TY - GEN A1 - Ehrlich, Elias A1 - Kath, Nadja Jeanette A1 - Gaedke, Ursula T1 - The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1390 KW - functional traits KW - community ecology KW - evolution KW - lake KW - mechanisms KW - diversity KW - plankton KW - fitness KW - maintenance KW - coexistence Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-513956 SN - 1866-8372 IS - 6 ER - TY - GEN A1 - Masigol, Hossein A1 - Khodaparast, Seyed Akbar A1 - Mostowfizadeh-Ghalamfarsa, Reza A1 - Rojas-Jimenez, Keilor A1 - Woodhouse, Jason Nicholas A1 - Neubauer, Darshan A1 - Grossart, Hans-Peter T1 - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1395 KW - Achlya KW - Saprolegnia KW - aquatic ecosystems KW - carbon cycling KW - polymer degradation KW - Saprolegniaceae KW - Achlyaceae Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515820 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Crawford, Tim A1 - Karamat, Fazeelat A1 - Lehotai, Nóra A1 - Rentoft, Matilda A1 - Blomberg, Jeanette A1 - Strand, Åsa A1 - Björklund, Stefan T1 - Specific functions for mediator complex subunits from different modules in the transcriptional response of arabidopsis thaliana to abiotic stress T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1399 KW - regulate gene expression KW - signal transduction KW - circadian clock KW - plant Mediator KW - salicylic-acid KW - activation KW - jasmonate KW - network KW - defense KW - MED16 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-513666 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Moradian, Hanieh A1 - Roch, Toralf A1 - Lendlein, Andreas A1 - Gossen, Manfred T1 - mRNA transfection-induced activation of primary human monocytes and macrophages BT - Dependence on carrier system and nucleotide modifcation T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1403 KW - sirna transfection KW - mediated delivery KW - gene delivery KW - efficient KW - immunogenicity KW - lipoplexes KW - cells KW - therapeutics KW - polarization KW - pathways Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515694 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Bäurle, Isabel A1 - Trindade, Inês T1 - Chromatin regulation of somatic abiotic stress memory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1408 KW - abiotic stress KW - chromatin regulation KW - heat stress memory KW - histone modifications, priming KW - transcriptional memory KW - vernalization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516668 SN - 1866-8372 IS - 17 ER - TY - GEN A1 - Obbard, Darren J. A1 - Shi, Mang A1 - Roberts, Katherine E. A1 - Longdon, Ben A1 - Dennis, Alice B. T1 - A new lineage of segmented RNA viruses infecting animals T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1411 KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516040 SN - 1866-8372 IS - 1 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 - GEN A1 - Amen, Rahma A1 - Nagel, Rebecca A1 - Hedt, Maximilian A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1416 KW - ecological speciation KW - feeding behaviour KW - electric fish KW - trophic apparatus KW - evolutionary ecology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-518714 SN - 1866-8372 IS - 3 ER - TY - GEN A1 - Moreno-Romero, Jordi A1 - Probst, Aline V. A1 - Trindade, Inês A1 - Kalyanikrishna, A1 - Engelhorn, Julia A1 - Farrona, Sara T1 - Looking At the Past and Heading to the Future BT - Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1423 KW - EWPC2019 KW - chromatin KW - epigenetics KW - transcription KW - nucleus Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-511942 SN - 1866-8372 ER - TY - GEN A1 - Cao, Xianyong A1 - Tian, Fang A1 - Andreev, Andrei A1 - Anderson, Patricia M. A1 - Lozhkin, Anatoly V. A1 - Bezrukova, Elena A1 - Ni, Jian A1 - Rudaya, Natalia A1 - Stobbe, Astrid A1 - Wieczorek, Mareike A1 - Herzschuh, Ulrike T1 - A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1427 KW - Late Quaternary vegetation KW - Holocene environmental history KW - eastern continental Asia KW - plant macrofossil data KW - late pleistocene KW - paleoenvironmental records KW - Verkhoyansk mountains KW - climate dynamics KW - glacial maximum KW - Northern Asia Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-512438 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Weyrich, Alexandra A1 - Yasar, Selma A1 - Lenz, Dorina A1 - Fickel, Jörns T1 - Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1431 KW - DNA methylation KW - gene-expression KW - CPG Islands KW - stress KW - hyperthermia KW - testis Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516525 SN - 1866-8372 IS - 5-6 ER - TY - GEN A1 - Fichtner, Franziska A1 - Olas, Justyna Jadwiga A1 - Feil, Regina A1 - Watanabe, Mutsumi A1 - Krause, Ursula A1 - Hoefgen, Rainer A1 - Stitt, Mark A1 - Lunn, John Edward T1 - Functional features of Trehalose-6-Phosphate Synthase 1 BT - an essential enzyme in Arabidopsis T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1432 KW - cyanobacterial sucrose-phosphatase KW - trehalose 6-phosphate KW - vegetative growth KW - crystal-structure KW - gene-expression KW - thaliana KW - metabolism KW - phosphorylation KW - reveals KW - proteins Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516532 SN - 1866-8372 IS - 6 ER - TY - GEN A1 - Leimkühler, Silke T1 - The biosynthesis of the molybdenum cofactors in Escherichia coli T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1433 KW - periplasmic nitrate reductase KW - biotin sulfoxide reductase KW - in-vitro-synthesis KW - n-oxide reductase KW - crystal-structure KW - molybdopterin synthase KW - formate dehydrogenase KW - rhodobacter-capsulatus KW - xanthine dehydrogenase KW - converting factor Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516559 SN - 1866-8372 IS - 6 ER - TY - GEN A1 - Weise, Hanna A1 - Auge, Harald A1 - Baessler, Cornelia A1 - Bärlund, Ilona A1 - Bennett, Elena M. A1 - Berger, Uta A1 - Bohn, Friedrich A1 - Bonn, Aletta A1 - Borchardt, Dietrich A1 - Brand, Fridolin A1 - Jeltsch, Florian A1 - Joshi, Jasmin Radha A1 - Grimm, Volker T1 - Resilience trinity BT - Safeguarding ecosystem functioning and services across three different time horizons and decision contexts T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1444 KW - concepts KW - ecosystems KW - ecosystem services provisioning KW - management KW - resilience Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515284 SN - 1866-8372 IS - 4 ER - TY - GEN A1 - Kunstmann, Ruth Sonja A1 - Engström, Olof A1 - Wehle, Marko A1 - Widmalm, Göran A1 - Santer, Mark A1 - Barbirz, Stefanie T1 - Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1417 KW - carbohydrates KW - molecular dynamics simulations KW - NMR spectroscopy KW - protein-carbohydrate interactions KW - surface plasmon resonance Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-519418 SN - 1866-8372 IS - 32 ER - TY - GEN A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Müller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1334 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439317 SN - 1866-8372 IS - 1334 ER - TY - GEN A1 - Gamba, Cristina A1 - Jones, Eppie R. A1 - Teasdale, Matthew D. A1 - McLaughlin, Russell L. A1 - González-Fortes, Gloria M. A1 - Mattiangeli, Valeria A1 - Domboróczki, László A1 - Kővári, Ivett A1 - Pap, Ildikó A1 - Anders, Alexandra A1 - Whittle, Alasdair A1 - Dani, János A1 - Raczky, Pál A1 - Higham, Thomas F. G. A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Pinhasi, Ron T1 - Genome flux and stasis in a five millennium transect of European prehistory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1332 KW - ancient DNA KW - lactase-persistence KW - positive selection KW - patterns KW - sequence KW - farmers KW - pigmentation KW - homozygosity KW - ancestry KW - skin Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437999 SN - 1866-8372 VL - 5 IS - 1332 ER - TY - GEN A1 - Hartmann, Stefanie A1 - Hasenkamp, Natascha A1 - Mayer, Jens A1 - Michaux, Johan A1 - Morand, Serge A1 - Mazzoni, Camila J. A1 - Roca, Alfred L. A1 - Greenwood, Alex D. T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1329 KW - murine leukemia virus KW - endogenous retrovirus KW - Xpr1 KW - XMRV KW - genomic evolution KW - Markov cluster algorithm Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431200 SN - 1866-8372 IS - 1329 ER - TY - GEN A1 - Pajoro, Alice A1 - Madrigal, Pedro A1 - Muiño, Jose M. A1 - Matus, José Tomás A1 - Jin, Jian A1 - Mecchia, Martin A. A1 - Debernardi, Juan M. A1 - Palatnik, Javier F. A1 - Balazadeh, Salma A1 - Arif, Muhammad A1 - Ó’Maoiléidigh, Diarmuid S. A1 - Wellmer, Frank A1 - Krajewski, Pawel A1 - Riechmann, José-Luis A1 - Angenent, Gerco C. A1 - Kaufmann, Kerstin T1 - Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1327 KW - flower development KW - floral organ KW - floral meristem KW - chromatin accessibility KW - growth regulate factor Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431139 SN - 1866-8372 VL - 15 ER - TY - GEN A1 - Meyer, Rhonda Christiane A1 - Kusterer, Barbara A1 - Lisec, Jan A1 - Steinfath, Matthias A1 - Becher, Martina A1 - Scharr, Hanno A1 - Melchinger, Albrecht E. A1 - Selbig, Joachim A1 - Schurr, Ulrich A1 - Willmitzer, Lothar A1 - Altmann, Thomas T1 - QTL analysis of early stage heterosis for biomass in Arabidopsis T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from −31 to 99% for dry weight and from −58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1330 KW - Quantitative Trait Locus KW - recombinant inbred line KW - Quantitative Trait Locus analysis KW - dominance effect KW - recombinant inbred line population Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431272 SN - 1866-8372 IS - 1330 ER -