TY - GEN A1 - Ślęzak, Jakub A1 - Metzler, Ralf A1 - Magdziarz, Marcin T1 - Codifference can detect ergodicity breaking and non-Gaussianity T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 748 KW - diffusion KW - anomalous diffusion KW - stochastic time series Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436178 IS - 748 ER - TY - JOUR A1 - Ślęzak, Jakub A1 - Metzler, Ralf A1 - Magdziarz, Marcin T1 - Codifference can detect ergodicity breaking and non-Gaussianity JF - New Journal of Physics N2 - We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement. KW - diffusion KW - stochastic time series KW - anomalous diffusion Y1 - 2019 U6 - https://doi.org/10.1088/1367-2630/ab13f3 SN - 1367-2630 VL - 21 PB - Deutsche Physikalische Gesellschaft CY - Bad Honnef ER - TY - GEN A1 - Ćwiek-Kupczyńska, Hanna A1 - Altmann, Thomas A1 - Arend, Daniel A1 - Arnaud, Elizabeth A1 - Chen, Dijun A1 - Cornut, Guillaume A1 - Fiorani, Fabio A1 - Frohmberg, Wojciech A1 - Junker, Astrid A1 - Klukas, Christian A1 - Lange, Matthias A1 - Mazurek, Cezary A1 - Nafissi, Anahita A1 - Neveu, Pascal A1 - van Oeveren, Jan A1 - Pommier, Cyril A1 - Poorter, Hendrik A1 - Rocca-Serra, Philippe A1 - Sansone, Susanna-Assunta A1 - Scholz, Uwe A1 - van Schriek, Marco A1 - Seren, Ümit A1 - Usadel, Björn A1 - Weise, Stephan A1 - Kersey, Paul A1 - Krajewski, Paweł T1 - Measures for interoperability of phenotypic data BT - minimum information requirements and formatting T2 - Plant methods N2 - Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time ‑consuming experiments, the findings can be fostered by reusing and combin‑ ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑ ment called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA ‑Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA ‑Tab ‑formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 450 KW - data standardisation and formatting KW - experimental metadata KW - minimum information recommendations KW - plant phenotyping KW - experiment description Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407299 ER - TY - GEN A1 - Üstün, Suayib A1 - Bartetzko, Verena A1 - Börnke, Frederik T1 - The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid T2 - Frontiers in plant science N2 - XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 432 KW - Xanthomonas KW - type-III effector KW - XopJ KW - avirulence KW - salicylic acid Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-406537 ER - TY - GEN A1 - Zwieback, Simon A1 - Kokelj, Steven V. A1 - Günther, Frank A1 - Boike, Julia A1 - Grosse, Guido A1 - Hajnsek, Irena T1 - Sub-seasonal thaw slump mass wasting is not consistently energy limited at the landscape scale T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Predicting future thaw slump activity requires a sound understanding of the atmospheric drivers and geomorphic controls on mass wasting across a range of timescales. On sub-seasonal timescales, sparse measurements indicate that mass wasting at active slumps is often limited by the energy available for melting ground ice, but other factors such as rainfall or the formation of an insulating veneer may also be relevant. To study the sub-seasonal drivers, we derive topographic changes from single-pass radar interferometric data acquired by the TanDEM-X satellites. The estimated elevation changes at 12m resolution complement the commonly observed planimetric retreat rates by providing information on volume losses. Their high vertical precision (around 30 cm), frequent observations (11 days) and large coverage (5000 km(2)) allow us to track mass wasting as drivers such as the available energy change during the summer of 2015 in two study regions. We find that thaw slumps in the Tuktoyaktuk coastlands, Canada, are not energy limited in June, as they undergo limited mass wasting (height loss of around 0 cm day 1) despite the ample available energy, suggesting the widespread presence of early season insulating snow or debris veneer. Later in summer, height losses generally increase (around 3 cm day 1), but they do so in distinct ways. For many slumps, mass wasting tracks the available energy, a temporal pattern that is also observed at coastal yedoma cliffs on the Bykovsky Peninsula, Russia. However, the other two common temporal trajectories are asynchronous with the available energy, as they track strong precipitation events or show a sudden speed-up in late August respectively. The observed temporal patterns are poorly related to slump characteristics like the headwall height. The contrasting temporal behaviour of nearby thaw slumps highlights the importance of complex local and temporally varying controls on mass wasting. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 926 KW - ground-ice KW - Tandem-X KW - Northeast Siberia KW - thermal regime KW - Peel Plateau KW - permafrost KW - erosion KW - Island KW - delta KW - yedoma Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-445688 SN - 1866-8372 IS - 926 SP - 549 EP - 564 ER - TY - GEN A1 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Chemotaxonomy of mycotoxigenic small-spored Alternaria fungi BT - do multitoxin mixtures act as an indicator for species differentiation? T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Necrotrophic as well as saprophytic small-spored Altemaria (A.) species are annually responsible for major losses of agricultural products, such as cereal crops, associated with the contamination of food and feedstuff with potential health-endangering Altemaria toxins. Knowledge of the metabolic capabilities of different species-groups to form mycotoxins is of importance for a reliable risk assessment. 93 Altemaria strains belonging to the four species groups Alternaria tenuissima, A. arborescens, A. altemata, and A. infectoria were isolated from winter wheat kernels harvested from fields in Germany and Russia and incubated under equal conditions. Chemical analysis by means of an HPLC-MS/MS multi-Alternaria-toxin-method showed that 95% of all strains were able to form at least one of the targeted 17 non-host specific Altemaria toxins. Simultaneous production of up to 15 (modified) Altemaria toxins by members of the A. tenuissima, A. arborescens, A. altemata species-groups and up to seven toxins by A. infectoria strains was demonstrated. Overall tenuazonic acid was the most extensively formed mycotoxin followed by alternariol and alternariol mono methylether, whereas altertoxin I was the most frequently detected toxin. Sulfoconjugated modifications of alternariol, alternariol mono methylether, altenuisol and altenuene were frequently determined. Unknown perylene quinone derivatives were additionally detected. Strains of the species-group A. infectoria could be segregated from strains of the other three species-groups due to significantly lower toxin levels and the specific production of infectopyrone. Apart from infectopyrone, alterperylenol was also frequently produced by 95% of the A. infectoria strains. Neither by the concentration nor by the composition of the targeted Altemaria toxins a differentiation between the species-groups A. altemata, A. tenuissima and A. arborescens was possible. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 696 KW - small-spored Alternaria fungi KW - Alternaria species-groups KW - Alternaria mycotoxins KW - chemotaxonomy KW - secondary metabolite profiling KW - LC-MS/MS KW - wheat KW - perylene quinone derivatives Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-426623 SN - 1866-8372 IS - 696 ER - TY - GEN A1 - Zurnic, Irena A1 - Hütter, Sylvia A1 - Rzeha, Ute A1 - Stanke, Nicole A1 - Reh, Juliane A1 - Müllers, Erik A1 - Hamann, Martin V. A1 - Kern, Tobias A1 - Gerresheim, Gesche K. A1 - Lindel, Fabian A1 - Serrao, Erik A1 - Lesbats, Paul A1 - Engelman, Alan N. A1 - Cherepanov, Peter A1 - Lindemann, Dirk T1 - Interactions of prototype foamy virus capsids with host cell polo-like kinases are important for efficient viral DNA integration T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Unlike for other retroviruses, only a few host cell factors that aid the replication of foamy viruses (FVs) via interaction with viral structural components are known. Using a yeast-two-hybrid (Y2H) screen with prototype FV (PFV) Gag protein as bait we identified human polo-like kinase 2 (hPLK2), a member of cell cycle regulatory kinases, as a new interactor of PFV capsids. Further Y2H studies confirmed interaction of PFV Gag with several PLKs of both human and rat origin. A consensus Ser-Thr/Ser-Pro (S-T/S-P) motif in Gag, which is conserved among primate FVs and phosphorylated in PFV virions, was essential for recognition by PLKs. In the case of rat PLK2, functional kinase and polo-box domains were required for interaction with PFV Gag. Fluorescently-tagged PFV Gag, through its chromatin tethering function, selectively relocalized ectopically expressed eGFP-tagged PLK proteins to mitotic chromosomes in a Gag STP motif-dependent manner, confirming a specific and dominant nature of the Gag-PLK interaction in mammalian cells. The functional relevance of the Gag-PLK interaction was examined in the context of replication-competent FVs and single-round PFV vectors. Although STP motif mutated viruses displayed wild type (wt) particle release, RNA packaging and intra-particle reverse transcription, their replication capacity was decreased 3-fold in single-cycle infections, and up to 20-fold in spreading infections over an extended time period. Strikingly similar defects were observed when cells infected with single-round wt Gag PFV vectors were treated with a pan PLK inhibitor. Analysis of entry kinetics of the mutant viruses indicated a post-fusion defect resulting in delayed and reduced integration, which was accompanied with an enhanced preference to integrate into heterochromatin. We conclude that interaction between PFV Gag and cellular PLK proteins is important for early replication steps of PFV within host cells. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 580 KW - core protein KW - HIV-1 infection KW - retroviral integration KW - reverse transcription KW - nuclear-localization KW - box domain KW - in-vivo KW - Gag KW - PLK1 KW - phosphorylation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-411317 SN - 1866-8372 IS - 580 ER - TY - GEN A1 - Zulawski, Monika A1 - Schulze, Gunnar A1 - Braginets, Rostyslav A1 - Hartmann, Stefanie A1 - Schulze, Waltraud X T1 - The Arabidopsis Kinome BT - phylogeny and evolutionary insights into functional diversification T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 861 KW - Hide Markov Model KW - Duplication Event KW - Kinase Family KW - Tandem Duplication KW - Segmental Duplication Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432907 SN - 1866-8372 IS - 861 ER - TY - GEN A1 - Zimmermann, Heike Hildegard A1 - Raschke, Elena A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Schwamborn, Georg A1 - Schirrmeister, Lutz A1 - Overduin, Pier Paul A1 - Herzschuh, Ulrike T1 - Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4-11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 670 KW - NE Siberia KW - vegetation patterns KW - environmental DNA KW - Arctic vegetation KW - frozen sediments KW - lake-sediments KW - gas-production KW - carbon KW - polygon KW - climate Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-417130 SN - 1866-8372 IS - 670 ER - TY - GEN A1 - Ziegler, Moritz O. A1 - Heidbach, Oliver A1 - Reinecker, John A1 - Przybycin, Anna M. A1 - Scheck-Wenderoth, Magdalena T1 - A multi-stage 3-D stress field modelling approach exemplified in the Bavarian Molasse Basin T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The knowledge of the contemporary in situ stress state is a key issue for safe and sustainable subsurface engineering. However, information on the orientation and magnitudes of the stress state is limited and often not available for the areas of interest. Therefore 3-D geomechanical-numerical modelling is used to estimate the in situ stress state and the distance of faults from failure for application in subsurface engineering. The main challenge in this approach is to bridge the gap in scale between the widely scattered data used for calibration of the model and the high resolution in the target area required for the application. We present a multi-stage 3-D geomechanical-numerical approach which provides a state-of-the-art model of the stress field for a reservoir-scale area from widely scattered data records. Therefore, we first use a large-scale regional model which is calibrated by available stress data and provides the full 3-D stress tensor at discrete points in the entire model volume. The modelled stress state is used subsequently for the calibration of a smaller-scale model located within the large-scale model in an area without any observed stress data records. We exemplify this approach with two-stages for the area around Munich in the German Molasse Basin. As an example of application, we estimate the scalar values for slip tendency and fracture potential from the model results as measures for the criticality of fault reactivation in the reservoir-scale model. The modelling results show that variations due to uncertainties in the input data are mainly introduced by the uncertain material properties and missing S-Hmax magnitude estimates needed for a more reliable model calibration. This leads to the conclusion that at this stage the model's reliability depends only on the amount and quality of available stress information rather than on the modelling technique itself or on local details of the model geometry. Any improvements in modelling and increases in model reliability can only be achieved using more high-quality data for calibration. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 556 KW - in-situ stress KW - induced seismicity KW - geothermal-reservoirs KW - geomechanical model KW - fault reactivation KW - alpine foreland KW - map project KW - km depth KW - orientation KW - system Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409806 SN - 1866-8372 IS - 556 ER -