@misc{ĆwiekKupczyńskaAltmannArendetal.2016, author = {Ćwiek-Kupczyńska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bj{\"o}rn and Weise, Stephan and Kersey, Paul and Krajewski, Paweł}, title = {Measures for interoperability of phenotypic data}, series = {Plant methods}, journal = {Plant methods}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407299}, pages = {18}, year = {2016}, abstract = {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.}, language = {en} } @article{UestuenSheikhGimenezIbanezetal.2016, author = {{\"U}st{\"u}n, Suayib and Sheikh, Arsheed and Gimenez-Ibanez, Selena and Jones, Alexandra and Ntoukakis, Vardis and B{\"o}rnke, Frederik}, title = {The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {172}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.00808}, pages = {1941 -- 1958}, year = {2016}, abstract = {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.}, language = {en} } @article{CwiekKupczynskaAltmannArendetal.2016, author = {´Cwiek-Kupczynska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bjorn and Weise, Stephan and Kersey, Paul and Krajewski, Pawel}, title = {Measures for interoperability of phenotypic data: minimum information requirements and formatting}, series = {Plant Methods}, volume = {12}, journal = {Plant Methods}, publisher = {BioMed Central}, address = {London}, issn = {1746-4811}, doi = {10.1186/s13007-016-0144-4}, pages = {18}, year = {2016}, abstract = {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.}, language = {en} } @article{ZuehlkeRiebeBeitzetal.2016, author = {Z{\"u}hlke, Martin and Riebe, Daniel and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Andreotti, Sandro and Reinert, Knut and Zenichowski, Karl and Diener, Marc}, title = {High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications}, series = {Journal of separation science}, volume = {39}, journal = {Journal of separation science}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1615-9306}, doi = {10.1002/jssc.201600749}, pages = {4756 -- 4764}, year = {2016}, abstract = {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.}, language = {en} } @article{ZoellerHolschneider2016, author = {Z{\"o}ller, Gert and Holschneider, Matthias}, title = {The Maximum Possible and the Maximum Expected Earthquake Magnitude for Production-Induced Earthquakes at the Gas Field in Groningen, The Netherlands}, series = {Bulletin of the Seismological Society of America}, volume = {106}, journal = {Bulletin of the Seismological Society of America}, publisher = {Seismological Society of America}, address = {Albany}, issn = {0037-1106}, doi = {10.1785/0120160220}, pages = {2917 -- 2921}, year = {2016}, abstract = {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.}, language = {en} } @article{ZoellerHolschneider2016, author = {Z{\"o}ller, Gert and Holschneider, Matthias}, title = {The Earthquake History in a Fault Zone Tells Us Almost Nothing about m(max)}, series = {Seismological research letters}, volume = {87}, journal = {Seismological research letters}, publisher = {Seismological Society of America}, address = {Albany}, issn = {0895-0695}, doi = {10.1785/0220150176}, pages = {132 -- 137}, year = {2016}, abstract = {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.}, language = {en} } @article{ZwickelKahlKlaffkeetal.2016, author = {Zwickel, Theresa and Kahl, Sandra M. and Klaffke, Horst and Rychlik, Michael and M{\"u}ller, Marina E. H.}, title = {Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions}, series = {Toxins}, volume = {8}, journal = {Toxins}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins8110344}, pages = {570 -- 583}, year = {2016}, abstract = {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.}, language = {en} } @misc{ZurnicHuetterRzehaetal.2016, author = {Zurnic, Irena and H{\"u}tter, Sylvia and Rzeha, Ute and Stanke, Nicole and Reh, Juliane and M{\"u}llers, Erik and Hamann, Martin V. and Kern, Tobias and Gerresheim, Gesche K. and Lindel, Fabian and Serrao, Erik and Lesbats, Paul and Engelman, Alan N. and Cherepanov, Peter and Lindemann, Dirk}, title = {Interactions of prototype foamy virus capsids with host cell polo-like kinases are important for efficient viral DNA integration}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {580}, issn = {1866-8372}, doi = {10.25932/publishup-41131}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-411317}, pages = {36}, year = {2016}, abstract = {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.}, language = {en} } @article{ZurnicHuetterRzehaetal.2016, author = {Zurnic, Irena and H{\"u}tter, Sylvia and Rzeha, Ute and Stanke, Nicole and Reh, Juliane and M{\"u}llers, Erik and Hamann, Martin V. and Kern, Tobias and Gerresheim, Gesche K. and Lindel, Fabian and Serrao, Erik and Lesbats, Paul and Engelman, Alan N. and Cherepanov, Peter and Lindemann, Dirk}, title = {Interactions of Prototype Foamy Virus Capsids with Host Cell Polo-Like Kinases Are Important for Efficient Viral DNA Integration}, series = {PLoS Pathogens}, volume = {12}, journal = {PLoS Pathogens}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7366}, doi = {10.1371/journal.ppat.1005860}, pages = {36}, year = {2016}, abstract = {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.}, language = {en} } @article{ZscheygeWeicker2016, author = {Zscheyge, Oliver and Weicker, Karsten}, title = {Werkzeugunterst{\"u}tzung bei der Vermittlung der Grundlagen wissenschaftlichen Schreibens}, series = {Commentarii informaticae didacticae (CID)}, journal = {Commentarii informaticae didacticae (CID)}, number = {10}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-376-3}, issn = {1868-0844}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94814}, pages = {57 -- 68}, year = {2016}, abstract = {Der Unterricht großer Studierendengruppen im wissenschaftlichen Schreiben birgt vielf{\"a}ltige organisatorische Herausforderungen und eine zeitintensive Betreuung durch die Dozenten. Diese Arbeit stellt ein Lehrkonzept mit Peer-Reviews vor, in dem das Feedback der Peers durch eine automatisierte Analyse erg{\"a}nzt wird. Die Software Confopy liefert metrik- und strukturbasierte Hinweise f{\"u}r die Verbesserung des wissenschaftlichen Schreibstils. Der Nutzen von Confopy wird an 47 studentischen Arbeiten in Draft- und Final-Version illustriert.}, language = {de} }