@misc{ZwiebackKokeljGuentheretal.2018,
  author    = {Zwieback, Simon and Kokelj, Steven V. and G{\"u}nther, Frank and Boike, Julia and Grosse, Guido and Hajnsek, Irena},
  title     = {Sub-seasonal thaw slump mass wasting is not consistently energy limited at the landscape scale},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {926},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44568},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445688},
  pages     = {549 -- 564},
  year      = {2018},
  abstract  = {Predicting future thaw slump activity requires a sound understanding of the atmospheric drivers and geomorphic controls on mass wasting across a range of timescales. On sub-seasonal timescales, sparse measurements indicate that mass wasting at active slumps is often limited by the energy available for melting ground ice, but other factors such as rainfall or the formation of an insulating veneer may also be relevant. To study the sub-seasonal drivers, we derive topographic changes from single-pass radar interferometric data acquired by the TanDEM-X satellites. The estimated elevation changes at 12m resolution complement the commonly observed planimetric retreat rates by providing information on volume losses. Their high vertical precision (around 30 cm), frequent observations (11 days) and large coverage (5000 km(2)) allow us to track mass wasting as drivers such as the available energy change during the summer of 2015 in two study regions. We find that thaw slumps in the Tuktoyaktuk coastlands, Canada, are not energy limited in June, as they undergo limited mass wasting (height loss of around 0 cm day 1) despite the ample available energy, suggesting the widespread presence of early season insulating snow or debris veneer. Later in summer, height losses generally increase (around 3 cm day 1), but they do so in distinct ways. For many slumps, mass wasting tracks the available energy, a temporal pattern that is also observed at coastal yedoma cliffs on the Bykovsky Peninsula, Russia. However, the other two common temporal trajectories are asynchronous with the available energy, as they track strong precipitation events or show a sudden speed-up in late August respectively. The observed temporal patterns are poorly related to slump characteristics like the headwall height. The contrasting temporal behaviour of nearby thaw slumps highlights the importance of complex local and temporally varying controls on mass wasting.},
  language  = {en}
}
@misc{MareljaLeimkuehlerMissirlis2018,
  author    = {Marelja, Zvonimir and Leimk{\"u}hler, Silke and Missirlis, Fanis},
  title     = {Iron sulfur and molybdenum cofactor enzymes regulate the Drosophila life cycle by controlling cell metabolism},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {925},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44567},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445670},
  pages     = {33},
  year      = {2018},
  abstract  = {Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.},
  language  = {en}
}
@misc{CuadratIonescuDavilaetal.2018,
  author    = {Cuadrat, Rafael R. C. and Ionescu, Danny and D{\´a}vila, Alberto M. R. and Grossart, Hans-Peter},
  title     = {Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {924},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445656},
  pages     = {15},
  year      = {2018},
  abstract  = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.},
  language  = {en}
}
@misc{SeyrichAlirezaeizanjaniBetaetal.2018,
  author    = {Seyrich, Maximilian and Alirezaeizanjani, Zahra and Beta, Carsten and Stark, Holger},
  title     = {Statistical parameter inference of bacterial swimming strategies},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {914},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44621},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446214},
  pages     = {23},
  year      = {2018},
  abstract  = {We provide a detailed stochastic description of the swimming motion of an E. coli bacterium in two dimension, where we resolve tumble events in time. For this purpose, we set up two Langevin equations for the orientation angle and speed dynamics. Calculating moments, distribution and autocorrelation functions from both Langevin equations and matching them to the same quantities determined from data recorded in experiments, we infer the swimming parameters of E. coli. They are the tumble rate lambda, the tumble time r(-1), the swimming speed v(0), the strength of speed fluctuations sigma, the relative height of speed jumps eta, the thermal value for the rotational diffusion coefficient D-0, and the enhanced rotational diffusivity during tumbling D-T. Conditioning the observables on the swimming direction relative to the gradient of a chemoattractant, we infer the chemotaxis strategies of E. coli. We confirm the classical strategy of a lower tumble rate for swimming up the gradient but also a smaller mean tumble angle (angle bias). The latter is realized by shorter tumbles as well as a slower diffusive reorientation. We also find that speed fluctuations are increased by about 30\% when swimming up the gradient compared to the reversed direction.},
  language  = {en}
}
@misc{TopcuFruehwirthMoseretal.2018,
  author    = {Top{\c{c}}u, {\c{C}}ağda{\c{s}} and Fr{\"u}hwirth, Matthias and Moser, Maximilian and Rosenblum, Michael and Pikovskij, Arkadij},
  title     = {Disentangling respiratory sinus arrhythmia in heart rate variability records},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {913},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43631},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436315},
  pages     = {15},
  year      = {2018},
  abstract  = {Objective: Several different measures of heart rate variability, and particularly of respiratory sinus arrhythmia, are widely used in research and clinical applications. For many purposes it is important to know which features of heart rate variability are directly related to respiration and which are caused by other aspects of cardiac dynamics. Approach: Inspired by ideas from the theory of coupled oscillators, we use simultaneous measurements of respiratory and cardiac activity to perform a nonlinear disentanglement of the heart rate variability into the respiratory-related component and the rest. Main results: The theoretical consideration is illustrated by the analysis of 25 data sets from healthy subjects. In all cases we show how the disentanglement is manifested in the different measures of heart rate variability. Significance: The suggested technique can be exploited as a universal preprocessing tool, both for the analysis of respiratory influence on the heart rate and in cases when effects of other factors on the heart rate variability are in focus.},
  language  = {en}
}
@misc{NakamuraGrebe2018,
  author    = {Nakamura, Moritaka and Grebe, Markus},
  title     = {Outer, inner and planar polarity in the Arabidopsis root},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {911},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44126},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441266},
  pages     = {46 -- 53},
  year      = {2018},
  abstract  = {Plant roots control uptake of water and nutrients and cope with environmental challenges. The root epidermis provides the first selective interface for nutrient absorption, while the endodermis produces the main apoplastic diffusion barrier in the form of a structure called the Casparian strip. The positioning of root hairs on epidermal cells, and of the Casparian strip around endodermal cells, requires asymmetries along cellular axes (cell polarity). Cell polarity is termed planar polarity, when coordinated within the plane of a given tissue layer. Here, we review recent molecular advances towards understanding both the polar positioning of the proteo-lipid membrane domain instructing root hair initiation, and the cytoskeletal, trafficking and polar tethering requirements of proteins at outer or inner plasma membrane domains. Finally, we highlight progress towards understanding mechanisms of Casparian strip formation and underlying endodermal cell polarity.},
  language  = {en}
}
@misc{JingHesseKumaretal.2018,
  author    = {Jing, Miao and Heße, Falk and Kumar, Rohini and Wang, Wenqing and Fischer, Thomas and Walther, Marc and Zink, Matthias and Zech, Alraune and Samaniego, Luis and Kolditz, Olaf and Attinger, Sabine},
  title     = {Improved regional-scale groundwater representation by the coupling of the mesoscale Hydrologic Model (mHM v5.7) to the groundwater model OpenGeoSys (OGS)},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {851},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42703},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427030},
  pages     = {1989 -- 2007},
  year      = {2018},
  abstract  = {Most large-scale hydrologic models fall short in reproducing groundwater head dynamics and simulating transport process due to their oversimplified representation of groundwater flow. In this study, we aim to extend the applicability of the mesoscale Hydrologic Model (mHM v5.7) to subsurface hydrology by coupling it with the porous media simulator OpenGeoSys (OGS). The two models are one-way coupled through model interfaces GIS2FEM and RIV2FEM, by which the grid-based fluxes of groundwater recharge and the river-groundwater exchange generated by mHM are converted to fixed-flux boundary conditions of the groundwater model OGS. Specifically, the grid-based vertical reservoirs in mHM are completely preserved for the estimation of land-surface fluxes, while OGS acts as a plug-in to the original mHM modeling framework for groundwater flow and transport modeling. The applicability of the coupled model (mHM-OGS v1.0) is evaluated by a case study in the central European mesoscale river basin - Nagelstedt. Different time steps, i.e., daily in mHM and monthly in OGS, are used to account for fast surface flow and slow groundwater flow. Model calibration is conducted following a two-step procedure using discharge for mHM and long-term mean of groundwater head measurements for OGS. Based on the model summary statistics, namely the Nash-Sutcliffe model efficiency (NSE), the mean absolute error (MAE), and the interquartile range error (QRE), the coupled model is able to satisfactorily represent the dynamics of discharge and groundwater heads at several locations across the study basin. Our exemplary calculations show that the one-way coupled model can take advantage of the spatially explicit modeling capabilities of surface and groundwater hydrologic models and provide an adequate representation of the spatiotemporal behaviors of groundwater storage and heads, thus making it a valuable tool for addressing water resources and management problems.},
  language  = {en}
}
@misc{MerksSwinarskiMeyeretal.2018,
  author    = {Merks, Anne Margarete and Swinarski, Marie and Meyer, Alexander Matthias and M{\"u}ller, Nicola Victoria and {\"O}zcan, Ismail and Donat, Stefan and Burger, Alexa and Gilbert, Stephen and Mosimann, Christian and Abdelilah-Seyfried, Salim and Pan{\´a}kov{\´a}, Daniela},
  title     = {Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {849},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42702},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427026},
  pages     = {17},
  year      = {2018},
  abstract  = {Development of a multiple-chambered heart from the linear heart tube is inherently linked to cardiac looping. Although many molecular factors regulating the process of cardiac chamber ballooning have been identified, the cellular mechanisms underlying the chamber formation remain unclear. Here, we demonstrate that cardiac chambers remodel by cell neighbour exchange of cardiomyocytes guided by the planar cell polarity (PCP) pathway triggered by two non-canonical Wnt ligands, Wnt5b and Wnt11. We find that PCP signalling coordinates the localisation of actomyosin activity, and thus the efficiency of cell neighbour exchange. On a tissue-scale, PCP signalling planar-polarises tissue tension by restricting the actomyosin contractility to the apical membranes of outflow tract cells. The tissue-scale polarisation of actomyosin contractility is required for cardiac looping that occurs concurrently with chamber ballooning. Taken together, our data reveal that instructive PCP signals couple cardiac chamber expansion with cardiac looping through the organ-scale polarisation of actomyosin-based tissue tension.},
  language  = {en}
}
@misc{MartensJuhlinBruckmanetal.2018,
  author    = {Martens, Sonja and Juhlin, Christopher and Bruckman, Viktor J. and Mitchell, Kristen and Griffiths, Luke and K{\"u}hn, Michael},
  title     = {Editorial: energy, resources and the environment},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {834},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42788},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427880},
  pages     = {6},
  year      = {2018},
  abstract  = {Every year, the European Geosciences Union (EGU) brings together experts from all over the world at its General Assembly, covering all disciplines of the Earth, planetary and space sciences. The EGU Division on Energy, Resources and the Environment (ERE) is concerned with one of the humankind's most challenging goals - providing affordable, reliable and sustainable energy and other georesources. A collection of contributions from the ERE Division at the EGU General Assembly 2018 is assembled within the present special issue in Advances in Geosciences.},
  language  = {en}
}
@misc{ZemellaThoringHoffmeisteretal.2018,
  author    = {Zemella, Anne and Thoring, Lena and Hoffmeister, Christian and Šamal{\´i}kov{\´a}, M{\´a}ria and Ehren, Patricia and W{\"u}stenhagen, Doreen Anja and Kubick, Stefan},
  title     = {Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {824},
  doi       = {10.25932/publishup-42701},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427017},
  pages     = {14},
  year      = {2018},
  abstract  = {As one of the most complex post-translational modification, glycosylation is widely involved in cell adhesion, cell proliferation and immune response. Nevertheless glycoproteins with an identical polypeptide backbone mostly differ in their glycosylation patterns. Due to this heterogeneity, the mapping of different glycosylation patterns to their associated function is nearly impossible. In the last years, glycoengineering tools including cell line engineering, chemoenzymatic remodeling and site-specific glycosylation have attracted increasing interest. The therapeutic hormone erythropoietin (EPO) has been investigated in particular by various groups to establish a production process resulting in a defined glycosylation pattern. However commercially available recombinant human EPO shows batch-to-batch variations in its glycoforms. Therefore we present an alternative method for the synthesis of active glycosylated EPO with an engineered O-glycosylation site by combining eukaryotic cell-free protein synthesis and site-directed incorporation of non-canonical amino acids with subsequent chemoselective modifications.},
  language  = {en}
}