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Ćwiek-Kupczyńska, Hanna ; Altmann, Thomas ; Arend, Daniel ; Arnaud, Elizabeth ; Chen, Dijun ; Cornut, Guillaume ; Fiorani, Fabio ; Frohmberg, Wojciech ; Junker, Astrid ; Klukas, Christian ; Lange, Matthias ; Mazurek, Cezary ; Nafissi, Anahita ; Neveu, Pascal ; van Oeveren, Jan ; Pommier, Cyril ; Poorter, Hendrik ; Rocca-Serra, Philippe ; Sansone, Susanna-Assunta ; Scholz, Uwe ; van Schriek, Marco ; Seren, Ümit ; Usadel, Björn ; Weise, Stephan ; Kersey, Paul ; Krajewski, Paweł
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.
The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors
(2016)
Üstün, Suayib ; Sheikh, Arsheed ; Gimenez-Ibanez, Selena ; Jones, Alexandra ; Ntoukakis, Vardis ; Börnke, Frederik
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.
Measures for interoperability of phenotypic data: minimum information requirements and formatting
(2016)
´Cwiek-Kupczynska, Hanna ; Altmann, Thomas ; Arend, Daniel ; Arnaud, Elizabeth ; Chen, Dijun ; Cornut, Guillaume ; Fiorani, Fabio ; Frohmberg, Wojciech ; Junker, Astrid ; Klukas, Christian ; Lange, Matthias ; Mazurek, Cezary ; Nafissi, Anahita ; Neveu, Pascal ; van Oeveren, Jan ; Pommier, Cyril ; Poorter, Hendrik ; Rocca-Serra, Philippe ; Sansone, Susanna-Assunta ; Scholz, Uwe ; van Schriek, Marco ; Seren, Ümit ; Usadel, Bjorn ; Weise, Stephan ; Kersey, Paul ; Krajewski, Pawel
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.
Zühlke, Martin ; Riebe, Daniel ; Beitz, Toralf ; Löhmannsröben, Hans-Gerd ; Andreotti, Sandro ; Reinert, Knut ; Zenichowski, Karl ; Diener, Marc
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.
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.
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.
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.
Zurnic, Irena ; Hütter, Sylvia ; Rzeha, Ute ; Stanke, Nicole ; Reh, Juliane ; Müllers, Erik ; Hamann, Martin V. ; Kern, Tobias ; Gerresheim, Gesche K. ; Lindel, Fabian ; Serrao, Erik ; Lesbats, Paul ; Engelman, Alan N. ; Cherepanov, Peter ; Lindemann, Dirk
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.
Zurnic, Irena ; Hütter, Sylvia ; Rzeha, Ute ; Stanke, Nicole ; Reh, Juliane ; Müllers, Erik ; Hamann, Martin V. ; Kern, Tobias ; Gerresheim, Gesche K. ; Lindel, Fabian ; Serrao, Erik ; Lesbats, Paul ; Engelman, Alan N. ; Cherepanov, Peter ; Lindemann, Dirk
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.
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.
Zohsel, Katrin ; Baldus, Christiane ; Schmidt, Martin H. ; Esser, Günter ; Banaschewski, Tobias ; Thomasius, Rainer ; Laucht, Manfred
Background: Cannabis is the most commonly used illegal substance among adolescents and young adults. Problematic cannabis use is often associated with comorbid psychopathological problems. The purpose of the current study was to elucidate the underlying developmental processes connecting externalizing and internalizing psychopathology in childhood and adolescence with problematic cannabis use in young adulthood. Methods: Data were drawn from the Mannheim Study of Children at Risk, an ongoing epidemiological cohort study from birth to adulthood. For n = 307 participants, symptom scores of conduct/oppositional defiant disorder, attention problems, hyperactivity/impulsivity, and internalizing disorders were available for the periods of childhood (4.5-11 years) and adolescence (15 years). At age 25 years, problematic cannabis use was assessed via clinical interview and a self-rating questionnaire. Results: At age 25 years, problematic cannabis use was identified in n = 28 participants (9.1%). Childhood conduct/oppositional behavior problems were predictive of problematic cannabis use during young adulthood when comorbid symptoms were controlled for. No such effect was found for childhood attention, hyperactivity/impulsivity or internalizing problems. With respect to psychopathological symptoms during adolescence, only attention problems were significantly related to later problematic cannabis use when controlling for comorbidity. Conclusions: The current study highlights the role of conduct/oppositional behavior problems during childhood and attention problems during adolescence in later problematic cannabis use. It sheds more light on the developmental sequence of childhood and adolescence psychopathology and young adult cannabis use, which is a prerequisite for effective prevention approaches. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
Article 15bis: Exercise of jurisdiction over the crime of aggression (State referal, proprio motu)
(2016)
In November 2015, the 14th Session of the Assembly of States Parties to the Rome Statute of the International Criminal Court (ICC) adopted, by consensus, an amendment providing for the deletion of Article 124 of the ICC Statute, which so far enables contracting parties, when joining the Statute, to opt out from the ICC’s treaty-based war crimes-related jurisdiction. After considering the genesis of the provision and the practice arising under Article 124 of the ICC Statute so far, this article considers the arguments for and against the deletion of Article 124 in light of the increasingly small number of accessions to the ICC Statute that have been forthcoming in the last few years. It also analyses the quite strict requirements for the entry into force of the amendment, as well as the effect of the entry into force of the amendment on possible declarations having been made pending such entry into force. It ends by considering the positive effect a continued applicability of Article 124 may have on states so far being reluctant to accede to the ICC Statute.
In November 2015, the 14th Session of the Assembly of States Parties to the Rome Statute of the International Criminal Court (ICC) adopted, by consensus, an amendment providing for the deletion of Article 124 of the ICC Statute, which so far enables contracting parties, when joining the Statute, to opt out from the ICC’s treaty-based war crimes-related jurisdiction. After considering the genesis of the provision and the practice arising under Article 124 of the ICC Statute so far, this article considers the arguments for and against the deletion of Article 124 in light of the increasingly small number of accessions to the ICC Statute that have been forthcoming in the last few years. It also analyses the quite strict requirements for the entry into force of the amendment, as well as the effect of the entry into force of the amendment on possible declarations having been made pending such entry into force. It ends by considering the positive effect a continued applicability of Article 124 may have on states so far being reluctant to accede to the ICC Statute.