TY - JOUR A1 - Terao, Mineko A1 - Garattini, Enrico A1 - Romão, Maria João A1 - Leimkühler, Silke T1 - Evolution, expression, and substrate specificities of aldehyde oxidase enzymes in eukaryotes JF - The journal of biological chemistry N2 - Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles. KW - metalloenzyme KW - molybdenum KW - mouse KW - drug metabolism KW - flavoprotein KW - xenobiotic KW - oxidase KW - oxygen radicals KW - iron-sulfur protein KW - aldehyde oxidase (AOX) KW - enzyme evolution KW - metal-containing enzyme KW - molybdenum cofactor (Moco) KW - molybdo-flavoenzyme KW - 2Fe-2S cluster KW - flavin adenine dinucleotide (FAD) Y1 - 2020 U6 - https://doi.org/10.1074/jbc.REV119.007741 SN - 0021-9258 SN - 1083-351X VL - 295 IS - 16 SP - 5377 EP - 5389 PB - American Society for Biochemistry and Molecular Biology CY - Rockville ER - TY - JOUR 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 JF - Chemistry – A European Journal 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. KW - carbohydrates KW - molecular dynamics simulations KW - NMR spectroscopy KW - protein-carbohydrate interactions KW - surface plasmon resonance Y1 - 2020 U6 - https://doi.org/10.1002/chem.202000495 SN - 0947-6539 SN - 1521-3765 VL - 26 IS - 32 SP - 7263 EP - 7273 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 JF - Autophagy N2 - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - https://doi.org/10.1080/15548627.2020.1820778 SN - 1554-8635 SN - 1554-8627 VL - 17 IS - 9 SP - 2184 EP - 2199 PB - Taylor & Francis CY - Abingdon ER - TY - JOUR A1 - Leins, Johannes A. A1 - Banitz, Thomas A1 - Grimm, Volker A1 - Drechsler, Martin T1 - High-resolution PVA along large environmental gradients to model the combined effects of climate change and land use timing BT - lessons from the large marsh grasshopper JF - Ecological modelling : international journal on ecological modelling and systems ecology N2 - Both climate change and land use regimes affect the viability of populations, but they are often studied separately. Moreover, population viability analyses (PVAs) often ignore the effects of large environmental gradients and use temporal resolutions that are too coarse to take into account that different stages of a population's life cycle may be affected differently by climate change. Here, we present the High-resolution Large Environmental Gradient (HiLEG) model and apply it in a PVA with daily resolution based on daily climate projections for Northwest Germany. We used the large marsh grasshopper (LMG) as the target species and investigated (1) the effects of climate change on the viability and spatial distribution of the species, (2) the influence of the timing of grassland mowing on the species and (3) the interaction between the effects of climate change and grassland mowing. The stageand cohort-based model was run for the spatially differentiated environmental conditions temperature and soil moisture across the whole study region. We implemented three climate change scenarios and analyzed the population dynamics for four consecutive 20-year periods. Climate change alone would lead to an expansion of the regions suitable for the LMG, as warming accelerates development and due to reduced drought stress. However, in combination with land use, the timing of mowing was crucial, as this disturbance causes a high mortality rate in the aboveground life stages. Assuming the same date of mowing throughout the region, the impact on viability varied greatly between regions due to the different climate conditions. The regional negative effects of the mowing date can be divided into five phases: (1) In early spring, the populations were largely unaffected in all the regions; (2) between late spring and early summer, they were severely affected only in warm regions; (3) in summer, all the populations were severely affected so that they could hardly survive; (4) between late summer and early autumn, they were severely affected in cold regions; and (5) in autumn, the populations were equally affected across all regions. The duration and start of each phase differed slightly depending on the climate change scenario and simulation period, but overall, they showed the same pattern. Our model can be used to identify regions of concern and devise management recommendations. The model can be adapted to the life cycle of different target species, climate projections and disturbance regimes. We show with our adaption of the HiLEG model that high-resolution PVAs and applications on large environmental gradients can be reconciled to develop conservation strategies capable of dealing with multiple stressors. KW - Climate change KW - Land use KW - Population viability analysis KW - Stage-based model KW - High resolution KW - Environmental gradients Y1 - 2020 U6 - https://doi.org/10.1016/j.ecolmodel.2020.109355 SN - 0304-3800 SN - 1872-7026 VL - 440 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Horn, Juliane A1 - Becher, Matthias A. A1 - Johst, Karin A1 - Kennedy, Peter J. A1 - Osborne, Juliet L. A1 - Radchuk, Viktoriia A1 - Grimm, Volker T1 - Honey bee colony performance affected by crop diversity and farmland structure BT - a modeling framework JF - Ecological applications N2 - Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps. KW - apis mellifera KW - BEEHAVE KW - colony viability KW - crop diversity KW - cropping system KW - decline KW - forage availability KW - forage gaps KW - honey bees KW - landscape generator KW - modeling Y1 - 2020 U6 - https://doi.org/10.1002/eap.2216 SN - 1939-5582 SN - 1051-0761 VL - 31 IS - 1 SP - 1 EP - 22 PB - Wiley Periodicals LLC CY - Washington DC ER - TY - JOUR A1 - Witzel, Katja A1 - Abu Risha, Marua A1 - Albers, Philip A1 - Börnke, Frederik A1 - Hanschen, Franziska S. T1 - Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; Börnke, Frederike; Hanschen, Franziska S. - Lausanne: Frontiers Media, 2019. - Frontiers in plant science : FPLS. - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552 JF - Frontiers in plant science : FPLS KW - epithionitrile KW - expression profile KW - functional complementation KW - glucosinolate hydrolysis KW - nitrile KW - specifier proteins KW - tissue KW - specificity Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2020.00523 SN - 1664-462X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR 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 JF - Aquatic Ecology 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. KW - Achlya KW - Saprolegnia KW - aquatic ecosystems KW - carbon cycling KW - polymer degradation KW - Saprolegniaceae KW - Achlyaceae Y1 - 2020 U6 - https://doi.org/10.1007/s10452-019-09745-w SN - 1573-5125 SN - 1386-2588 VL - 54 IS - 1 SP - 323 EP - 336 PB - Springer Science CY - Dordrecht ER - TY - JOUR 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 JF - Scientific reports 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. 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 - https://doi.org/10.1038/s41598-020-60506-4 SN - 2045-2322 VL - 10 IS - 1 SP - 1 EP - 15 PB - Springer Nature CY - London ER - TY - JOUR 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 JF - Virus Evolution 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. KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - https://doi.org/10.1093/ve/vez061 SN - 2057-1577 VL - 6 IS - 1 SP - 1 EP - 10 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR 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 JF - Metabolites 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. 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 - https://doi.org/10.3390/metabo10040148 SN - 2218-1989 VL - 10 IS - 4 SP - 1 EP - 18 PB - MDPI CY - Basel ER - TY - JOUR 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 JF - Evolutionary Ecology 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. KW - ecological speciation KW - feeding behaviour KW - electric fish KW - trophic apparatus KW - evolutionary ecology Y1 - 2020 U6 - https://doi.org/10.1007/s10682-020-10043-3 SN - 0269-7653 SN - 1573-8477 VL - 34 IS - 3 SP - 427 EP - 437 PB - Springer Science CY - Dordrecht ER - TY - JOUR 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 JF - Frontiers in Plant Science 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. KW - EWPC2019 KW - chromatin KW - epigenetics KW - transcription KW - nucleus Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2019.01795 SN - 1664-462X VL - 10 IS - 1795 SP - 1 EP - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR 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 JF - Earth System Science Data 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. 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 - https://doi.org/10.5194/essd-12-119-2020 SN - 1866-3508 SN - 1866-3516 VL - 12 IS - 1 SP - 119 EP - 135 PB - Copernics Publications CY - Katlenburg-Lindau ER - TY - JOUR 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 JF - The Plant Cell 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. 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 - https://doi.org/10.1105/tpc.19.00837 SN - 0032-0781 SN - 1471-9053 VL - 32 IS - 6 SP - 1949 EP - 1972 PB - Oxford University Press CY - Oxford ER - TY - JOUR 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 JF - Oikos 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. KW - concepts KW - ecosystems KW - ecosystem services provisioning KW - management KW - resilience Y1 - 2020 U6 - https://doi.org/10.1111/oik.07213 SN - 0030-1299 SN - 1600-0706 VL - 129 IS - 4 SP - 445 EP - 456 PB - Wiley-Blackwell CY - Oxford ER - TY - JOUR A1 - Gryzik, Stefanie A1 - Hoang, Yen A1 - Lischke, Timo A1 - Mohr, Elodie A1 - Venzke, Melanie A1 - Kadner, Isabelle A1 - Pötzsch, Josephine A1 - Groth, Detlef A1 - Radbruch, Andreas A1 - Hutloff, Andreas A1 - Baumgrass, Ria T1 - Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception JF - eLife N2 - Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21(+) IFN-gamma(high) PD-1(low) CD40L(high) CXCR5(-) Bcl-6(-) T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-alpha and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties. Y1 - 2020 U6 - https://doi.org/10.7554/eLife.53226 SN - 2050-084X VL - 9 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Yuan, Junxia A1 - Sheng, Guilian A1 - Preick, Michaela A1 - Sun, Boyang A1 - Hou, Xindong A1 - Chen, Shungang A1 - Taron, Ulrike Helene A1 - Barlow, Axel A1 - Wang, Linying A1 - Hu, Jiaming A1 - Deng, Tao A1 - Lai, Xulong A1 - Hofreiter, Michael T1 - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species. KW - Equus dalianensis KW - Equus przewalskii KW - Pleistocene caballine horses KW - ancient DNA KW - phylogenetic relationship KW - divergence time Y1 - 2020 U6 - https://doi.org/10.1016/j.quascirev.2020.106691 SN - 0277-3791 VL - 250 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Botero, David A1 - Monk, Jonathan A1 - Rodriguez Cubillos, Maria Juliana A1 - Rodriguez Cubillos, Andres Eduardo A1 - Restrepo, Mariana A1 - Bernal-Galeano, Vivian A1 - Reyes, Alejandro A1 - Gonzalez Barrios, Andres A1 - Palsson, Bernhard O. A1 - Restrepo, Silvia A1 - Bernal, Adriana T1 - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis BT - an approach to elucidate pathogenicity at the metabolic level JF - Frontiers in genetics N2 - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species. KW - Xanthomonas KW - Xpm KW - cassava bacterial blight KW - genome-scale metabolic KW - model KW - quorum sensing Y1 - 2020 U6 - https://doi.org/10.3389/fgene.2020.00837 SN - 1664-8021 VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Navazo, Bárbara A1 - Oyhenart, Evelia A1 - Dahinten, Silvia A1 - Mumm, Rebekka A1 - Scheffler, Christiane T1 - Decrease of external skeletal robustness (Frame Index) between two cohorts of school children living in Puerto Madryn, Argentina at the beginning of the 21st century JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger N2 - Background: It has been shown that modern life style with reduced physical activity can lead to lower bone accumulation. Also a decline trend in external skeletal robustness in children and young adolescents, measured by the Frame Index (FI), seems to have a parallel trend with the increase in overweight and obesity. Based on these findings we estimate that likely, the FI should be changed after a decade in the Argentinean population as well as in others population of the world. Thereby, the aim of the present study was to describe, using the FI, the pattern of external skeletal robustness in school children aged 6-14 years from two cohorts of Argentina (Puerto Madryn, Chubut) and to compare them with the European reference (Czech Republic, Germany, Poland and Russia). Methods: Elbow breadth and height of Puerto Madryn school children were collected in two cross-sectional studies conducted between 2001-2006 (cohort 1 = C1) and 2014-2016 (cohort 2 = C2). Percentiles (P) values, for males and females, from C1 and C2 were calculated combining the LMSmethod and its extension. A t-test has been used to compare, by age and sex, the FI values between the Argentinean cohorts and the European reference (ER). Then, in order to know the percentage of the variation of the percentiles values between cohorts, as well as with ER, percent differences between means (PDM%) were employed. Results: FI from Argentinean cohorts differed significantly from ER. Even more, C2 was not only smaller than ER, but also than C1. In males, C1-C2 showed significant differences at 6-8, 11 and 12 years and in females at all ages. Then, respect to ER each Argentinean cohort showed significant differences in males of C1 at 6, 12-14 years and in females at 6 and 11-14 years; and of C2, in both sexes, from 6 to 14 years. The PDM% values for elbow breadth of male were negative in ER-C1 in all percentiles analyzed; in ER-C2 positive (P3 and P50) and negative (P97) and C1-C2 recorded positive values. In females, elbow breadth showed negative values for ER-C1 (P50 and P97), and positive for the remaining values. Finally, height registered, in both sexes, negative values in ER-C1 (except P97 in females), ER-C2 and C1-C2. Conclusions: After ten years of the first study carried on in Puerto Madryn, school children show a negative trend in the external skeletal robustness. Additionally, the children of both Argentinean cohorts have lower values compared to the European reference, and mainly the actual cohort. This situation would be explained, in part, by the progressive increase over time of overweight and obesity as consequence, among others, of the change in the quantity and/or quality of the food that children have access to and with the physical activity they do at school and outside. KW - elbow breadth KW - height KW - skeletal robustness KW - school children KW - Argentina Y1 - 2020 U6 - https://doi.org/10.1127/anthranz/2020/1182 SN - 0003-5548 SN - 2363-7099 VL - 77 IS - 5 SP - 405 EP - 413 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - De Cahsan, Binia A1 - Nagel, Rebecca A1 - Schedina, Ina-Maria A1 - King, James J. A1 - Bianco, Pier G. A1 - Tiedemann, Ralph A1 - Ketmaier, Valerio T1 - Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data JF - Journal of fish biology N2 - The European river lamprey Lampetra fluviatilis and the European brook lamprey Lampetra planeri (Block 1784) are classified as a paired species, characterized by notably different life histories but morphological similarities. Previous work has further shown limited genetic differentiation between these two species at the mitochondrial DNA level. Here, we expand on this previous work, which focused on lamprey species from the Iberian Peninsula in the south and mainland Europe in the north, by sequencing three mitochondrial marker regions of Lampetra individuals from five river systems in Ireland and five in southern Italy. Our results corroborate the previously identified pattern of genetic diversity for the species pair. We also show significant genetic differentiation between Irish and mainland European lamprey populations, suggesting another ichthyogeographic district distinct from those previously defined. Finally, our results stress the importance of southern Italian L. planeri populations, which maintain several private alleles and notable genetic diversity. KW - European lamprey KW - Lampetra KW - paired species KW - phylogeography KW - population KW - structure Y1 - 2020 U6 - https://doi.org/10.1111/jfb.14279 SN - 0022-1112 SN - 1095-8649 VL - 96 IS - 4 SP - 905 EP - 912 PB - Wiley-Blackwell CY - Oxford [u.a.] ER -