TY - GEN A1 - Olayide, Priscilla A1 - Large, Annabel A1 - Stridh, Linnea A1 - Rabbi, Ismail A1 - Baldermann, Susanne A1 - Stavolone, Livia A1 - Alexandersson, Erik T1 - Gene expression and metabolite profiling of thirteen Nigerian cassava landraces to elucidate starch and carotenoid composition T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The prevalence of vitamin A deficiency in sub-Saharan Africa necessitates effective approaches to improve provitamin A content of major staple crops. Cassava holds much promise for food security in sub-Saharan Africa, but a negative correlation between beta-carotene, a provitamin A carotenoid, and dry matter content has been reported, which poses a challenge to cassava biofortification by conventional breeding. To identify suitable material for genetic transformation in tissue culture with the overall aim to increase beta-carotene and maintain starch content as well as better understand carotenoid composition, root and leaf tissues from thirteen field-grown cassava landraces were analyzed for agronomic traits, carotenoid, chlorophyll, and starch content. The expression of five genes related to carotenoid biosynthesis were determined in selected landraces. Analysis revealed a weak negative correlation between starch and beta-carotene content, whereas there was a strong positive correlation between root yield and many carotenoids including beta-carotene. Carotenoid synthesis genes were expressed in both white and yellow cassava roots, but phytoene synthase 2 (PSY2), lycopene-epsilon-cyclase (LCY epsilon), and beta-carotenoid hydroxylase (CHY beta) expression were generally higher in yellow roots. This study identified lines with reasonably high content of starch and beta-carotene that could be candidates for biofortification by further breeding or plant biotechnological means. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1415 KW - carotenoid biosynthesis KW - ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) KW - provitamin A KW - biofortification Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-517834 SN - 1866-8372 IS - 3 ER - TY - GEN A1 - Riaño-Pachón, Diego Mauricio A1 - Kleessen, Sabrina A1 - Neigenfind, Jost A1 - Durek, Pawel A1 - Weber, Elke A1 - Engelsberger, Wolfgang R. A1 - Walther, Dirk A1 - Selbig, Joachim A1 - Schulze, Waltraud X. A1 - Kersten, Birgit T1 - Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. Results: From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented. These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. Conclusions: We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1328 KW - Gene Ontology KW - Phosphorylation Site KW - phosphorylated amino acid KW - slim term KW - single nucleotide polymorphism mapping Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431181 SN - 1866-8372 IS - 1328 ER - TY - GEN A1 - Schwarze, Thomas A1 - Riemer, Janine A1 - Müller, Holger A1 - John, Leonard A1 - Holdt, Hans‐Jürgen A1 - Wessig, Pablo T1 - Na+ Selective Fluorescent Tools Based on Fluorescence Intensity Enhancements, Lifetime Changes, and on a Ratiometric Response T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Over the years, we developed highly selective fluorescent probes for K+ in water, which show K+-induced fluorescence intensity enhancements, lifetime changes, or a ratiometric behavior at two emission wavelengths (cf. Scheme 1, K1-K4). In this paper, we introduce selective fluorescent probes for Na+ in water, which also show Na+ induced signal changes, which are analyzed by diverse fluorescence techniques. Initially, we synthesized the fluorescent probes 2, 4, 5, 6 and 10 for a fluorescence analysis by intensity enhancements at one wavelength by varying the Na+ responsive ionophore unit and the fluorophore moiety to adjust different K-d values for an intra- or extracellular Na+ analysis. Thus, we found that 2, 4 and 5 are Na+ selective fluorescent tools, which are able to measure physiologically important Na+ levels at wavelengths higher than 500 nm. Secondly, we developed the fluorescent probes 7 and 8 to analyze precise Na+ levels by fluorescence lifetime changes. Herein, only 8 (K-d=106 mm) is a capable fluorescent tool to measure Na+ levels in blood samples by lifetime changes. Finally, the fluorescent probe 9 was designed to show a Na+ induced ratiometric fluorescence behavior at two emission wavelengths. As desired, 9 (K-d=78 mm) showed a ratiometric fluorescence response towards Na+ ions and is a suitable tool to measure physiologically relevant Na+ levels by the intensity change of two emission wavelengths at 404 nm and 492 nm. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1136 KW - crown compounds KW - fluorescence lifetime KW - fluorescent probes KW - ratiometric KW - sodium Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437482 SN - 1866-8372 IS - 1136 ER - TY - GEN A1 - Pauly, Maren A1 - Helle, Gerhard A1 - Miramont, Cécile A1 - Büntgen, Ulf A1 - Treydte, Kerstin A1 - Reinig, Frederick A1 - Guibal, Frédéric A1 - Sivan, Olivier A1 - Heinrich, Ingo A1 - Riedel, Frank A1 - Kromer, Bernd A1 - Balanzategui, Daniel A1 - Wacker, Lukas A1 - Sookdeo, Adam Sookdeo A1 - Brauer, Achim T1 - Subfossil trees suggest enhanced Mediterranean hydroclimate variability at the onset of the Younger Dryas T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Nearly 13,000 years ago, the warming trend into the Holocene was sharply interrupted by a reversal to near glacial conditions. Climatic causes and ecological consequences of the Younger Dryas (YD) have been extensively studied, however proxy archives from the Mediterranean basin capturing this period are scarce and do not provide annual resolution. Here, we report a hydroclimatic reconstruction from stable isotopes (delta O-18, delta C-13) in subfossil pines from southern France. Growing before and during the transition period into the YD (12 900-12 600 cal BP), the trees provide an annually resolved, continuous sequence of atmospheric change. Isotopic signature of tree sourcewater (delta O-18(sw)) and estimates of relative air humidity were reconstructed as a proxy for variations in air mass origin and precipitation regime. We find a distinct increase in inter-annual variability of sourcewater isotopes (delta O-18(sw)), with three major downturn phases of increasing magnitude beginning at 12 740 cal BP. The observed variation most likely results from an amplified intensity of North Atlantic (low delta O-18(sw)) versus Mediterranean (high delta O-18(sw)) precipitation. This marked pattern of climate variability is not seen in records from higher latitudes and is likely a consequence of atmospheric circulation oscillations at the margin of the southward moving polar front. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1135 KW - annually laminated sediments KW - lake Meerfelder Maar KW - isotopic composition KW - oxygen isotope KW - climate KW - cellulose KW - radiocarbon KW - temperature KW - record KW - model Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459169 SN - 1866-8372 IS - 1135 ER - TY - GEN A1 - Manzoni, Stefano A1 - Čapek, Petr A1 - Porada, Philipp A1 - Thurner, Martin A1 - Winterdahl, Mattias A1 - Beer, Christian A1 - Brüchert, Volker A1 - Frouz, Jan A1 - Herrmann, Anke M. A1 - Lindahl, Björn D. A1 - Lyon, Steve W. A1 - Šantrůčková, Hana A1 - Vico, Giulia A1 - Way, Danielle T1 - Reviews and syntheses BT - carbon use efficiency from organisms to ecosystems – definitions, theories, and empirical evidence T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The cycling of carbon (C) between the Earth surface and the atmosphere is controlled by biological and abiotic processes that regulate C storage in biogeochemical compartments and release to the atmosphere. This partitioning is quantified using various forms of C-use efficiency (CUE) - the ratio of C remaining in a system to C entering that system. Biological CUE is the fraction of C taken up allocated to biosynthesis. In soils and sediments, C storage depends also on abiotic processes, so the term C-storage efficiency (CSE) can be used. Here we first review and reconcile CUE and CSE definitions proposed for autotrophic and heterotrophic organisms and communities, food webs, whole ecosystems and watersheds, and soils and sediments using a common mathematical framework. Second, we identify general CUE patterns; for example, the actual CUE increases with improving growth conditions, and apparent CUE decreases with increasing turnover. We then synthesize > 5000CUE estimates showing that CUE decreases with increasing biological and ecological organization - from uni-cellular to multicellular organisms and from individuals to ecosystems. We conclude that CUE is an emergent property of coupled biological-abiotic systems, and it should be regarded as a flexible and scale-dependent index of the capacity of a given system to effectively retain C. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1134 KW - gross primary production KW - net primary production KW - plant respiration KW - microbial carbon KW - stoichiometric controls KW - growth efficiency KW - bacterial growth KW - excess carbon KW - soil KW - matter Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446386 SN - 1866-8372 IS - 1134 ER - TY - GEN A1 - Odongo, Grace Akinyi A1 - Schlotz, Nina A1 - Baldermann, Susanne A1 - Neugart, Susanne A1 - Huyskens-Keil, Susanne A1 - Ngwene, Benard A1 - Trierweiler, Bernhard A1 - Schreiner, Monika A1 - Lamy, Evelyn T1 - African nightshade (Solanum scabrum Mill.) BT - impact of cultivation and plant processing on its health promoting potential as determined in a human liver cell model T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Plant cultivation and processing may impact nutrient and phytochemical content of vegetables. The present study aimed at determining the influence of cultivation and processing on the health promoting capacity of African nightshade (Solanum scabrum Mill.) leaves, an indigenous vegetable, rich in nutrients and phytochemicals. Anti-genotoxicity against the human liver carcinogen aflatoxin B1 (AFB1) as determined by the comet assay and radical oxygen species (ROS) scavenging capacity of ethanolic and aqueous extracts were investigated in human derived liver (HepG2) cells. ROS scavenging activity was assessed using electron paramagnetic spin resonance and quantification of ARE/Nrf2 mediated gene expression. The cultivation was done under different environmental conditions. The processing included fermentation and cooking; postharvest ultraviolet irradiation (UV-C) treatment was also investigated. Overall, S. scabrum extracts showed strong health promoting potential, the highest potential was observed with the fermented extract, which showed a 60% reduction of AFB1 induced DNA damage and a 38% reduction in FeSO4 induced oxidative stress. The content of total polyphenols, carotenoids and chlorophylls was indeed affected by cultivation and processing. Based on the present in vitro findings consumption of S. scabrum leaves could be further encouraged, preferentially after cooking or fermentation of the plant. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1133 KW - aflatoxin B1 KW - African indigenous vegetables KW - anti-genotoxicity KW - anti-oxidant activity KW - cancer chemoprevention KW - Solanaceae Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459114 SN - 1866-8372 IS - 1133 ER - TY - GEN A1 - Asgarimehr, Milad A1 - Wickert, Jens A1 - Reich, Sebastian T1 - Evaluating impact of rain attenuation on space-borne GNSS Reflectometry wind speeds T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The novel space-borne Global Navigation Satellite System Reflectometry (GNSS-R) technique has recently shown promise in monitoring the ocean state and surface wind speed with high spatial coverage and unprecedented sampling rate. The L-band signals of GNSS are structurally able to provide a higher quality of observations from areas covered by dense clouds and under intense precipitation, compared to those signals at higher frequencies from conventional ocean scatterometers. As a result, studying the inner core of cyclones and improvement of severe weather forecasting and cyclone tracking have turned into the main objectives of GNSS-R satellite missions such as Cyclone Global Navigation Satellite System (CYGNSS). Nevertheless, the rain attenuation impact on GNSS-R wind speed products is not yet well documented. Evaluating the rain attenuation effects on this technique is significant since a small change in the GNSS-R can potentially cause a considerable bias in the resultant wind products at intense wind speeds. Based on both empirical evidence and theory, wind speed is inversely proportional to derived bistatic radar cross section with a natural logarithmic relation, which introduces high condition numbers (similar to ill-posed conditions) at the inversions to high wind speeds. This paper presents an evaluation of the rain signal attenuation impact on the bistatic radar cross section and the derived wind speed. This study is conducted simulating GNSS-R delay-Doppler maps at different rain rates and reflection geometries, considering that an empirical data analysis at extreme wind intensities and rain rates is impossible due to the insufficient number of observations from these severe conditions. Finally, the study demonstrates that at a wind speed of 30 m/s and incidence angle of 30 degrees, rain at rates of 10, 15, and 20 mm/h might cause overestimation as large as approximate to 0.65 m/s (2%), 1.00 m/s (3%), and 1.3 m/s (4%), respectively, which are still smaller than the CYGNSS required uncertainty threshold. The simulations are conducted in a pessimistic condition (severe continuous rainfall below the freezing height and over the entire glistening zone) and the bias is expected to be smaller in size in real environments. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1132 KW - GNSS Reflectometry KW - wind speed KW - rain effect KW - rain attenuation KW - DDM simulation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-473441 SN - 1866-8372 IS - 1132 ER - TY - GEN A1 - Hildebrandt, Dieter T1 - A software reference architecture for service-oriented 3D geovisualization systems T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Modern 3D geovisualization systems (3DGeoVSs) are complex and evolving systems that are required to be adaptable and leverage distributed resources, including massive geodata. This article focuses on 3DGeoVSs built based on the principles of service-oriented architectures, standards and image-based representations (SSI) to address practically relevant challenges and potentials. Such systems facilitate resource sharing and agile and efficient system construction and change in an interoperable manner, while exploiting images as efficient, decoupled and interoperable representations. The software architecture of a 3DGeoVS and its underlying visualization model have strong effects on the system's quality attributes and support various system life cycle activities. This article contributes a software reference architecture (SRA) for 3DGeoVSs based on SSI that can be used to design, describe and analyze concrete software architectures with the intended primary benefit of an increase in effectiveness and efficiency in such activities. The SRA integrates existing, proven technology and novel contributions in a unique manner. As the foundation for the SRA, we propose the generalized visualization pipeline model that generalizes and overcomes expressiveness limitations of the prevalent visualization pipeline model. To facilitate exploiting image-based representations (IReps), the SRA integrates approaches for the representation, provisioning and styling of and interaction with IReps. Five applications of the SRA provide proofs of concept for the general applicability and utility of the SRA. A qualitative evaluation indicates the overall suitability of the SRA, its applications and the general approach of building 3DGeoVSs based on SSI. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1131 KW - 3D geovisualization KW - software reference architecture KW - spatial data infrastructure KW - service-oriented architecture KW - standardization KW - image-based representation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-475831 SN - 1866-8372 IS - 1131 ER - TY - GEN A1 - Reindl, Nicole A1 - Finch, Nicolle L. A1 - Schaffenroth, Veronika A1 - Barstow, Martin A. A1 - Casewell, Sarah L. A1 - Geier, Stephan Alfred A1 - Bertolami Miller, Marcelo Miguel A1 - Taubenberger, Stefan T1 - Revealing the true nature of Hen2-428 T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The nucleus of Hen 2-428 is a short orbital period (4.2 h) spectroscopic binary, whose status as potential supernovae type Ia progenitor has raised some controversy in the literature. We present preliminary results of a thorough analysis of this interesting system, which combines quantitative non-local thermodynamic (non-LTE) equilibrium spectral modelling, radial velocity analysis, multi-band light curve fitting, and state-of-the art stellar evolutionary calculations. Importantly, we find that the dynamical system mass that is derived by using all available He II lines does not exceed the Chandrasekhar mass limit. Furthermore, the individual masses of the two central stars are too small to lead to an SN Ia in case of a dynamical explosion during the merger process. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1129 KW - binaries: spectroscopic KW - stars: atmospheres KW - stars: abundances KW - Supernovae Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459703 SN - 1866-8372 IS - 1129 ER - TY - GEN A1 - Hodgkins, Suzanne B. A1 - Richardson, Curtis J. A1 - Dommain, René A1 - Wang, Hongjun A1 - Glaser, Paul H. A1 - Verbeke, Brittany A1 - Winkler, B. Rose A1 - Cobb, Alexander R. A1 - Rich, Virginia I. A1 - Missilmani, Malak A1 - Flanagan, Neal A1 - Ho, Mengchi A1 - Hoyt, Alison M. A1 - Harvey, Charles F. A1 - Vining, S. Rose A1 - Hough, Moira A. A1 - Moore, Tim R. A1 - Richard, Pierre J. H. A1 - De La Cruz, Florentino B. A1 - Toufaily, Joumana A1 - Hamdan, Rasha A1 - Cooper, William T. A1 - Chanton, Jeffrey P. T1 - Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Peatlands represent large terrestrial carbon banks. Given that most peat accumulates in boreal regions, where low temperatures and water saturation preserve organic matter, the existence of peat in (sub)tropical regions remains enigmatic. Here we examined peat and plant chemistry across a latitudinal transect from the Arctic to the tropics. Near-surface low-latitude peat has lower carbohydrate and greater aromatic content than near-surface high-latitude peat, creating a reduced oxidation state and resulting recalcitrance. This recalcitrance allows peat to persist in the (sub)tropics despite warm temperatures. Because we observed similar declines in carbohydrate content with depth in high-latitude peat, our data explain recent field-scale deep peat warming experiments in which catotelm (deeper) peat remained stable despite temperature increases up to 9 degrees C. We suggest that high-latitude deep peat reservoirs may be stabilized in the face of climate change by their ultimately lower carbohydrate and higher aromatic composition, similar to tropical peats. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1125 KW - dissolved organic matter KW - greenhouse gas fluxes KW - permafrost thaw KW - Northern Minnesota KW - FTIR spectroscopy KW - lignin content KW - brown rot KW - decomposition KW - chemistry KW - dynamics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459658 SN - 1866-8372 IS - 1125 ER - TY - GEN A1 - Couto, Rafael C. A1 - Cruz, Vinicius V. A1 - Ertan, Emelie A1 - Eckert, Sebastian A1 - Fondell, Mattis A1 - Dantz, Marcus A1 - Kennedy, Brian A1 - Schmitt, Thorsten A1 - Pietzsch, Annette A1 - Guimarães, Freddy F. A1 - Ågren, Hans A1 - Gel’mukhanov, Faris A1 - Odelius, Michael A1 - Kimberg, Victor A1 - Föhlisch, Alexander T1 - Selective gating to vibrational modes through resonant X-ray scattering T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1124 KW - potential-energy surface KW - raman-scattering KW - water-vapor KW - spectroscopy KW - chemistry KW - molecule KW - spectrum KW - CM(-1) KW - states KW - NM Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436926 SN - 1866-8372 IS - 1124 ER - TY - GEN A1 - Prát, Tomáš A1 - Hajny ́, Jakub A1 - Grunewald, Wim A1 - Vasileva, Mina A1 - Molnár, Gergely A1 - Tejos, Ricardo A1 - Schmid, Markus A1 - Sauer, Michael A1 - Friml, Jiří T1 - WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17-and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain-and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1123 KW - apical-basal axis KW - arabidopsis-thaliana KW - root gravitropism KW - DNA-binding KW - gene-expression KW - transport KW - efflux KW - canalization KW - plants KW - phosphorylation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446331 SN - 1866-8372 IS - 1123 ER - TY - GEN A1 - Küken, Anika A1 - Sommer, Frederik A1 - Yaneva-Roder, Liliya A1 - Mackinder, Luke C.M. A1 - Höhne, Melanie A1 - Geimer, Stefan A1 - Jonikas, Martin C. A1 - Schroda, Michael A1 - Stitt, Mark A1 - Nikoloski, Zoran A1 - Mettler-Altmann, Tabea T1 - Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1122 KW - carbon concentrating mechanism KW - B12-dependent 1,2-propanediol degradation KW - green algae KW - co2 concentrating mechanism KW - salmonella typhimurium KW - co2 concentration KW - enzyme activities KW - anhydrase CAH3 KW - protein KW - expression Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446358 SN - 1866-8372 IS - 1122 ER - TY - GEN A1 - Eckert, Sebastian A1 - Norell, Jesper A1 - Miedema, Piter S. A1 - Beye, Martin A1 - Fondell, Mattis A1 - Quevedo, Wilson A1 - Kennedy, Brian A1 - Hantschmann, Markus A1 - Pietzsch, Annette A1 - van Kuiken, Benjamin E. A1 - Ross, Matthew A1 - Minitti, Michael P. A1 - Moeller, Stefan P. A1 - Schlotter, William F. A1 - Khalil, Munira A1 - Odelius, Michael A1 - Föhlisch, Alexander T1 - Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort time-scale. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1115 KW - nitrogen KW - photochemistry KW - protonation KW - RIXS (resonant inelastic X-ray scattering) KW - selective bond cleavage Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436873 SN - 1866-8372 IS - 1115 ER - TY - GEN A1 - Licht, Alexis A1 - Dupont-Nivet, Guillaume A1 - Pullen, Alex A1 - Kapp, Paul A1 - Abels, Hemmo A. A1 - Lai, Zulong A1 - Guo, ZhaoJie A1 - Abell, Jordan A1 - Giesler, Dominique T1 - Resilience of the Asian atmospheric circulation shown by paleogene dust provenance T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The onset of modern central Asian atmospheric circulation is traditionally linked to the interplay of surface uplift of the Mongolian and Tibetan-Himalayan orogens, retreat of the Paratethys sea from central Asia and Cenozoic global cooling. Although the role of these players has not yet been unravelled, the vast dust deposits of central China support the presence of arid conditions and modern atmospheric pathways for the last 25 million years (Myr). Here, we present provenance data from older (42-33 Myr) dust deposits, at a time when the Tibetan Plateau was less developed, the Paratethys sea still present in central Asia and atmospheric pCO(2) much higher. Our results show that dust sources and near-surface atmospheric circulation have changed little since at least 42 Myr. Our findings indicate that the locus of central Asian high pressures and concurrent aridity is a resilient feature only modulated by mountain building, global cooling and sea retreat. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1114 KW - Chinese Loess Plateau KW - last glacial maximum KW - Tibetan Plateau KW - Yellow-River KW - climate KW - basin KW - evolution KW - ardification KW - monsoons KW - desert Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436381 SN - 1866-8372 IS - 1114 ER - TY - GEN A1 - Xiong, Chao A1 - Stolle, Claudia A1 - Lühr, Hermann A1 - Park, Jaeheung A1 - Fejer, Bela G. A1 - Kervalishvili, Guram N. T1 - Scale analysis of equatorial plasma irregularities derived from Swarm constellation T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In this study, we investigated the scale sizes of equatorial plasma irregularities (EPIs) using measurements from the Swarm satellites during its early mission and final constellation phases. We found that with longitudinal separation between Swarm satellites larger than 0.4°, no significant correlation was found any more. This result suggests that EPI structures include plasma density scale sizes less than 44 km in the zonal direction. During the Swarm earlier mission phase, clearly better EPI correlations are obtained in the northern hemisphere, implying more fragmented irregularities in the southern hemisphere where the ambient magnetic field is low. The previously reported inverted-C shell structure of EPIs is generally confirmed by the Swarm observations in the northern hemisphere, but with various tilt angles. From the Swarm spacecrafts with zonal separations of about 150 km, we conclude that larger zonal scale sizes of irregularities exist during the early evening hours (around 1900 LT). T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1112 KW - Equatorial plasma irregularities KW - ionospheric scale lengths KW - Swarm constellation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431842 SN - 1866-8372 IS - 1112 ER - TY - GEN A1 - Wurzbacher, Christian A1 - Fuchs, Andrea A1 - Attermeyer, Katrin A1 - Frindte, Katharina A1 - Grossart, Hans-Peter A1 - Hupfer, Michael A1 - Casper, Peter A1 - Monaghan, Michael T. T1 - Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1–4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5–14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper “replacement horizon” is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower “depauperate horizon” is characterized by low taxonomic richness, more stable “low-energy” conditions, and a dominance of enigmatic Archaea. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1111 KW - Archaea KW - Eukaryota KW - Bacteria KW - community KW - freshwater KW - lake KW - DNA metabarcoding KW - beta-diversity KW - sediment KW - turnover Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431965 SN - 1866-8372 IS - 1111 ER - TY - GEN A1 - Plöhn, Svenja A1 - Edelmann, Bärbel A1 - Japtok, Lukasz A1 - He, Xingxuan A1 - Hose, Matthias A1 - Hansen, Wiebke A1 - Schuchman, Edward H. A1 - Eckstein, Anja A1 - Berchner-Pfannschmidt, Utta T1 - CD40 enhances sphingolipids in orbital fibroblasts BT - potential role of sphingosine-1-phosphate in inflammatory T-cell migration in Graves' orbitopathy T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - PURPOSE. Graves' orbitopathy (GO) is an autoimmune orbital disorder associated with Graves' disease caused by thyrotropin receptor autoantibodies. Orbital fibroblasts (OFs) and CD40 play a key role in disease pathogenesis. The bioactive lipid sphingosine-1-phosphate (S1P) has been implicated in promoting adipogenesis, fibrosis, and inflammation in OFs. We investigated the role of CD40 signaling in inducing S1P activity in orbital inflammation. METHODS. OFs and T cells were derived from GO patients and healthy control (Ctl) persons. S1P abundance in orbital tissues was evaluated by immunofluorescence. OFs were stimulated with CD40 ligand and S1P levels were determined by ELISA. Further, activities of acid sphingomyelinase (ASM), acid ceramidase, and sphingosine kinase were measured by ultraperformance liquid chromatography. Sphingosine and ceramide contents were analyzed by mass spectrometry. Finally, the role for S1P in T-cell attraction was investigated by T-cell migration assays. RESULTS. GO orbital tissue showed elevated amounts of S1P as compared to control samples. Stimulation of CD40 induced S1P expression in GO-derived OFs, while Ctl-OFs remained unaffected. A significant increase of ASM and sphingosine kinase activities, as well as lipid formation, was observed in GO-derived OFs. Migration assay of T cells in the presence of SphK inhibitor revealed that S1P released by GO-OFs attracted T cells for migration. CONCLUSIONS. The results demonstrated that CD40 ligand stimulates GO fibroblast to produce S1P, which is a driving force for T-cell migration. The results support the use of S1P receptor signaling modulators in GO management. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1099 KW - Grave’s orbitopathy KW - sphingosine-1-phosphate KW - sphingolipids KW - inflammation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468837 SN - 1866-8372 IS - 1099 ER - TY - GEN A1 - Schieferdecker, Anne A1 - Wendler, Petra T1 - Structural mapping of missense mutations in the Pex1/Pex6 complex T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1072 KW - Zellweger syndrome spectrum disorder (ZSSD) KW - Zellweger KW - structure KW - Pex1 KW - Pex6 KW - mutation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472843 SN - 1866-8372 IS - 1072 ER - TY - GEN A1 - Ayzel, Georgy A1 - Izhitskiy, Alexander T1 - Climate change impact assessment on freshwater inflow into the Small Aral Sea T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - During the last few decades, the rapid separation of the Small Aral Sea from the isolated basin has changed its hydrological and ecological conditions tremendously. In the present study, we developed and validated the hybrid model for the Syr Darya River basin based on a combination of state-of-the-art hydrological and machine learning models. Climate change impact on freshwater inflow into the Small Aral Sea for the projection period 2007–2099 has been quantified based on the developed hybrid model and bias corrected and downscaled meteorological projections simulated by four General Circulation Models (GCM) for each of three Representative Concentration Pathway scenarios (RCP). The developed hybrid model reliably simulates freshwater inflow for the historical period with a Nash–Sutcliffe efficiency of 0.72 and a Kling–Gupta efficiency of 0.77. Results of the climate change impact assessment showed that the freshwater inflow projections produced by different GCMs are misleading by providing contradictory results for the projection period. However, we identified that the relative runoff changes are expected to be more pronounced in the case of more aggressive RCP scenarios. The simulated projections of freshwater inflow provide a basis for further assessment of climate change impacts on hydrological and ecological conditions of the Small Aral Sea in the 21st Century. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1071 KW - Small Aral Sea KW - hydrology KW - climate change KW - modeling KW - machine learning Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472794 SN - 1866-8372 IS - 1071 ER - TY - GEN A1 - Metin, Ayse Duha A1 - Dung, Nguyen Viet A1 - Schröter, Kai A1 - Guse, Björn A1 - Apel, Heiko A1 - Kreibich, Heidi A1 - Vorogushyn, Sergiy A1 - Merz, Bruno T1 - How do changes along the risk chain affect flood risk? T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Flood risk is impacted by a range of physical and socio-economic processes. Hence, the quantification of flood risk ideally considers the complete flood risk chain, from atmospheric processes through catchment and river system processes to damage mechanisms in the affected areas. Although it is generally accepted that a multitude of changes along the risk chain can occur and impact flood risk, there is a lack of knowledge of how and to what extent changes in influencing factors propagate through the chain and finally affect flood risk. To fill this gap, we present a comprehensive sensitivity analysis which considers changes in all risk components, i.e. changes in climate, catchment, river system, land use, assets, and vulnerability. The application of this framework to the mesoscale Mulde catchment in Germany shows that flood risk can vary dramatically as a consequence of plausible change scenarios. It further reveals that components that have not received much attention, such as changes in dike systems or in vulnerability, may outweigh changes in often investigated components, such as climate. Although the specific results are conditional on the case study area and the selected assumptions, they emphasize the need for a broader consideration of potential drivers of change in a comprehensive way. Hence, our approach contributes to a better understanding of how the different risk components influence the overall flood risk. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1067 KW - global sensitivity analysis KW - climate change KW - river floods KW - frequency KW - Europe KW - model KW - vulnerability KW - adaptation KW - strategies KW - catchment Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468790 SN - 1866-8372 IS - 1067 ER - TY - GEN A1 - Weiskirchen, Sabine A1 - Weiper, Katharina A1 - Tolba, René H. A1 - Weiskirchen, Ralf T1 - All you can feed BT - some comments on production of mouse diets used in biomedical research with special emphasis on non-alcoholic fatty liver disease research T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The laboratory mouse is the most common used mammalian research model in biomedical research. Usually these animals are maintained in germ-free, gnotobiotic, or specific-pathogen-free facilities. In these facilities, skilled staff takes care of the animals and scientists usually don’t pay much attention about the formulation and quality of diets the animals receive during normal breeding and keeping. However, mice have specific nutritional requirements that must be met to guarantee their potential to grow, reproduce and to respond to pathogens or diverse environmental stress situations evoked by handling and experimental interventions. Nowadays, mouse diets for research purposes are commercially manufactured in an industrial process, in which the safety of food products is addressed through the analysis and control of all biological and chemical materials used for the different diet formulations. Similar to human food, mouse diets must be prepared under good sanitary conditions and truthfully labeled to provide information of all ingredients. This is mandatory to guarantee reproducibility of animal studies. In this review, we summarize some information on mice research diets and general aspects of mouse nutrition including nutrient requirements of mice, leading manufacturers of diets, origin of nutrient compounds, and processing of feedstuffs for mice including dietary coloring, autoclaving and irradiation. Furthermore, we provide some critical views on the potential pitfalls that might result from faulty comparisons of grain-based diets with purified diets in the research data production resulting from confounding nutritional factors. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1066 KW - animal experimentation KW - diet KW - nutrition KW - ingredients KW - lard KW - fibers KW - fructose KW - diet coloring KW - autoclaving KW - irradiation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472460 SN - 1866-8372 IS - 1066 ER - TY - GEN A1 - Al-Halbouni, Djamil A1 - Holohan, Eoghan P. A1 - Taheri, Abbas A1 - Schöpfer, Martin P. J. A1 - Emam, Sacha A1 - Dahm, Torsten T1 - Geomechanical modelling of sinkhole development using distinct elements BT - model verification for a single void space and application to the Dead Sea area T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Mechanical and/or chemical removal of material from the subsurface may generate large subsurface cavities, the destabilisation of which can lead to ground collapse and the formation of sinkholes. Numerical simulation of the interaction of cavity growth, host material deformation and overburden collapse is desirable to better understand the sinkhole hazard but is a challenging task due to the involved high strains and material discontinuities. Here, we present 2-D distinct element method numerical simulations of cavity growth and sinkhole development. Firstly, we simulate cavity formation by quasi-static, stepwise removal of material in a single growing zone of an arbitrary geometry and depth. We benchmark this approach against analytical and boundary element method models of a deep void space in a linear elastic material. Secondly, we explore the effects of properties of different uniform materials on cavity stability and sinkhole development. We perform simulated biaxial tests to calibrate macroscopic geotechnical parameters of three model materials representative of those in which sinkholes develop at the Dead Sea shoreline: mud, alluvium and salt. We show that weak materials do not support large cavities, leading to gradual sagging or suffusion-style subsidence. Strong materials support quasi-stable to stable cavities, the overburdens of which may fail suddenly in a caprock or bedrock collapse style. Thirdly, we examine the consequences of layered arrangements of weak and strong materials. We find that these are more susceptible to sinkhole collapse than uniform materials not only due to a lower integrated strength of the overburden but also due to an inhibition of stabilising stress arching. Finally, we compare our model sinkhole geometries to observations at the Ghor Al-Haditha sinkhole site in Jordan. Sinkhole depth ∕ diameter ratios of 0.15 in mud, 0.37 in alluvium and 0.33 in salt are reproduced successfully in the calibrated model materials. The model results suggest that the observed distribution of sinkhole depth ∕ diameter values in each material type may partly reflect sinkhole growth trends. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1061 KW - rock mass KW - karst KW - dissolution KW - reflection KW - subsidence KW - subrosion KW - collapse KW - simulation KW - scale KW - fault Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468435 SN - 1866-8372 IS - 1061 ER - TY - GEN A1 - Omori, Toshihiro A1 - Winter, Katja A1 - Shinohara, Kyosuke A1 - Hamada, Hiroshi A1 - Ishikawa, Takuji T1 - Simulation of the nodal flow of mutant embryos with a small number of cilia BT - comparison of mechanosensing and vesicle transport hypotheses T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Left-right (L-R) asymmetry in the body plan is determined by nodal flow in vertebrate embryos. Shinohara et al. (Shinohara K et al. 2012 Nat. Commun. 3, 622 (doi:10.1038/ncomms1624)) used Dpcd and Rfx3 mutant mouse embryos and showed that only a few cilia were sufficient to achieve L-R asymmetry. However, the mechanism underlying the breaking of symmetry by such weak ciliary flow is unclear. Flow-mediated signals associated with the L-R asymmetric organogenesis have not been clarified, and two different hypotheses-vesicle transport and mechanosensing-are now debated in the research field of developmental biology. In this study, we developed a computational model of the node system reported by Shinohara et al. and examined the feasibilities of the two hypotheses with a small number of cilia. With the small number of rotating cilia, flow was induced locally and global strong flow was not observed in the node. Particles were then effectively transported only when they were close to the cilia, and particle transport was strongly dependent on the ciliary positions. Although the maximum wall shear rate was also influenced by ciliary position, the mean wall shear rate at the perinodal wall increased monotonically with the number of cilia. We also investigated the membrane tension of immotile cilia, which is relevant to the regulation of mechanotransduction. The results indicated that tension of about 0.1 mu Nm(-1) was exerted at the base even when the fluid shear rate was applied at about 0.1 s(-1). The area of high tension was also localized at the upstream side, and negative tension appeared at the downstream side. Such localization may be useful to sense the flow direction at the periphery, as time-averaged anticlockwise circulation was induced in the node by rotation of a few cilia. Our numerical results support the mechanosensing hypothesis, and we expect that our study will stimulate further experimental investigations of mechanotransduction in the near future. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1056 KW - nodal flow KW - left-right asymmetry KW - boundary element method KW - fluid-structure interaction Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468734 SN - 1866-8372 IS - 1056 ER - TY - GEN A1 - Kashkarov, Egor B. A1 - Obrosov, Aleksei A1 - Sutygina, Alina N. A1 - Uludintceva, Elena A1 - Mitrofanov, Andrei A1 - Weiß, Sabine T1 - Hydrogen permeation, and mechanical and tribological behavior, of CrNx coatings deposited at various bias voltages on IN718 by direct current reactive sputtering T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - In the current work, the microstructure, hydrogen permeability, and properties of chromium nitride (CrNx) thin films deposited on the Inconel 718 superalloy using direct current reactive sputtering are investigated. The influence of the substrate bias voltage on the crystal structure, mechanical, and tribological properties before and after hydrogen exposure was studied. It was found that increasing the substrate bias voltage leads to densification of the coating. X-ray diffraction (XRD) results reveal a change from mixed fcc-CrN + hcp-Cr2N to the approximately stoichiometric hcp-Cr2N phase with increasing substrate bias confirmed by wavelength-dispersive X-ray spectroscopy (WDS). The texture coefficients of (113), (110), and (111) planes vary significantly with increasing substrate bias voltage. The hydrogen permeability was measured by gas-phase hydrogenation. The CrN coating deposited at 60 V with mixed c-CrN and (113) textured hcp-Cr2N phases exhibits the lowest hydrogen absorption at 873 K. It is suggested that the crystal orientation is only one parameter influencing the permeation resistance of the CrNx coating together with the film structure, the presence of mixing phases, and the packing density of the structure. After hydrogenation, the hardness increased for all coatings, which could be related to the formation of a Cr2O3 oxide film on the surface, as well as the defect formation after hydrogen loading. Tribological tests reveal that hydrogenation leads to a decrease of the friction coefficient by up to 40%. The lowest value of 0.25 +/- 0.02 was reached for the CrNx coating deposited at 60 V after hydrogenation. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1017 KW - CrNx coatings KW - Physical Vapour Deposition (PVD) KW - hydrogenation KW - Tribology KW - mechanical properties KW - X-ray diffraction Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459846 SN - 1866-8372 IS - 1017 ER - TY - GEN A1 - Schaal, Frederik A1 - Rutloh, Michael A1 - Weidenfeld, Susanne A1 - Stumpe, Joachim A1 - Michler, Peter A1 - Pruss, Christof A1 - Osten, Wolfgang T1 - Optically addressed modulator for tunable spatial polarization control T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present an optically addressed non-pixelated spatial light modulator. The system is based on reversible photoalignment of a LC cell using a red light sensitive novel azobenzene photoalignment layer. It is an electrode-free device that manipulates the liquid crystal orientation and consequently the polarization via light without artifacts caused by electrodes. The capability to miniaturize the spatial light modulator allows the integration into a microscope objective. This includes a miniaturized 200 channel optical addressing system based on a VCSEL array and hybrid refractive-diffractive beam shapers. As an application example, the utilization as a microscope objective integrated analog phase contrast modulator is shown. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1001 KW - nematic liquid crystals KW - command surfaces KW - light modulator KW - alignment KW - films KW - polymer Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-446263 SN - 1866-8372 IS - 1001 SP - 28119 EP - 28130 ER - TY - GEN A1 - Radosavljevic, Boris A1 - Lantuit, Hugues A1 - Pollard, Wayne A1 - Overduin, Pier Paul A1 - Couture, Nicole A1 - Sachs, Torsten A1 - Helm, Veit A1 - Fritz, Michael T1 - Erosion and flooding-threats to coastal Infrastructure in the Arctic BT - a case study from Herschel Island, Yukon Territory, Canada T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Arctic coastal infrastructure and cultural and archeological sites are increasingly vulnerable to erosion and flooding due to amplified warming of the Arctic, sea level rise, lengthening of open water periods, and a predicted increase in frequency of major storms. Mitigating these hazards necessitates decision-making tools at an appropriate scale. The objectives of this paper are to provide such a tool by assessing potential erosion and flood hazards at Herschel Island, a UNESCO World Heritage candidate site. This study focused on Simpson Point and the adjacent coastal sections because of their archeological, historical, and cultural significance. Shoreline movement was analyzed using the Digital Shoreline Analysis System (DSAS) after digitizing shorelines from 1952, 1970, 2000, and 2011. For purposes of this analysis, the coast was divided in seven coastal reaches (CRs) reflecting different morphologies and/or exposures. Using linear regression rates obtained from these data, projections of shoreline position were made for 20 and 50 years into the future. Flood hazard was assessed using a least cost path analysis based on a high-resolution light detection and ranging (LiDAR) dataset and current Intergovernmental Panel on Climate Change sea level estimates. Widespread erosion characterizes the study area. The rate of shoreline movement in different periods of the study ranges from −5.5 to 2.7 m·a⁻¹ (mean −0.6 m·a⁻¹). Mean coastal retreat decreased from −0.6 m·a⁻¹ to −0.5 m·a⁻¹, for 1952–1970 and 1970–2000, respectively, and increased to −1.3 m·a⁻¹ in the period 2000–2011. Ice-rich coastal sections most exposed to wave attack exhibited the highest rates of coastal retreat. The geohazard map combines shoreline projections and flood hazard analyses to show that most of the spit area has extreme or very high flood hazard potential, and some buildings are vulnerable to coastal erosion. This study demonstrates that transgressive forcing may provide ample sediment for the expansion of depositional landforms, while growing more susceptible to overwash and flooding. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 996 KW - Arctic KW - coastal erosion KW - UNESCO KW - vulnerability mapping; KW - permafrost coasts Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432279 SN - 1866-8372 IS - 996 ER - TY - GEN A1 - Ribeiro Martins, Renata Filipa A1 - Fickel, Jörns A1 - Le, Minh A1 - Nguyen, Thanh van A1 - Nguyen, Ha M. A1 - Timmins, Robert A1 - Gan, Han Ming A1 - Rovie-Ryan, Jeffrine J. A1 - Lenz, Dorina A1 - Förster, Daniel W. A1 - Wilting, Andreas T1 - Phylogeography of red muntjacs reveals three distinct mitochondrial lineages T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia. Results We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. Conclusions Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 973 KW - phylogeography KW - archival DNA KW - Muntjac KW - Southeast Asia KW - species complex Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430780 SN - 1866-8372 IS - 973 ER - TY - GEN A1 - Fairey, Brenton J. A1 - Timmerman, Martin Jan A1 - Sudo, Masafumi A1 - Tsikos, Harilaos T1 - The role of hydrothermal activity in the formation of Karst-hosted manganese deposits of the Postmasburg Mn Field, Northern Cape Province, South Africa T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Postmasburg Manganese Field (PMF), Northern Cape Province, South Africa, once represented one of the largest sources of manganese ore worldwide. Two belts of manganese ore deposits have been distinguished in the PMF, namely the Western Belt of ferruginous manganese ores and the Eastern Belt of siliceous manganese ores. Prevailing models of ore formation in these two belts invoke karstification of manganese-rich dolomites and residual accumulation of manganese wad which later underwent diagenetic and low-grade metamorphic processes. For the most part, the role of hydrothermal processes and metasomatic alteration towards ore formation has not been adequately discussed. Here we report an abundance of common and some rare Al-, Na-, K- and Ba-bearing minerals, particularly aegirine, albite, microcline, banalsite, sérandite-pectolite, paragonite and natrolite in Mn ores of the PMF, indicative of hydrothermal influence. Enrichments in Na, K and/or Ba in the ores are generally on a percentage level for most samples analysed through bulk-rock techniques. The presence of As-rich tokyoite also suggests the presence of As and V in the hydrothermal fluid. The fluid was likely oxidized and alkaline in nature, akin to a mature basinal brine. Various replacement textures, particularly of Na- and K- rich minerals by Ba-bearing phases, suggest sequential deposition of gangue as well as ore-minerals from the hydrothermal fluid, with Ba phases being deposited at a later stage. The stratigraphic variability of the studied ores and their deviation from the strict classification of ferruginous and siliceous ores in the literature, suggests that a re-evaluation of genetic models is warranted. New Ar-Ar ages for K-feldspars suggest a late Neoproterozoic timing for hydrothermal activity. This corroborates previous geochronological evidence for regional hydrothermal activity that affected Mn ores at the PMF but also, possibly, the high-grade Mn ores of the Kalahari Manganese Field to the north. A revised, all-encompassing model for the development of the manganese deposits of the PMF is then proposed, whereby the source of metals is attributed to underlying carbonate rocks beyond the Reivilo Formation of the Campbellrand Subgroup. The main process by which metals are primarily accumulated is attributed to karstification of the dolomitic substrate. The overlying Asbestos Hills Subgroup banded iron formation (BIF) is suggested as a potential source of alkali metals, which also provides a mechanism for leaching of these BIFs to form high-grade residual iron ore deposits. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 966 KW - manganese ore KW - Postmasburg manganese field KW - hydrothermal KW - karst KW - South Africa Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-473304 SN - 1866-8372 IS - 966 ER - TY - GEN A1 - Alter, S. Elizabeth A1 - Meyer, Matthias A1 - Post, Klaas A1 - Czechowski, Paul A1 - Gravlund, Peter A1 - Gaines, Cork A1 - Rosenbaum, Howard C. A1 - Kaschner, Kristin A1 - Turvey, Samuel T. A1 - van der Plicht, Johannes A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100 T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 965 KW - ancient DNA KW - climate change KW - last glacial maximum KW - marine mammal Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438920 SN - 1866-8372 IS - 965 SP - 1510 EP - 1522 ER - TY - GEN A1 - Krstic, Jelena A1 - Galhuber, Markus A1 - Schulz, Tim Julius A1 - Schupp, Michael A1 - Prokesch, Andreas T1 - p53 as a dichotomous regulator of liver disease BT - the dose makes the medicine T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Lifestyle-related disorders, such as the metabolic syndrome, have become a primary risk factor for the development of liver pathologies that can progress from hepatic steatosis, hepatic insulin resistance, steatohepatitis, fibrosis and cirrhosis, to the most severe condition of hepatocellular carcinoma (HCC). While the prevalence of liver pathologies is steadily increasing in modern societies, there are currently no approved drugs other than chemotherapeutic intervention in late stage HCC. Hence, there is a pressing need to identify and investigate causative molecular pathways that can yield new therapeutic avenues. The transcription factor p53 is well established as a tumor suppressor and has recently been described as a central metabolic player both in physiological and pathological settings. Given that liver is a dynamic tissue with direct exposition to ingested nutrients, hepatic p53, by integrating cellular stress response, metabolism and cell cycle regulation, has emerged as an important regulator of liver homeostasis and dysfunction. The underlying evidence is reviewed herein, with a focus on clinical data and animal studies that highlight a direct influence of p53 activity on different stages of liver diseases. Based on current literature showing that activation of p53 signaling can either attenuate or fuel liver disease, we herein discuss the hypothesis that, while hyper-activation or loss of function can cause disease, moderate induction of hepatic p53 within physiological margins could be beneficial in the prevention and treatment of liver pathologies. Hence, stimuli that lead to a moderate and temporary p53 activation could present new therapeutic approaches through several entry points in the cascade from hepatic steatosis to HCC. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 963 KW - p53 KW - liver disease KW - insulin resistance KW - non-alcoholic fatty liver disease KW - non-alcoholic steatohepatitis KW - hepatocellular carcinoma KW - liver regeneration KW - mouse models Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-468127 SN - 1866-8372 IS - 963 ER - TY - GEN A1 - Totz, Sonja Juliana A1 - Löber, Jakob A1 - Totz, Jan Frederik A1 - Engel, Harald T1 - Control of transversal instabilities in reaction-diffusion systems T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In two-dimensional reaction-diffusion systems, local curvature perturbations on traveling waves are typically damped out and vanish. However, if the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated waves and to spreading spiral turbulence. Here, we propose a scheme to induce or inhibit these instabilities via a spatio-temporal feedback loop. In a piecewise-linear version of the FitzHugh-Nagumo model, transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilizing plane wave propagation. Conversely, in numerical simulations with the modified Oregonator model for the photosensitive Belousov-Zhabotinsky reaction, which does not exhibit transversal instabilities on its own, we demonstrate the feasibility of inducing transversal instabilities and study the emerging wave patterns in a well-controlled manner. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 962 KW - traveling waves KW - control KW - transversal instabilities Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-469762 SN - 1866-8372 IS - 962 ER - TY - GEN A1 - López de Guereñu, Anna A1 - Bastian, Philipp A1 - Wessig, Pablo A1 - John, Leonard A1 - Kumke, Michael Uwe T1 - Energy transfer between tm-doped upconverting nanoparticles and a small organic dye with large stokes shift T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51%) despite the compromised luminescence due to surface quenching. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 961 KW - resonance energy transfer KW - DBD dye KW - core shell UCNP KW - time-resolved luminescence Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472240 SN - 1866-8372 IS - 961 ER - TY - GEN A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - How reliable is the electrochemical readout of MIP-sensors? T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 960 KW - molecularly imprinted polymers KW - electropolymerization KW - direct electron transfer KW - catalysis KW - redox marker KW - gate effect Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-471608 SN - 1866-8372 IS - 960 ER - TY - GEN A1 - Sadovnichii, V. A. A1 - Panasyuk, M. I. A1 - Amelyushkin, A. M. A1 - Benghin, V. V. A1 - Garipov, G. K. A1 - Kalegaev, V. V. A1 - Klimov, P. A. A1 - Khrenov, B. A. A1 - Petrov, V. L. A1 - Sharakin, S. A. A1 - Shirokov, A. V. A1 - Svertilov, S. I. A1 - Zotov, M. Y. A1 - Yashin, I. V. A1 - Gorbovskoy, E. S. A1 - Lipunov, V. M. A1 - Park, I. H. A1 - Lee, J. A1 - Jeong, S. A1 - Kim, M. B. A1 - Jeong, H. M. A1 - Shprits, Yuri Y. A1 - Angelopoulos, V. A1 - Russell, C. T. A1 - Runov, A. A1 - Turner, D. A1 - Strangeway, R. J. A1 - Caron, R. A1 - Biktemerova, S. A1 - Grinyuk, A. A1 - Lavrova, M. A1 - Tkachev, L. A1 - Tkachenko, A. A1 - Martinez, O. A1 - Salazar, H. A1 - Ponce, E. T1 - "Lomonosov" satellite-space observatory to study extreme phenomena in space T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The "Lomonosov" space project is lead by Lomonosov Moscow State University in collaboration with the following key partners: Joint Institute for Nuclear Research, Russia, University of California, Los Angeles (USA), University of Pueblo (Mexico), Sungkyunkwan University (Republic of Korea) and with Russian space industry organi-zations to study some of extreme phenomena in space related to astrophysics, astroparticle physics, space physics, and space biology. The primary goals of this experiment are to study: -Ultra-high energy cosmic rays (UHECR) in the energy range of the Greizen-ZatsepinKuzmin (GZK) cutoff; -Ultraviolet (UV) transient luminous events in the upper atmosphere; -Multi-wavelength study of gamma-ray bursts in visible, UV, gamma, and X-rays; -Energetic trapped and precipitated radiation (electrons and protons) at low-Earth orbit (LEO) in connection with global geomagnetic disturbances; -Multicomponent radiation doses along the orbit of spacecraft under different geomagnetic conditions and testing of space segments of optical observations of space-debris and other space objects; -Instrumental vestibular-sensor conflict of zero-gravity phenomena during space flight. This paper is directed towards the general description of both scientific goals of the project and scientific equipment on board the satellite. The following papers of this issue are devoted to detailed descriptions of scientific instruments. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 959 KW - gamma-ray bursts KW - ultra-high energy cosmic rays KW - radiation belts KW - space mission Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428185 SN - 1866-8372 IS - 959 SP - 1705 EP - 1738 ER - TY - GEN A1 - Krippendorff, Ben-Fillippo A1 - Oyarzún, Diego A. A1 - Huisinga, Wilhelm T1 - Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cell-level kinetic models for therapeutically relevant processes increasingly benefit the early stages of drug development. Later stages of the drug development processes, however, rely on pharmacokinetic compartment models while cell-level dynamics are typically neglected. We here present a systematic approach to integrate cell-level kinetic models and pharmacokinetic compartment models. Incorporating target dynamics into pharmacokinetic models is especially useful for the development of therapeutic antibodies because their effect and pharmacokinetics are inherently interdependent. The approach is illustrated by analysing the F(ab)-mediated inhibitory effect of therapeutic antibodies targeting the epidermal growth factor receptor. We build a multi-level model for anti-EGFR antibodies by combining a systems biology model with in vitro determined parameters and a pharmacokinetic model based on in vivo pharmacokinetic data. Using this model, we investigated in silico the impact of biochemical properties of anti-EGFR antibodies on their F(ab)-mediated inhibitory effect. The multi-level model suggests that the F(ab)-mediated inhibitory effect saturates with increasing drug-receptor affinity, thereby limiting the impact of increasing antibody affinity on improving the effect. This indicates that observed differences in the therapeutic effects of high affinity antibodies in the market and in clinical development may result mainly from Fc-mediated indirect mechanisms such as antibody-dependent cell cytotoxicity. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 958 KW - cell-level kinetics KW - pharmacokinetic models KW - therapeutic proteins KW - EGFR Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431051 SN - 1866-8372 IS - 958 SP - 125 EP - 139 ER - TY - GEN A1 - Lamprecht, Anna-Lena A1 - Naujokat, Stefan A1 - Margaria, Tiziana A1 - Steffen, Bernhard T1 - Semantics-based composition of EMBOSS services T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions. Results In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized. Conclusions Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 956 KW - service description KW - synthesis algorithm KW - input type KW - synthesis methodology KW - electronic tool integration Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431830 SN - 1866-8372 IS - 956 ER - TY - GEN A1 - Yang, Lei A1 - Tang, Renjie A1 - Zhu, Jinqi A1 - Liu, Hua A1 - Mueller-Roeber, Bernd A1 - Xia, Huijun A1 - Zhang, Hongxia T1 - Enhancement of stress tolerance in transgenic tobacco plants constitutively expressing AtIpk2β, an inositol polyphosphate 6-/3-kinase from Arabidopsis thaliana T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Inositol phosphates (IPs) and their turnover products have been implicated to play important roles in stress signaling in eukaryotic cells. In higher plants genes encoding inositol polyphosphate kinases have been identified previously, but their physiological functions have not been fully resolved. Here we expressed Arabidopsis inositol polyphosphate 6-/3-kinase (AtIpk2 beta) in two heterologous systems, i.e. the yeast Saccharomyces cerevisiae and in tobacco (Nicotiana tabacum), and tested the effect on abiotic stress tolerance. Expression of AtIpk2 beta rescued the salt-, osmotic- and temperature-sensitive growth defects of a yeast mutant strain (arg82 Delta) that lacks inositol polyphosphate multikinase activity encoded by the ARG82/IPK2 gene. Transgenic tobacco plants constitutively expressing AtIpk2 beta under the control of the Cauliflower Mosaic Virus 35S promoter were generated and found to exhibit improved tolerance to diverse abiotic stresses when compared to wild type plants. Expression patterns of various stress responsive genes were enhanced, and the activities of anti-oxidative enzymes were elevated in transgenic plants, suggesting a possible involvement of AtIpk2 beta in plant stress responses. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 954 KW - arabidopsis thaliana KW - AtIpk2 beta KW - inositol phosphate KW - IP3 KW - stress tolerance KW - transgenic tobacco Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431225 SN - 1866-8372 IS - 954 ER - TY - GEN A1 - Eckert, Sebastian A1 - Miedema, Piter A1 - Quevedo, Wilson A1 - O'Cinneide, B. A1 - Fondell, Mattis A1 - Beye, Martin A1 - Pietzsch, Annette A1 - Ross, Matthew R. A1 - Khalil, Munira A1 - Föhlisch, Alexander T1 - Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms. (C) 2016 The Authors. Published by Elsevier B.V. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 953 KW - ray-emission-spectroscopy KW - x-ray KW - hydroxypyridine-pyridone KW - protomeric equilibria KW - self-association KW - CU(110) KW - valence Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437473 SN - 1866-8372 IS - 953 SP - 103 EP - 106 ER - TY - GEN A1 - Gallego-Llorente, Marcos A1 - Sarah, Connell A1 - Jones, Eppie R. A1 - Merrett, Deborah C. A1 - Jeon, Y. A1 - Eriksson, Anders A1 - Siska, Veronika A1 - Gamba, Cristina A1 - Meiklejohn, Christopher A1 - Beyer, Robert A1 - Jeon, Sungwon A1 - Cho, Yun Sung A1 - Hofreiter, Michael A1 - Bhak, Jong A1 - Manica, Andrea A1 - Pinhasi, Ron T1 - The genetics of an early Neolithic pastoralist from the Zagros, Iran T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 952 KW - whole-genome association KW - ancient KW - domestication KW - agriculture KW - mountains KW - diffusion KW - migration KW - admixture KW - patterns KW - sequence KW - archaeology KW - biological anthropology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439355 SN - 1866-8372 IS - 952 ER - TY - GEN A1 - Kaminski, Jakob A. A1 - Schlagenhauf, Florian A1 - Rapp, Michael Armin A1 - Awasthi, Swapnil A1 - Ruggeri, Barbara A1 - Deserno, Lorenz A1 - Banaschewski, Tobias A1 - Bokde, Arun L. W. A1 - Bromberg, Uli A1 - Büchel, Christian A1 - Quinlan, Erin Burke A1 - Desrivières, Sylvane A1 - Flor, Herta A1 - Frouin, Vincent A1 - Garavan, Hugh A1 - Gowland, Penny A1 - Ittermann, Bernd A1 - Martinot, Jean-Luc A1 - Paillère Martinot, Marie-Laure A1 - Nees, Frauke A1 - Papadopoulos Orfanos, Dimitri A1 - Paus, Tomáš A1 - Poustka, Luise A1 - Smolka, Michael N. A1 - Fröhner, Juliane H. A1 - Walter, Henrik A1 - Whelan, Robert A1 - Ripke, Stephan A1 - Schumann, Gunter A1 - Heinz, Andreas T1 - Epigenetic variance in dopamine D2 receptor BT - a marker of IQ malleability? T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Genetic and environmental factors both contribute to cognitive test performance. A substantial increase in average intelligence test results in the second half of the previous century within one generation is unlikely to be explained by genetic changes. One possible explanation for the strong malleability of cognitive performance measure is that environmental factors modify gene expression via epigenetic mechanisms. Epigenetic factors may help to understand the recent observations of an association between dopamine-dependent encoding of reward prediction errors and cognitive capacity, which was modulated by adverse life events. The possible manifestation of malleable biomarkers contributing to variance in cognitive test performance, and thus possibly contributing to the "missing heritability" between estimates from twin studies and variance explained by genetic markers, is still unclear. Here we show in 1475 healthy adolescents from the IMaging and GENetics (IMAGEN) sample that general IQ (gIQ) is associated with (1) polygenic scores for intelligence, (2) epigenetic modification of DRD2 gene, (3) gray matter density in striatum, and (4) functional striatal activation elicited by temporarily surprising reward-predicting cues. Comparing the relative importance for the prediction of gIQ in an overlapping subsample, our results demonstrate neurobiological correlates of the malleability of gIQ and point to equal importance of genetic variance, epigenetic modification of DRD2 receptor gene, as well as functional striatal activation, known to influence dopamine neurotransmission. Peripheral epigenetic markers are in need of confirmation in the central nervous system and should be tested in longitudinal settings specifically assessing individual and environmental factors that modify epigenetic structure. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 950 KW - genome-wide association KW - reward anticipation KW - human intelligence KW - human brain KW - stress KW - metaanalysis KW - striatum KW - psychopathology KW - prediction KW - volume KW - epigenetics and behaviour KW - human behaviour KW - learning and memory Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-425687 SN - 1866-8372 IS - 950 ER - TY - GEN A1 - Andorf, Sandra A1 - Gärtner, Tanja A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Altmann, Thomas A1 - Repsilber, Dirk T1 - Towards systems biology of heterosis BT - a hypothesis about molecular network structure applied for the Arabidopsis metabolome T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 949 KW - partial correlation KW - biological network KW - metabolite profile KW - molecular network KW - significant edge Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436274 SN - 1866-8372 IS - 949 ER - TY - GEN A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background Nucleic acid amplification is the most sensitive and specific method to detect Plasmodium falciparum. However the polymerase chain reaction remains laboratory-based and has to be conducted by trained personnel. Furthermore, the power dependency for the thermocycling process and the costly equipment necessary for the read-out are difficult to cover in resource-limited settings. This study aims to develop and evaluate a combination of isothermal nucleic acid amplification and simple lateral flow dipstick detection of the malaria parasite for point-of-care testing. Methods A specific fragment of the 18S rRNA gene of P. falciparum was amplified in 10 min at a constant 38°C using the isothermal recombinase polymerase amplification (RPA) method. With a unique probe system added to the reaction solution, the amplification product can be visualized on a simple lateral flow strip without further labelling. The combination of these methods was tested for sensitivity and specificity with various Plasmodium and other protozoa/bacterial strains, as well as with human DNA. Additional investigations were conducted to analyse the temperature optimum, reaction speed and robustness of this assay. Results The lateral flow RPA (LF-RPA) assay exhibited a high sensitivity and specificity. Experiments confirmed a detection limit as low as 100 fg of genomic P. falciparum DNA, corresponding to a sensitivity of approximately four parasites per reaction. All investigated P. falciparum strains (n = 77) were positively tested while all of the total 11 non-Plasmodium samples, showed a negative test result. The enzymatic reaction can be conducted under a broad range of conditions from 30-45°C with high inhibitory concentration of known PCR inhibitors. A time to result of 15 min from start of the reaction to read-out was determined. Conclusions Combining the isothermal RPA and the lateral flow detection is an approach to improve molecular diagnostic for P. falciparum in resource-limited settings. The system requires none or only little instrumentation for the nucleic acid amplification reaction and the read-out is possible with the naked eye. Showing the same sensitivity and specificity as comparable diagnostic methods but simultaneously increasing reaction speed and dramatically reducing assay requirements, the method has potential to become a true point-of-care test for the malaria parasite. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 948 KW - Plasmodium falciparum KW - Recombinase polymerase amplification KW - RPA KW - PCR KW - lateral flow KW - point-of-care testing KW - rapid test KW - isothermal nucleic acid amplification Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431562 SN - 1866-8372 IS - 948 ER - TY - GEN A1 - Zaourar, Naima A1 - Hamoudi, Mohamed A1 - Mandea, Mioara A1 - Balasis, Georgios A1 - Holschneider, Matthias T1 - Wavelet-based multiscale analysis of geomagnetic disturbance T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The dynamics of external contributions to the geomagnetic field is investigated by applying time-frequency methods to magnetic observatory data. Fractal models and multiscale analysis enable obtaining maximum quantitative information related to the short-term dynamics of the geomagnetic field activity. The stochastic properties of the horizontal component of the transient external field are determined by searching for scaling laws in the power spectra. The spectrum fits a power law with a scaling exponent β, a typical characteristic of self-affine time-series. Local variations in the power-law exponent are investigated by applying wavelet analysis to the same time-series. These analyses highlight the self-affine properties of geomagnetic perturbations and their persistence. Moreover, they show that the main phases of sudden storm disturbances are uniquely characterized by a scaling exponent varying between 1 and 3, possibly related to the energy contained in the external field. These new findings suggest the existence of a long-range dependence, the scaling exponent being an efficient indicator of geomagnetic activity and singularity detection. These results show that by using magnetogram regularity to reflect the magnetosphere activity, a theoretical analysis of the external geomagnetic field based on local power-law exponents is possible. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 947 KW - geomagnetic field KW - magnetosphere KW - geomagnetic storm KW - multiscale analysis KW - spectral exponent Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436912 SN - 1866-8372 VL - 65 IS - 12 SP - 1525 EP - 1540 ER - TY - GEN A1 - Schell, Mareike A1 - Chudoba, Chantal A1 - Leboucher, Antoine A1 - Alfine, Eugenia A1 - Flore, Tanina A1 - Ritter, Katrin A1 - Weiper, Katharina A1 - Wernitz, Andreas A1 - Henkel, Janin A1 - Kleinridders, André T1 - Interplay of Dietary Fatty Acids and Cholesterol Impacts Brain Mitochondria and Insulin Action T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Overconsumption of high-fat and cholesterol-containing diets is detrimental for metabolism and mitochondrial function, causes inflammatory responses and impairs insulin action in peripheral tissues. Dietary fatty acids can enter the brain to mediate the nutritional status, but also to influence neuronal homeostasis. Yet, it is unclear whether cholesterol-containing high-fat diets (HFDs) with different combinations of fatty acids exert metabolic stress and impact mitochondrial function in the brain. To investigate whether cholesterol in combination with different fatty acids impacts neuronal metabolism and mitochondrial function, C57BL/6J mice received different cholesterol-containing diets with either high concentrations of long-chain saturated fatty acids or soybean oil-derived poly-unsaturated fatty acids. In addition, CLU183 neurons were stimulated with combinations of palmitate, linoleic acid and cholesterol to assess their effects on metabolic stress, mitochondrial function and insulin action. The dietary interventions resulted in a molecular signature of metabolic stress in the hypothalamus with decreased expression of occludin and subunits of mitochondrial electron chain complexes, elevated protein carbonylation, as well as c-Jun N-terminal kinase (JNK) activation. Palmitate caused mitochondrial dysfunction, oxidative stress, insulin and insulin-like growth factor-1 (IGF-1) resistance, while cholesterol and linoleic acid did not cause functional alterations. Finally, we defined insulin receptor as a novel negative regulator of metabolically stress-induced JNK activation. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 946 KW - cholesterol KW - insulin signaling KW - mitochondria KW - brain KW - inflammation KW - fatty acids KW - JNK KW - insulin receptor Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-470773 SN - 1866-8372 IS - 946 ER - TY - GEN A1 - Spricigo, Roberto A1 - Dronov, Roman A1 - Lisdat, Fred A1 - Leimkühler, Silke A1 - Scheller, Frieder W. A1 - Wollenberger, Ursula T1 - Electrocatalytic sulfite biosensor with human sulfite oxidase co-immobilized with cytochrome c in a polyelectrolyte-containing multilayer T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - An efficient electrocatalytic biosensor for sulfite detection was developed by co-immobilizing sulfite oxidase and cytochrome c with polyaniline sulfonic acid in a layer-by-layer assembly. QCM, UV-Vis spectroscopy and cyclic voltammetry revealed increasing loading of electrochemically active protein with the formation of multilayers. The sensor operates reagentless at low working potential. A catalytic oxidation current was detected in the presence of sulfite at the modified gold electrode, polarized at +0.1 V ( vs. Ag/AgCl 1 M KCl). The stability of the biosensor performance was characterized and optimized. A 17-bilayer electrode has a linear range between 1 and 60 mu M sulfite with a sensitivity of 2.19 mA M-1 sulfite and a response time of 2 min. The electrode retained a stable response for 3 days with a serial reproducibility of 3.8% and lost 20% of sensitivity after 5 days of operation. It is possible to store the sensor in a dry state for more than 2 months. The multilayer electrode was used for determination of sulfite in unspiked and spiked samples of red and white wine. The recovery and the specificity of the signals were evaluated for each sample. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 945 KW - bioelectrocatalysis KW - sulfite KW - sulfite oxidase KW - cytochrome c KW - multilayer Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431176 SN - 1866-8372 IS - 945 SP - 225 EP - 233 ER - TY - GEN A1 - Karpuz, Eylem Guzel A1 - Çevik, Ahmet Sinan A1 - Koppitz, Jörg A1 - Cangul, Ismail Naci T1 - Some fixed-point results on (generalized) Bruck-Reilly ∗-extensions of monoids T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In this paper, we determine necessary and sufficient conditions for Bruck-Reilly and generalized Bruck-Reilly ∗-extensions of arbitrary monoids to be regular, coregular and strongly π-inverse. These semigroup classes have applications in various field of mathematics, such as matrix theory, discrete mathematics and p-adic analysis (especially in operator theory). In addition, while regularity and coregularity have so many applications in the meaning of boundaries (again in operator theory), inverse monoids and Bruck-Reilly extensions contain a mixture fixed-point results of algebra, topology and geometry within the purposes of this journal. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 942 KW - Bruck-Reilly extension KW - generalized Bruck-Reilly ∗-extension KW - π -inverse monoid KW - regular monoid Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432701 SN - 1866-8372 IS - 942 ER - TY - GEN A1 - Werner, Peter A1 - Münzberg, Marvin A1 - Hass, Roland A1 - Reich, Oliver T1 - Process analytical approaches for the coil-to-globule transition of poly(N-isopropylacrylamide) in a concentrated aqueous suspension T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM) microgel particles suspended in water has been investigated in situ as a function of heating and cooling rate with four optical process analytical technologies (PAT), sensitive to structural changes of the polymer. Photon Density Wave (PDW) spectroscopy, Focused Beam Reflectance Measurements (FBRM), turbidity measurements, and Particle Vision Microscope (PVM) measurements are found to be powerful tools for the monitoring of the temperature-dependent transition of such thermo-responsive polymers. These in-line technologies allow for monitoring of either the reduced scattering coefficient and the absorption coefficient, the chord length distribution, the reflected intensities, or the relative backscatter index via in-process imaging, respectively. Varying heating and cooling rates result in rate-dependent lower critical solution temperatures (LCST), with different impact of cooling and heating. Particularly, the data obtained by PDW spectroscopy can be used to estimate the thermodynamic transition temperature of PNIPAM for infinitesimal heating or cooling rates. In addition, an inverse hysteresis and a reversible building of micrometer-sized agglomerates are observed for the PNIPAM transition process. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 944 KW - poly(N-isopropylacrylamide) KW - Photon Density Wave spectroscopy KW - Focused Beam Reflectance Measurement KW - turbidity measurement KW - Particle Vision Microscope measurement KW - rate-dependent lower critical solution temperature Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431162 SN - 1866-8372 IS - 944 SP - 807 EP - 819 ER - TY - GEN A1 - Arvidsson, Samuel Janne A1 - Kwasniewski, Miroslaw A1 - Riaño- Pachón, Diego Mauricio A1 - Mueller-Roeber, Bernd T1 - QuantPrime BT - a flexible tool for reliable high-throughput primer design for quantitative PCR T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. Conclusion QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 943 KW - prime pair KW - genome annotation KW - specific prime pair KW - primer pair design KW - quantification protocol Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431531 SN - 1866-8372 IS - 943 ER - TY - GEN A1 - Göritz, Anna A1 - Berger, Stella A. A1 - Gege, Peter A1 - Grossart, Hans-Peter A1 - Nejstgaard, Jens C. A1 - Riedel, Sebastian A1 - Röttgers, Rüdiger A1 - Utschig, Christian T1 - Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover BT - a case study at lake Stechlin (Germany) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 941 KW - remote sensing KW - inland water KW - hyperspectral measurements KW - in-situ KW - cloud KW - surface reflection KW - inversion KW - bio-optical modeling Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459837 SN - 1866-8372 IS - 941 ER -