Zimmermann, Bernhard T1 - Subcellular organization of agonist-evoked Ca2+ waves in the blowfly salivary gland Y1 - 2000 ER - TY - JOUR A1 - Zilliges, Yvonne A1 - Kehr, Jan-Christoph A1 - Meissner, Sven A1 - Ishida, Keishi A1 - Mikkat, Stefan A1 - Hagemann, Martin A1 - Kaplan, Aaron A1 - Börner, Thomas A1 - Dittmann-Thünemann, Elke T1 - The cyanobacterial hepatotoxin microcystin binds to proteins and increases the fitness of microcystis under oxidative stress conditions JF - PLoS one N2 - Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant Delta mcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0017615 SN - 1932-6203 VL - 6 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Ziemert, Nadine A1 - Ishida, Keishi A1 - Weiz, Annika A1 - Hertweck, Christian A1 - Dittmann-Thünemann, Elke T1 - Exploiting the natural diversity of microviridin gene clusters for discovery of novel tricyclic depsipeptides N2 - Microviridins are ribosomally synthesized tricyclic depsipeptides produced by different genera of cyanobacteria. The prevalence of the microviridin gene clusters and the natural diversity of microviridin precursor sequences are currently unknown. Screening of laboratory strains and field samples of the bloom-forming freshwater cyanobacterium Microcystis via PCR revealed global occurrence of the microviridin pathway and an unexpected natural variety. We could detect 15 new variants of the precursor gene mdnA encoding microviridin backbones that differ in up to 4 amino acid positions from known isoforms of the peptide. The survey not only provides insights into the versatility of the biosynthetic enzymes in a closely related group of cyanobacteria, but also facilitates the discovery and characterization of cryptic microviridin variants. This is demonstrated for microviridin L in Microcystis aeruginosa strain NIES843 and heterologously produced variants. Y1 - 2010 UR - http://aem.asm.org/ U6 - https://doi.org/10.1128/AEM.02858-09 SN - 0099-2240 ER - TY - JOUR A1 - Zielhofer, Christoph A1 - Schmidt, Johannes A1 - Reiche, Niklas A1 - Tautenhahn, Marie A1 - Ballasus, Helen A1 - Burkart, Michael A1 - Linstädter, Anja A1 - Dietze, Elisabeth A1 - Kaiser, Knut A1 - Mehler, Natascha T1 - The lower Havel River Region (Brandenburg, Germany) BT - a 230-Year-Long historical map record indicates a decrease in surface water areas and groundwater levels JF - Water N2 - Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas. KW - long-term hydrological changes KW - historical maps KW - review of written KW - sources KW - preindustrial to industrial period KW - hydro-engineering history; KW - effects of global warming KW - drying trend KW - wetlands KW - drainage works to KW - create cropland KW - Lower Havel River Region KW - Brandenburg KW - Germany Y1 - 2022 U6 - https://doi.org/10.3390/w14030480 SN - 2073-4441 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - THES A1 - Ziege, Ricardo T1 - Growth dynamics and mechanical properties of E. coli biofilms T1 - Wachstumsdynamik und mechanische Eigenschaften von E. coli Biofilmen N2 - Biofilms are complex living materials that form as bacteria get embedded in a matrix of self-produced protein and polysaccharide fibres. The formation of a network of extracellular biopolymer fibres contributes to the cohesion of the biofilm by promoting cell-cell attachment and by mediating biofilm-substrate interactions. This sessile mode of bacteria growth has been well studied by microbiologists to prevent the detrimental effects of biofilms in medical and industrial settings. Indeed, biofilms are associated with increased antibiotic resistance in bacterial infections, and they can also cause clogging of pipelines or promote bio-corrosion. However, biofilms also gained interest from biophysics due to their ability to form complex morphological patterns during growth. Recently, the emerging field of engineered living materials investigates biofilm mechanical properties at multiple length scales and leverages the tools of synthetic biology to tune the functions of their constitutive biopolymers. This doctoral thesis aims at clarifying how the morphogenesis of Escherichia coli (E. coli) biofilms is influenced by their growth dynamics and mechanical properties. To address this question, I used methods from cell mechanics and materials science. I first studied how biological activity in biofilms gives rise to non-uniform growth patterns. In a second study, I investigated how E. coli biofilm morphogenesis and its mechanical properties adapt to an environmental stimulus, namely the water content of their substrate. Finally, I estimated how the mechanical properties of E. coli biofilms are altered when the bacteria express different extracellular biopolymers. On nutritive hydrogels, micron-sized E. coli cells can build centimetre-large biofilms. During this process, bacterial proliferation and matrix production introduce mechanical stresses in the biofilm, which release through the formation of macroscopic wrinkles and delaminated buckles. To relate these biological and mechanical phenomena, I used time-lapse fluorescence imaging to track cell and matrix surface densities through the early and late stages of E. coli biofilm growth. Colocalization of high cell and matrix densities at the periphery precede the onset of mechanical instabilities at this annular region. Early growth is detected at this outer annulus, which was analysed by adding fluorescent microspheres to the bacterial inoculum. But only when high rates of matrix production are present in the biofilm centre, does overall biofilm spreading initiate along the solid-air interface. By tracking larger fluorescent particles for a long time, I could distinguish several kinematic stages of E. coli biofilm expansion and observed a transition from non-linear to linear velocity profiles, which precedes the emergence of wrinkles at the biofilm periphery. Decomposing particle velocities to their radial and circumferential components revealed a last kinematic stage, where biofilm movement is mostly directed towards the radial delaminated buckles, which verticalize. The resulting compressive strains computed in these regions were observed to substantially deform the underlying agar substrates. The co-localization of higher cell and matrix densities towards an annular region and the succession of several kinematic stages are thus expected to promote the emergence of mechanical instabilities at the biofilm periphery. These experimental findings are predicted to advance future modelling approaches of biofilm morphogenesis. E. coli biofilm morphogenesis is further anticipated to depend on external stimuli from the environment. To clarify how the water could be used to tune biofilm material properties, we quantified E. coli biofilm growth, wrinkling dynamics and rigidity as a function of the water content of the nutritive substrates. Time-lapse microscopy and computational image analysis revealed that substrates with high water content promote biofilm spreading kinetics, while substrates with low water content promote biofilm wrinkling. The wrinkles observed on biofilm cross-sections appeared more bent on substrates with high water content, while they tended to be more vertical on substrates with low water content. Both wet and dry biomass, accumulated over 4 days of culture, were larger in biofilms cultured on substrates with high water content, despite extra porosity within the matrix layer. Finally, the micro-indentation analysis revealed that substrates with low water content supported the formation of stiffer biofilms. This study shows that E. coli biofilms respond to the water content of their substrate, which might be used for tuning their material properties in view of further applications. Biofilm material properties further depend on the composition and structure of the matrix of extracellular proteins and polysaccharides. In particular, E. coli biofilms were suggested to present tissue-like elasticity due to a dense fibre network consisting of amyloid curli and phosphoethanolamine-modified cellulose. To understand the contribution of these components to the emergent mechanical properties of E. coli biofilms, we performed micro-indentation on biofilms grown from bacteria of several strains. Besides showing higher dry masses, larger spreading diameters and slightly reduced water contents, biofilms expressing both main matrix components also presented high rigidities in the range of several hundred kPa, similar to biofilms containing only curli fibres. In contrast, a lack of amyloid curli fibres provides much higher adhesive energies and more viscoelastic fluid-like material behaviour. Therefore, the combination of amyloid curli and phosphoethanolamine-modified cellulose fibres implies the formation of a composite material whereby the amyloid curli fibres provide rigidity to E. coli biofilms, whereas the phosphoethanolamine-modified cellulose rather acts as a glue. These findings motivate further studies involving purified versions of these protein and polysaccharide components to better understand how their interactions benefit biofilm functions. All three studies depict different aspects of biofilm morphogenesis, which are interrelated. The first work reveals the correlation between non-uniform biological activities and the emergence of mechanical instabilities in the biofilm. The second work acknowledges the adaptive nature of E. coli biofilm morphogenesis and its mechanical properties to an environmental stimulus, namely water. Finally, the last study reveals the complementary role of the individual matrix components in the formation of a stable biofilm material, which not only forms complex morphologies but also functions as a protective shield for the bacteria it contains. Our experimental findings on E. coli biofilm morphogenesis and their mechanical properties can have further implications for fundamental and applied biofilm research fields. N2 - Biofilme sind komplexe lebende Materialien, die sich bilden, wenn Bakterien in eine Matrix aus selbstproduzierten Protein- und Polysaccharidfasern eingebettet werden. Die Bildung eines Netzwerks aus extrazellulären Biopolymerfasern trägt zum Zusammenhalt des Biofilms bei, indem sie die Zell-Zell-Anhaftung fördert und die Wechselwirkungen zwischen Biofilm und Substrat vermittelt. Diese sessile Form des Bakterienwachstums wurde von Mikrobiologen eingehend untersucht, um die schädlichen Auswirkungen von Biofilmen in der Medizin und Industrie zu verhindern. Biofilme werden nämlich mit einer erhöhten Antibiotikaresistenz bei bakteriellen Infektionen in Verbindung gebracht, und sie können auch zur Verstopfung von Rohrleitungen führen oder Biokorrosion fördern. Biofilme sind jedoch auch für die Biophysik von Interesse, da sie während ihres Wachstums komplexe morphologische Muster bilden können. In jüngster Zeit werden auf dem aufstrebenden Gebiet der künstlich hergestellten lebenden Materialien die mechanischen Eigenschaften von Biofilmen auf verschiedenen Längenskalen untersucht und die Werkzeuge der synthetischen Biologie genutzt, um die Funktionen ihrer konstitutiven Biopolymere zu beeinflussen. In dieser Doktorarbeit soll geklärt werden, wie die Morphogenese von Escherichia coli (E. coli)-Biofilmen durch deren Wachstumsdynamik und mechanische Eigenschaften beeinflusst wird. Um dieser Frage nachzugehen, habe ich Methoden aus der Zellmechanik und der Materialwissenschaft verwendet. Zunächst habe ich untersucht, wie die biologische Aktivität in Biofilmen zu ungleichmäßigen Wachstumsmustern führt. In einer zweiten Studie untersuchte ich, wie sich die Morphogenese von E. coli-Biofilmen und ihre mechanischen Eigenschaften an einen Umweltstimulus, nämlich den Wassergehalt des Substrats, anpassen. Schließlich habe ich abgeschätzt, wie sich die mechanischen Eigenschaften von E. coli-Biofilmen verändern, wenn die Bakterien verschiedene extrazelluläre Biopolymere exprimieren. Auf nährstoffhaltigen Hydrogelen können mikrometergroße E. coli-Zellen zentimetergroße Biofilme bilden. Während dieses Prozesses führen die bakterielle Vermehrung und die Matrixproduktion zu mechanischen Spannungen im Biofilm, die sich durch die Bildung von makroskopischen Falten und delaminierten Knicken entladen. Um diese biologischen und mechanischen Phänomene miteinander in Beziehung zu setzen, habe ich mit Hilfe von Zeitraffer-Fluoreszenzaufnahmen die Zell- und Matrixoberflächendichte in den frühen und späten Phasen des E. coli-Biofilmwachstums verfolgt. Die Kolokalisierung hoher Zell- und Matrixdichten an der Peripherie geht dem Auftreten mechanischer Instabilitäten in diesem ringförmigen Bereich voraus. An diesem äußeren Ring wird ein frühes Wachstum festgestellt, das durch Zugabe von fluoreszierenden Mikrokugeln zum bakteriellen Inokulum analysiert wurde. Aber nur wenn im Zentrum des Biofilms hohe Raten der Matrixproduktion vorhanden sind, beginnt die Ausbreitung des gesamten Biofilms entlang der Feststoff-Luft-Grenzfläche. Indem ich größere fluoreszierende Partikel über einen längeren Zeitraum verfolgte, konnte ich mehrere kinematische Stadien der E. coli-Biofilmexpansion unterscheiden und einen Übergang von nichtlinearen zu linearen Geschwindigkeitsprofilen beobachten, der dem Auftreten von Falten an der Biofilmperipherie vorausgeht. Die Zerlegung der Partikelgeschwindigkeiten in ihre radialen und umlaufenden Komponenten ergab ein letztes kinematisches Stadium, in dem die Bewegung des Biofilms hauptsächlich auf die radialen delaminierten Knicke gerichtet ist, die sich vertikalisieren. Die in diesen Regionen berechneten Druckspannungen verformen die darunter liegenden Agarsubstrate erheblich. Die gleichzeitige Ansammlung höherer Zell- und Matrixdichten in einer ringförmigen Region und die Abfolge mehrerer kinematischer Stadien dürften somit das Entstehen mechanischer Instabilitäten an der Biofilm-Peripherie fördern. Diese experimentellen Ergebnisse werden voraussichtlich zukünftige Modellierungsansätze der Biofilmmorphogenese voranbringen. Die Morphogenese des E. coli-Biofilms wird voraussichtlich auch von externen Stimuli aus der Umwelt abhängen. Um zu klären, wie das Wasser zur Einstellung der Materialeigenschaften von Biofilmen genutzt werden könnte, haben wir das Wachstum, die Faltenbildung und die Steifigkeit von E. coli-Biofilmen in Abhängigkeit vom Wassergehalt der Nährsubstrate quantifiziert. Zeitraffermikroskopie und computergestützte Bildanalyse zeigten, dass Substrate mit hohem Wassergehalt die Ausbreitungskinetik des Biofilms fördern, während Substrate mit niedrigem Wassergehalt die Faltenbildung des Biofilms begünstigen. Die auf Biofilm-Querschnitten beobachteten Falten erschienen auf Substraten mit hohem Wassergehalt stärker gebogen, während sie auf Substraten mit niedrigem Wassergehalt eher vertikal verliefen. Sowohl die feuchte als auch die trockene Biomasse, die während der 4-tägigen Kultur akkumuliert wurde, war in Biofilmen, die auf Substraten mit hohem Wassergehalt gezüchtet wurden, größer, trotz der zusätzlichen Porosität innerhalb der Matrixschicht. Schließlich ergab die Mikroindentationsanalyse, dass Substrate mit niedrigem Wassergehalt die Bildung von steiferen Biofilmen begünstigten. Diese Studie zeigt, dass E. coli-Biofilme auf den Wassergehalt ihres Substrats reagieren, was für die Abstimmung ihrer Materialeigenschaften im Hinblick auf weitere Anwendungen genutzt werden könnte. Die Materialeigenschaften von Biofilmen hängen außerdem von der Zusammensetzung und Struktur der Matrix aus extrazellulären Proteinen und Polysacchariden ab. Insbesondere wurde vermutet, dass E. coli-Biofilme aufgrund eines dichten Fasernetzwerks aus Amyloid-Curli und Phosphoethanolamin-modifizierter Cellulose eine gewebeähnliche Elastizität aufweisen. Um den Beitrag dieser Komponenten zu den entstehenden mechanischen Eigenschaften von E. coli-Biofilmen zu verstehen, führten wir an Biofilmen, die aus Bakterien verschiedener Stämme gewachsen waren, Mikroeindrücke durch. Biofilme, die beide Hauptmatrixkomponenten enthalten, wiesen nicht nur eine höhere Trockenmasse, einen größeren Ausbreitungsdurchmesser und einen leicht verringerten Wassergehalt auf, sondern auch eine hohe Steifigkeit im Bereich von mehreren hundert kPa, ähnlich wie Biofilme, die nur Curli-Fasern enthalten. Das Fehlen von Amyloid-Curli-Fasern führt dagegen zu deutlich höheren Adhäsionsenergien und einem viskoelastischeren, flüssigkeitsähnlichen Materialverhalten. Die Kombination von Amyloid-Curli-Fasern und Phosphoethanolamin-modifizierten Cellulosefasern impliziert daher die Bildung eines Verbundmaterials, bei dem die Amyloid-Curli-Fasern den E. coli-Biofilmen Steifigkeit verleihen, während die Phosphoethanolamin-modifizierte Cellulose eher als Klebstoff wirkt. Diese Ergebnisse motivieren zu weiteren Studien mit gereinigten Versionen dieser Protein- und Polysaccharidkomponenten, um besser zu verstehen, wie ihre Interaktionen die Funktionen des Biofilms unterstützen. Alle drei Studien zeigen verschiedene Aspekte der Biofilm-Morphogenese, die miteinander verbunden sind. Die erste Arbeit zeigt den Zusammenhang zwischen ungleichmäßigen biologischen Aktivitäten und dem Auftreten mechanischer Instabilitäten im Biofilm auf. Die zweite Arbeit bestätigt die Anpassungsfähigkeit der Morphogenese des E. coli-Biofilms und seiner mechanischen Eigenschaften an einen Umweltreiz, nämlich Wasser. Die letzte Studie schließlich zeigt die komplementäre Rolle der einzelnen Matrixkomponenten bei der Bildung eines stabilen Biofilmmaterials, das nicht nur komplexe Morphologien bildet, sondern auch als Schutzschild für die darin enthaltenen Bakterien fungiert. Unsere experimentellen Erkenntnisse über die Morphogenese von E. coli-Biofilmen und ihre mechanischen Eigenschaften können weitere Auswirkungen auf grundlegende und angewandte Biofilm-Forschungsbereiche haben. KW - biofilm KW - E. coli KW - living materials KW - mechanobiology KW - E. coli KW - Biofilm KW - lebende Materialien KW - Mechanobiologie Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-559869 ER - TY - GEN A1 - Ziege, Madlen A1 - Mahlow, Kristin A1 - Hennige-Sulz, Carmen A1 - Kronmarck, Claudia A1 - Tiedemann, Ralph A1 - Streit, Bruno A1 - Plath, Martin T1 - Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk? N2 - Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 143 KW - Siamese fighting fish KW - Guppies poecilia-reticulata KW - Betta-splendens KW - Public information KW - Mating preferences Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45171 ER - TY - JOUR A1 - Ziege, Madlen A1 - Hermann, Bernd Timo A1 - Kriesten, Stefanie A1 - Merker, Stefan A1 - Ullmann, Wiebke A1 - Streit, Bruno A1 - Wenninger, Sandra A1 - Plath, Martin T1 - Ranging behavior of European rabbits (Oryctolagus cuniculus) in urban and suburban landscapes JF - Mammal research / Mammal Research Institute, Polish Academy of Sciences N2 - Various mammals, particularly carnivores, reportedly establish smaller home ranges in urban compared with rural areas. This may be because urban environments provide optimal resources within a small area, negating the requirement to range further, or because habitat fragmentation constrains ranging behavior. Comparable information on urban populations of herbivorous mammalian species (such as European rabbits) is scarce. To fill this knowledge gap, we radio-tracked 13 individuals (seven females and six males) equipped with radio collars in a suburban and an urban study site in the city of Frankfurt am Main in Germany during the reproductive season (March to September) of 2012. The study sites differed in levels of habitat fragmentation. We report the smallest home ranges ever described for this species, with mean 95% minimum convex polygons (MCPs) covering 0.50 ha, while no consistent differences between sites were uncovered. We occasionally tracked individuals crossing streets underground (in burrows), suggesting that streets may restrict the ranging behavior of rabbits-and possibly other burrowing species-to a much lesser extent than previously thought. We conclude that heterogeneous landscape structures, made up of a diverse mosaic of buildings, parks, and gardens, provide sufficient food and shelter in close proximity to burrows at both study sites. Therefore, our data support the hypothesis that optimal resources constrain ranges in this case rather than habitat fragmentation. KW - Habitat fragmentation KW - Home range KW - Urbanization KW - Urban ecology KW - Minimum convex polygons (MCPs) Y1 - 2020 U6 - https://doi.org/10.1007/s13364-020-00490-2 SN - 2199-2401 SN - 2199-241X VL - 65 IS - 3 SP - 607 EP - 614 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Ziege, Madlen A1 - Hennige-Schulz, Carmen A1 - Muecksch, Frauke A1 - Bierbach, David A1 - Tiedemann, Ralph A1 - Streit, Bruno A1 - Plath, Martin T1 - A comparison of two methods to assess audience-induced changes in male mate choice JF - Current zoology N2 - Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk: interacting more equally with different females may be advantageous because rivals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains unknown if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males' mating preferences by scoring pre-mating (nipping) and mating behavior (gonopodial thrusting). Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male's behavior. A reduction in the strength of focal males' preferences was also seen after the rival male had an opportunity to mate with the focal male's preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both stimulus females not only the male's motivational state is reflected but also females' behavior such as avoidance of male sexual harassment. KW - Communication networks KW - Male mate choice KW - Non-independent mate choice KW - Sexual selection KW - Sperm competition risk KW - Audience effect Y1 - 2012 SN - 1674-5507 VL - 58 IS - 1 SP - 84 EP - 94 PB - Current Zoology CY - Beijing ER - TY - JOUR A1 - Zibulski, Romy A1 - Wesener, Felix A1 - Wilkes, Heinz A1 - Plessen, Birgit A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - C / N ratio, stable isotope (delta C-13, delta N-15), and n-alkane patterns of brown mosses along hydrological gradients of low-centred polygons of the Siberian Arctic JF - Biogeosciences N2 - Mosses are a major component of the arctic vegetation, particularly in wetlands. We present C / N atomic ratio, delta C-13 and delta N-15 data of 400 brown-moss samples belonging to 10 species that were collected along hydrological gradients within polygonal mires located on the southern Taymyr Peninsula and the Lena River delta in northern Siberia. Additionally, n-alkane patterns of six of these species (16 samples) were investigated. The aim of the study is to see whether the inter-and intraspecific differences in C / N, isotopic compositions and n-alkanes are indicative of habitat, particularly with respect to water level. Overall, we find high variability in all investigated parameters for two different moisture-related groups of moss species. The C / N ratios range between 11 and 53 (median: 32) and show large variations at the intraspecific level. However, species preferring a dry habitat (xero-mesophilic mosses) show higher C / N ratios than those preferring a wet habitat (meso-hygrophilic mosses). The delta C-13 values range between 37.0 and 22.5% (median D 27.8 %). The delta N-15 values range between 6.6 and C 1.7%(median D 2.2 %). We find differences in delta C-13 and delta N-15 compositions between both habitat types. For some species of the meso-hygrophilic group, we suggest that a relationship between the individ-ual habitat water level and isotopic composition can be inferred as a function of microbial symbiosis. The n-alkane distribution also shows differences primarily between xeromesophilic and meso-hygrophilic mosses, i. e. having a dominance of n-alkanes with long (n-C29, n-C31 /and intermediate (n-C25 /chain lengths, respectively. Overall, our results reveal that C / N ratios, isotopic signals and n-alkanes of studied brown-moss taxa from polygonal wetlands are characteristic of their habitat. Y1 - 2017 U6 - https://doi.org/10.5194/bg-14-1617-2017 SN - 1726-4170 SN - 1726-4189 VL - 14 SP - 1617 EP - 1630 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa) JF - PLoS one N2 - The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0186411 SN - 1932-6203 VL - 12 IS - 10 SP - 1 EP - 14 PB - PLoS CY - Lawrence, Kan. ER - TY - JOUR A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors JF - PLoS one N2 - The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs’ embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess–as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0156209 SN - 1932-6203 VL - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors JF - PLoS one N2 - The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs’ embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess–as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as. Y1 - 2016 U6 - https://doi.org/10.1371/JOURNAL.PONE.0156209 SN - 1932-6203 VL - 11 IS - 6 PB - PLoS CY - Lawrence, Kan. ER - TY - GEN A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors N2 - The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs’ embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess–as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 265 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-97119 ER - TY - GEN A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa) N2 - The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 395 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403875 ER - TY - THES A1 - Zhu, Fangjun T1 - Gene evolution and expression patterns in the all-female fish Amazon molly: Poecilia formosa Y1 - 2016 ER - TY - THES A1 - Zhou, Fei T1 - Optimization of foreign gene expression in plastids Y1 - 2008 ER - TY - JOUR A1 - Zhivkova, Veselina A1 - Kiecker, Felix A1 - Langer, Peter A1 - Eberle, Jürgen T1 - Crucial role of reactive oxygen species (ROS) for the proapoptotic effects of indirubin derivative DKP-073 in melanoma cells JF - Molecular carcinogenesis N2 - Melanoma represents a prime example demonstrating the success of targeted therapy in cancer. Nevertheless, it remained a deadly disease until now, and the identification of new, independent strategies as well as the understanding of their molecular mechanisms may help to finally overcome the high mortality. Both indirubins and TNF-related apoptosis-inducing ligand (TRAIL) represent promising candidates. Here, the indirubin derivative DKP-073 is shown to trigger apoptosis in melanoma cells, which is enhanced by the combination with TRAIL and is accompanied by complete loss of cell viability. Addressing the signaling cascade, characteristic molecular steps were identified as caspase-3 activation, downregulation of XIAP, upregulation of p53 and TRAIL receptor 2, loss of mitochondrial membrane potential, and STAT-3 dephosphorylation. The decisive step, however, turned out to be the early production of ROS already at 1 h. This was proven by antioxidant pretreatment, which completely abolished apoptosis induction and loss of cell viability as well as abrogated all signaling effects listed above. Thus, ROS appeared as upstream of all proapoptotic signaling. The data indicate a dominant role of ROS in apoptosis regulation, and the new pathway may expose a possible Achilles heel of melanoma. KW - apoptosis KW - kinase pathway KW - melanoma KW - stat 3 Y1 - 2018 U6 - https://doi.org/10.1002/mc.22924 SN - 0899-1987 SN - 1098-2744 VL - 58 IS - 2 SP - 258 EP - 269 PB - Wiley CY - Hoboken ER -