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 - JOUR A1 - Üstün, Suayib A1 - Sheikh, Arsheed A1 - Gimenez-Ibanez, Selena A1 - Jones, Alexandra A1 - Ntoukakis, Vardis A1 - Börnke, Frederik T1 - The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Recent evidence suggests that the ubiquitin-proteasome system is involved in several aspects of plant immunity and that a range of plant pathogens subvert the ubiquitin-proteasome system to enhance their virulence. Here, we show that proteasome activity is strongly induced during basal defense in Arabidopsis (Arabidopsis thaliana). Mutant lines of the proteasome subunits RPT2a and RPN12a support increased bacterial growth of virulent Pseudomonas syringae pv tomato DC3000 (Pst) and Pseudomonas syringae pv maculicola ES4326. Both proteasome subunits are required for pathogen-associated molecular pattern-triggered immunity responses. Analysis of bacterial growth after a secondary infection of systemic leaves revealed that the establishment of systemic acquired resistance (SAR) is impaired in proteasome mutants, suggesting that the proteasome also plays an important role in defense priming and SAR. In addition, we show that Pst inhibits proteasome activity in a type III secretion-dependent manner. A screen for type III effector proteins from Pst for their ability to interfere with proteasome activity revealed HopM1, HopAO1, HopA1, and HopG1 as putative proteasome inhibitors. Biochemical characterization of HopM1 by mass spectrometry indicates that HopM1 interacts with several E3 ubiquitin ligases and proteasome subunits. This supports the hypothesis that HopM1 associates with the proteasome, leading to its inhibition. Thus, the proteasome is an essential component of pathogen-associated molecular pattern-triggered immunity and SAR, which is targeted by multiple bacterial effectors. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.00808 SN - 0032-0889 SN - 1532-2548 VL - 172 SP - 1941 EP - 1958 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - ´Cwiek-Kupczynska, 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, Bjorn A1 - Weise, Stephan A1 - Kersey, Paul A1 - Krajewski, Pawel T1 - Measures for interoperability of phenotypic data: minimum information requirements and formatting JF - 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 combining 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 document 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. KW - Data standardisation and formatting KW - Experimental metadata KW - Minimum information recommendations KW - Plant phenotyping KW - Experiment description Y1 - 2016 U6 - https://doi.org/10.1186/s13007-016-0144-4 SN - 1746-4811 VL - 12 PB - BioMed Central CY - London ER - TY - JOUR A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd A1 - Andreotti, Sandro A1 - Reinert, Knut A1 - Zenichowski, Karl A1 - Diener, Marc T1 - High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications JF - Journal of separation science N2 - The combination of high-performance liquid chromatography and electrospray ionization ion mobility spectrometry facilitates the two-dimensional separation of complex mixtures in the retention and drift time plane. The ion mobility spectrometer presented here was optimized for flow rates customarily used in high-performance liquid chromatography between 100 and 1500 mu L/min. The characterization of the system with respect to such parameters as the peak capacity of each time dimension and of the 2D spectrum was carried out based on a separation of a pesticide mixture containing 24 substances. While the total ion current chromatogram is coarsely resolved, exhibiting coelutions for a number of compounds, all substances can be separately detected in the 2D plane due to the orthogonality of the separations in retention and drift dimensions. Another major advantage of the ion mobility detector is the identification of substances based on their characteristic mobilities. Electrospray ionization allows the detection of substances lacking a chromophore. As an example, the separation of a mixture of 18 amino acids is presented. A software built upon the free mass spectrometry package OpenMS was developed for processing the extensive 2D data. The different processing steps are implemented as separate modules which can be arranged in a graphic workflow facilitating automated processing of data. KW - Amino acids KW - Electrospray ionization KW - Ion mobility spectrometry KW - Pesticides KW - Two-dimensional separations Y1 - 2016 U6 - https://doi.org/10.1002/jssc.201600749 SN - 1615-9306 SN - 1615-9314 VL - 39 SP - 4756 EP - 4764 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Zöller, Gert A1 - Holschneider, Matthias T1 - The Maximum Possible and the Maximum Expected Earthquake Magnitude for Production-Induced Earthquakes at the Gas Field in Groningen, The Netherlands JF - Bulletin of the Seismological Society of America N2 - The Groningen gas field serves as a natural laboratory for production-induced earthquakes, because no earthquakes were observed before the beginning of gas production. Increasing gas production rates resulted in growing earthquake activity and eventually in the occurrence of the 2012M(w) 3.6 Huizinge earthquake. At least since this event, a detailed seismic hazard and risk assessment including estimation of the maximum earthquake magnitude is considered to be necessary to decide on the future gas production. In this short note, we first apply state-of-the-art methods of mathematical statistics to derive confidence intervals for the maximum possible earthquake magnitude m(max). Second, we calculate the maximum expected magnitude M-T in the time between 2016 and 2024 for three assumed gas-production scenarios. Using broadly accepted physical assumptions and 90% confidence level, we suggest a value of m(max) 4.4, whereas M-T varies between 3.9 and 4.3, depending on the production scenario. Y1 - 2016 U6 - https://doi.org/10.1785/0120160220 SN - 0037-1106 SN - 1943-3573 VL - 106 SP - 2917 EP - 2921 PB - Seismological Society of America CY - Albany ER - TY - JOUR A1 - Zöller, Gert A1 - Holschneider, Matthias T1 - The Earthquake History in a Fault Zone Tells Us Almost Nothing about m(max) JF - Seismological research letters N2 - In the present study, we summarize and evaluate the endeavors from recent years to estimate the maximum possible earthquake magnitude m(max) from observed data. In particular, we use basic and physically motivated assumptions to identify best cases and worst cases in terms of lowest and highest degree of uncertainty of m(max). In a general framework, we demonstrate that earthquake data and earthquake proxy data recorded in a fault zone provide almost no information about m(max) unless reliable and homogeneous data of a long time interval, including several earthquakes with magnitude close to m(max), are available. Even if detailed earthquake information from some centuries including historic and paleoearthquakes are given, only very few, namely the largest events, will contribute at all to the estimation of m(max), and this results in unacceptably high uncertainties. As a consequence, estimators of m(max) in a fault zone, which are based solely on earthquake-related information from this region, have to be dismissed. Y1 - 2016 U6 - https://doi.org/10.1785/0220150176 SN - 0895-0695 SN - 1938-2057 VL - 87 SP - 132 EP - 137 PB - Seismological Society of America CY - Albany ER - 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 - 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 - JOUR 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 JF - PLoS Pathogens 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. Y1 - 2016 U6 - https://doi.org/10.1371/journal.ppat.1005860 SN - 1553-7366 SN - 1553-7374 VL - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Zoref, Arye T1 - Journeys for God in Ṣūfī and Judeo Arabic Literature JF - PaRDeS : Journal of the Association of Jewish Studies [22 (2016)] = Muslim-Jewish Dialogue JF - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien [22 (2016)] = Muslim-Jewish Dialogue N2 - Das Konzept der drei Reisen als einen Weg zur spirituellen Entwicklung wurde von einem der Gründerväter der islamischen Mystik, Dhu al-Nun, eingeführt. Später wurde die Anwendung des Konzepts verfeinert, indem es mit der sufischen Technik verschiedene Präpositionen hinzuzufügen kombiniert wurde, um dadurch zwischen den spirituellen Stufen zu unterscheiden. Mit der Verwendung der Wörter Reise (Safar) und Gott (Allah) und dem Hinzufügen einer Präposition zum Wort Gott konnten sufische Schriftsteller die verschiedenen Wege zu Gott oder die Stationen (Maqamat) auf diesem Weg aufzeichnen. Ibn al-’Arabi spricht Anfang des dreizehnten Jahrhunderts von drei verschiedenen Wegen: von Gott, zu Gott und in Gott. Am Ende des dreizehnten Jahrhunderts spricht der jüdisch-arabische Bibelkommentator Tanchum ha-Yerushalmi von den drei Reisen als drei Stationen eines kontinuierlichen Weges. Eine nahezu identische Beschreibung ist eine Generation danach beim muslimischen Gelehrten Qayyim al-Jawziyya zu finden. Aus den drei Reisen werden im vierzehnten Jahrhundert in den Schriften des sufischen Schriftstellers al-Qashani vier, wobei das Schema der drei Präpositionen beibehalten wurde. Kurz vor dem Ende des vierzehnten Jahrhunderts sind in den Schriften von R. David ha-Nagid nur noch zwei Reisen zu finden: zu Gott und in Gott. All dies zeigt uns, dass uns die jüdisch-arabische Literatur dabei helfen kann die geschichtliche Entwicklung der sufischen Ideen genauer nachzuzeichnen. N2 - The concept of three journeys as a way to denote spiritual development was introduced by Dhu al-Nun, one of the founding fathers of Islamic mysticism. The use of this concept was later refined by combining it with the Sufi technique of adding different prepositions to a certain term, in order to differentiate between spiritual stages. By using the words journey (Safar) and God (Allah) and inserting a preposition before the word God, Sufi writers could map the different roads to God or the stations (Maqamat) on this road. Ibn al-'Arabi, in the beginning of the thirteenth century, speaks of three different ways: from God, toward God and in God. Tanchum ha-Yerushalmi, the Judeo Arabic biblical commentator from the end of this century, speaks of the three journeys as three stations of one continuous way. A nearly identical description we can find in the writing of the Muslim scholar Ibn Qayyim al-Jawziyya, a generation later. Later in the fourteenth century, in the writing of the Sufi writer al-Qashani, the three travels become four, although the scheme of three prepositions is preserved. Near the end of the fourteenth century, in the writings of R. David ha-Nagid, we find only two journeys: to God and in God. All this tells us that Judeo Arabic literature can help us map with greater precision the historical development of Sufi ideas. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99635 SN - 978-3-86956-370-1 SN - 1614-6492 SN - 1862-7684 VL - 22 SP - 109 EP - 119 PB - Universitätsverlag Potsdam CY - Potsdam ER -