TY - GEN A1 - Mao, Hailiang A1 - Nakamura, Moritaka A1 - Viotti, Corrado A1 - Grebe, Markus T1 - A framework for lateral membrane trafficking and polar tethering of the PEN3 ATP-Binding cassette transporter T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 909 KW - precursor indole-3-butyric acid KW - GNOM ARF-GEF KW - plasma-membrane KW - exocyst complex KW - auxin transport KW - planar polarity KW - Arabidopsis-thaliana KW - fluorescent protein KW - soil interface KW - cell polarity Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441302 SN - 1866-8372 IS - 909 SP - 2245 EP - 2260 ER - TY - GEN A1 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann-Thünemann, Elke T1 - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. T2 - Frontiers in microbiology N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434 KW - cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179 ER - TY - GEN A1 - Clusella, Pau A1 - Politi, Antonio A1 - Rosenblum, Michael T1 - A minimal model of self-consistent partial synchrony T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - We show that self-consistent partial synchrony in globally coupled oscillatory ensembles is a general phenomenon. We analyze in detail appearance and stability properties of this state in possibly the simplest setup of a biharmonic Kuramoto-Daido phase model as well as demonstrate the effect in limit-cycle relaxational Rayleigh oscillators. Such a regime extends the notion of splay state from a uniform distribution of phases to an oscillating one. Suitable collective observables such as the Kuramoto order parameter allow detecting the presence of an inhomogeneous distribution. The characteristic and most peculiar property of self-consistent partial synchrony is the difference between the frequency of single units and that of the macroscopic field. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 890 KW - synchronization KW - collective dynamics KW - coupled oscillators Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436266 SN - 1866-8372 IS - 890 ER - TY - GEN A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, André A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites T2 - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 435 KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407181 ER - TY - GEN A1 - Ziegler, Moritz O. A1 - Heidbach, Oliver A1 - Reinecker, John A1 - Przybycin, Anna M. A1 - Scheck-Wenderoth, Magdalena T1 - A multi-stage 3-D stress field modelling approach exemplified in the Bavarian Molasse Basin T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The knowledge of the contemporary in situ stress state is a key issue for safe and sustainable subsurface engineering. However, information on the orientation and magnitudes of the stress state is limited and often not available for the areas of interest. Therefore 3-D geomechanical-numerical modelling is used to estimate the in situ stress state and the distance of faults from failure for application in subsurface engineering. The main challenge in this approach is to bridge the gap in scale between the widely scattered data used for calibration of the model and the high resolution in the target area required for the application. We present a multi-stage 3-D geomechanical-numerical approach which provides a state-of-the-art model of the stress field for a reservoir-scale area from widely scattered data records. Therefore, we first use a large-scale regional model which is calibrated by available stress data and provides the full 3-D stress tensor at discrete points in the entire model volume. The modelled stress state is used subsequently for the calibration of a smaller-scale model located within the large-scale model in an area without any observed stress data records. We exemplify this approach with two-stages for the area around Munich in the German Molasse Basin. As an example of application, we estimate the scalar values for slip tendency and fracture potential from the model results as measures for the criticality of fault reactivation in the reservoir-scale model. The modelling results show that variations due to uncertainties in the input data are mainly introduced by the uncertain material properties and missing S-Hmax magnitude estimates needed for a more reliable model calibration. This leads to the conclusion that at this stage the model's reliability depends only on the amount and quality of available stress information rather than on the modelling technique itself or on local details of the model geometry. Any improvements in modelling and increases in model reliability can only be achieved using more high-quality data for calibration. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 556 KW - in-situ stress KW - induced seismicity KW - geothermal-reservoirs KW - geomechanical model KW - fault reactivation KW - alpine foreland KW - map project KW - km depth KW - orientation KW - system Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409806 SN - 1866-8372 IS - 556 ER - TY - GEN A1 - Levermann, Anders A1 - Winkelmann, Ricarda T1 - A simple equation for the melt elevation feedback of ice sheets T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In recent decades, the Greenland Ice Sheet has been losing mass and has thereby contributed to global sea-level rise. The rate of ice loss is highly relevant for coastal protection worldwide. The ice loss is likely to increase under future warming. Beyond a critical temperature threshold, a meltdown of the Greenland Ice Sheet is induced by the self-enforcing feedback between its lowering surface elevation and its increasing surface mass loss: the more ice that is lost, the lower the ice surface and the warmer the surface air temperature, which fosters further melting and ice loss. The computation of this rate so far relies on complex numerical models which are the appropriate tools for capturing the complexity of the problem. By contrast we aim here at gaining a conceptual understanding by deriving a purposefully simple equation for the self-enforcing feedback which is then used to estimate the melt time for different levels of warming using three observable characteristics of the ice sheet itself and its surroundings. The analysis is purely conceptual in nature. It is missing important processes like ice dynamics for it to be useful for applications to sea-level rise on centennial timescales, but if the volume loss is dominated by the feedback, the resulting logarithmic equation unifies existing numerical simulations and shows that the melt time depends strongly on the level of warming with a critical slow-down near the threshold: the median time to lose 10% of the present-day ice volume varies between about 3500 years for a temperature level of 0.5 degrees C above the threshold and 500 years for 5 degrees C. Unless future observations show a significantly higher melting sensitivity than currently observed, a complete meltdown is unlikely within the next 2000 years without significant ice-dynamical contributions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 529 KW - sea-level rise KW - mass-balance KW - climate-change KW - Greenland KW - model KW - glacier KW - projections KW - dynamics KW - impact KW - 21st-Century Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409834 SN - 1866-8372 IS - 529 ER - TY - GEN A1 - Kuik, Friderike A1 - Lauer, Axel A1 - Churkina, Galina A1 - Denier Van der Gon, Hugo Anne Cornelis A1 - Fenner, Daniel A1 - Mar, Kathleen A. A1 - Butler, Tim M. T1 - Air quality modelling in the Berlin–Brandenburg region using WRF-Chem v3.7.1 BT - sensitivity to resolution of model grid and input data T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Air pollution is the number one environmental cause of premature deaths in Europe. Despite extensive regulations, air pollution remains a challenge, especially in urban areas. For studying summertime air quality in the Berlin-Brandenburg region of Germany, the Weather Research and Forecasting Model with Chemistry (WRF-Chem) is set up and evaluated against meteorological and air quality observations from monitoring stations as well as from a field campaign conducted in 2014. The objective is to assess which resolution and level of detail in the input data is needed for simulating urban background air pollutant concentrations and their spatial distribution in the Berlin-Brandenburg area. The model setup includes three nested domains with horizontal resolutions of 15, 3 and 1 km and anthropogenic emissions from the TNO-MACC III inventory. We use RADM2 chemistry and the MADE/SORGAM aerosol scheme. Three sensitivity simulations are conducted updating input parameters to the single-layer urban canopy model based on structural data for Berlin, specifying land use classes on a sub-grid scale (mosaic option) and downscaling the original emissions to a resolution of ca. 1 km x 1 km for Berlin based on proxy data including traffic density and population density. The results show that the model simulates meteorology well, though urban 2m temperature and urban wind speeds are biased high and nighttime mixing layer height is biased low in the base run with the settings described above. We show that the simulation of urban meteorology can be improved when specifying the input parameters to the urban model, and to a lesser extent when using the mosaic option. On average, ozone is simulated reasonably well, but maximum daily 8 h mean concentrations are underestimated, which is consistent with the results from previous modelling studies using the RADM2 chemical mechanism. Particulate matter is underestimated, which is partly due to an underestimation of secondary organic aerosols. NOx (NO + NO2) concentrations are simulated reasonably well on average, but nighttime concentrations are overestimated due to the model's underestimation of the mixing layer height, and urban daytime concentrations are underestimated. The daytime underestimation is improved when using downscaled, and thus locally higher emissions, suggesting that part of this bias is due to deficiencies in the emission input data and their resolution. The results further demonstrate that a horizontal resolution of 3 km improves the results and spatial representativeness of the model compared to a horizontal resolution of 15 km. With the input data (land use classes, emissions) at the level of detail of the base run of this study, we find that a horizontal resolution of 1 km does not improve the results compared to a resolution of 3 km. However, our results suggest that a 1 km horizontal model resolution could enable a detailed simulation of local pollution patterns in the Berlin-Brandenburg region if the urban land use classes, together with the respective input parameters to the urban canopy model, are specified with a higher level of detail and if urban emissions of higher spatial resolution are used. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 531 KW - urban canopy model KW - aqmeii phase-2 KW - Mexico-City KW - Heat-Island KW - ozone KW - performance KW - transport KW - chemistry KW - meteorology KW - simulation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-410131 SN - 1866-8372 IS - 531 ER - TY - GEN A1 - Volckmar, Anna-Lena A1 - Han, Chung-Ting A1 - Pütter, Carolin A1 - Haas, Stefan A1 - Vogel, Carla I. G. A1 - Knoll, Nadja A1 - Struve, Christoph A1 - Göbel, Maria A1 - Haas, Katharina A1 - Herrfurth, Nikolas A1 - Jarick, Ivonne A1 - Grallert, Harald A1 - Schürmann, Annette A1 - Al- Hasani, Hadi A1 - Hebebrand, Johannes A1 - Sauer, Sascha A1 - Hinney, Anke T1 - Analysis of genes involved in body weight regulation by targeted re-sequencing T2 - PLoS ONE N2 - Introduction Genes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing. Methods We enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) >= 99th percentile and 176 lean adults (BMI <= 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults. Results and Conclusion We detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (p(TDT) = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 423 KW - melanocortin-4 receptor gene KW - stimulated glucose-uptake KW - life-style intervention KW - onset extreme obesity KW - genome-wide analysis KW - mass index KW - FTO gene KW - fat mass KW - overweight children KW - diabetes-melllitus Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-410289 ER - TY - GEN A1 - Memczak, Henry A1 - Lauster, Daniel A1 - Kar, Parimal A1 - Di Lella, Santiago A1 - Volkmer, Rudolf A1 - Knecht, Volker A1 - Herrmann, Andreas A1 - Ehrentreich-Förster, Eva A1 - Bier, Frank Fabian A1 - Stöcklein, Walter F. M. T1 - Anti-hemagglutinin antibody derived lead peptides for inhibitors of influenza virus binding T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/MuteSwan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 536 KW - receptor-binding KW - A viruses KW - neutralizing antibody KW - avian influenza KW - origin KW - neuraminidase KW - invection KW - entry KW - sites KW - identification Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-410872 SN - 1866-8372 IS - 536 ER - TY - GEN A1 - Roggenbuck, Dirk A1 - Borghi, Maria Orietta A1 - Somma, Valentina A1 - Büttner, Thomas A1 - Schierack, Peter A1 - Hanack, Katja A1 - Grossi, Claudia A1 - Bodio, Caterina A1 - Macor, Paolo A1 - von Landenberg, Philipp A1 - Boccellato, Francesco A1 - Mahler, Michael A1 - Meroni, Pier Luigi T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption. Results Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs. Conclusions The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 436 KW - Antiphospholipid syndrome KW - Antiphospholipid antibody KW - Phospholipid binding proteins KW - Beta2 - glycoprotein I KW - Line immunoassay Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407211 SN - 1866-8372 IS - 436 ER -