TY - THES A1 - Matzk, Sören T1 - Predictive analysis of metabolic and preventive patient data T1 - Prädiktive Analyse metabolischer und präventiver Patienten Daten N2 - Every day huge amounts of medical records are stored by means of hospitals’ and medical offices’ software. These data are generally unconsidered in research. In this work anonymized everyday medical records ascertained in a physician’s office, cov- ering holistic internal medicine in combination with orthomolecular medicine, are analyzed. Due to the lack of cooperation by the provider of the medical practice software a selection of diagnoses and anthropometric parameters was extracted manually. Information about patients’ treatment are not available in this study. Nevertheless, data mining approaches in- cluding machine learning techniques are used to enable research, prevention and monitoring of patients’ course of treatment. The potential of these everyday medical data is demonstrated by investigating co-morbidity and pyroluria which is a metabolic dysfunction indicated by increased levels of hydroxy- hemopyrrolin-2-one (HPL). It points out that the metabolic syndrome forms a cluster of its components and cancer, as well as mental disorders are grouped with thyroid diseases including autoimmune thyroid diseases. In contrast to prevailing assumptions in which it was estimated that approximately 10 % of the population show increased levels of HPL, in this analysis 84.9 % of the tested patients have an increased concentration of HPL. Prevention is illustrated by using decision tree models to predict diseases. Evaluation of the obtained model for Hashimoto’s disease yield an accuracy of 87.5 %. The model generated for hypothyroidism (accuracy of 60.9 %) reveals shortcomings due to missing information about the treatment. Dynamics in the biomolecular status of 20 patients who have visited the medical office at least one time a year between 2010 and 2014 for laboratory tests are visualized by STATIS, a consensus analysis based on an extension to principal component analysis. Thereby, one can obtain patterns which are predestinated for specific diseases as hypertension. This study demonstrates that these often overlooked everyday data are challenging due to its sparsity and heterogeneity but its analysis is a great possibility to do research on disease profiles of real patients. N2 - Jeden Tag werden unzählige Mengen an medizinischen Patientendaten in Krankenhäusern und Arztpraxen digital gespeichert. Für Forschungszwecke werden diese Daten bisher größtenteils nicht verwendet. Ziel dieser Arbeit ist es täglich anfallende anonymisierte Patientendaten, die aus einer Praxis für ganzheitliche Innere Medizin stammen, zu analysieren. Aufgrund mangelnder Kooperation seitens des Anbieters der Praxissoftware konnten die Patientendaten nicht automatisch extrahiert werden. Daher wurde eine Auswahl an Diagnosen und anthropometrischen Parametern manuell in eine Datenbank übertragen. Informationen über die Behandlung wurden dabei nicht berücksichtigt. Data-Mining Verfahren ermöglichen die Forschung auf der Grundlage von alltäglichen Patientendaten. Durch die Anwendung maschinellen Lernens kann Präventionsmedizin und die Überwachung von Behandlungsverläufen unterstützt werden. Das Potenzial der Analyse dieser sonst weitgehend ungenutzten Daten wird anhand von Untersuchungen zur Komorbidität verdeutlicht. Dabei zeigt sich, dass einerseits das Metabolische Syndrom und dessen Komponenten zusammen mit Krebserkrankungen ein Cluster bilden und andererseits psychosomatische Störungen vermehrt mit Autoimmunerkrankungen der Schilddrüse auftreten. Außerdem wird eine noch nicht schulmedizinisch anerkannte Stoffwechselerkrankung, die Hämopyrrollaktamurie (HPU) untersucht. Diese lässt sich durch eine vermehrte Ausscheidung von Pyrrolen im Urin nachweisen. Bezüglich der Patienten bei denen ein HPU-Test vorliegt, weisen 84 % einen erhöhten Titer auf. Diese Beobachtung steht im Widerspruch zur vorherigen Annahme, dass in etwa 10 % der Bevölkerung von HPU betroffen sind. Präventives Handeln ermöglicht es Gesundheit zu erhalten. Zu diesem Zweck ist es notwen- dig Krankheiten möglichst früh zu erkennen. In dieser Studie können Entscheidungsbaum-Modelle die Hashimoto Thyreoiditis mit einer Genauigkeit von 87.5 % bei einem Patienten diagnostizieren. Defizite durch die fehlenden Informationen über die medikamentöse Behandlung werden anhand des Modells zur Vorhersage von Hypothyreoiditis (Genauigkeit von 60.9 %) aufgezeigt. Mit Hilfe von STATIS, das auf einer Erweiterung der Hauptkomponentenanalyse basiert, die es ermöglicht mehrere Tabellen simultan zu vergleichen, wurde der Behandlungsverlauf von 20 Patienten über einen Zeitraum von fünf Jahren überwacht. Anhand von Hypertonie wird gezeigt, dass sich sich die Patenten bezüglich Ihrer Laborwerte voneinander unterscheiden und sich Muster für Krankheiten erkennen lassen. Diese Arbeit demonstriert den Nutzen, der durch die vermehrte Analyse alltäglicher hochdimensionaler und heterogener Daten erbracht werden kann. KW - predictive analysis KW - database KW - personalised medicine KW - prädiktive Analyse KW - Datenbank KW - personalisierte Medizin Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-406103 ER - TY - GEN A1 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann-Thünemann, Elke T1 - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. T2 - Frontiers in microbiology N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434 KW - cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179 ER - TY - GEN A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, André A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites T2 - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 435 KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407181 ER - TY - GEN A1 - Lukoszek, Radoslaw A1 - Feist, Peter A1 - Ignatova, Zoya T1 - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq T2 - BMC plant biology N2 - Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 438 KW - translation KW - ribosome profiling KW - transcription KW - RNA-Seq KW - secondary structure KW - G-quadruplexes, KW - heat stress response Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407262 ER - TY - JOUR A1 - Feoktistova, Natalia A1 - Rose, Jürgen A1 - Prokopovic, Vladimir Z. A1 - Vikulina, Anna S. A1 - Skirtach, Andre A1 - Volodkin, Dmitry T1 - Controlling the Vaterite CaCO3 Crystal Pores. Design of Tailor-Made Polymer Based Microcapsules by Hard Templating JF - Langmuir N2 - The spherical vaterite CaCO3 microcrystals are nowadays widely used as sacrificial templates for fabrication of various microcarriers made of biopolymers (e.g., proteins, nucleic acids, enzymes) due to porous structure and mild template elimination conditions. Here, we demonstrated for the first time that polymer microcarriers with tuned internal nanoarchitecture can be designed by employing the CaCO3 crystals of controlled porosity. The layer-by-layer deposition has been utilized to assemble shell-like (hollow) and matrix-like (filled) polymer capsules due to restricted and free polymer diffusion through the crystal pores, respectively. The crystal pore size in the range of few tens of nanometers can be adjusted without any additives by variation of the crystal preparation temperature in the range 745 degrees C. The temperature-mediated growth mechanism is explained by the Ostwald ripening of nanocrystallites forming the crystal secondary structure. Various techniques including SEM, AFM, CLSM, Raman microscopy, nitrogen adsorptiondesorption, and XRD have been employed for crystal and microcapsule analysis. A three-dimensional model is introduced to describe the crystal internal structure and predict the pore cutoff and available surface for the pore diffusing molecules. Inherent biocompatibility of CaCO3 and a possibility to scale the porosity in the size range of typical biomacromolecules make the CaCO3 crystals extremely attractive tools for template assisted designing tailor-made biopolymer-based architectures in 2D to 3D targeted at drug delivery and other bioapplications. Y1 - 2016 U6 - https://doi.org/10.1021/acs.langmuir.6b00717 SN - 0743-7463 VL - 32 SP - 4229 EP - 4238 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Erdossy, Julia A1 - Horvath, Viola A1 - Yarman, Aysu A1 - Scheller, Frieder W. A1 - Gyurcsanyi, Robert E. T1 - Electrosynthesized molecularly imprinted polymers for protein recognition JF - Trends in Analytical Chemistry N2 - Molecularly imprinted polymers (MIPs) for the recognition of proteins are expected to possess high affinity through the establishment of multiple interactions between the polymer matrix and the large number of functional groups of the target. However, while highly affine recognition sites need building blocks rich in complementary functionalities to their target, such units are likely to generate high levels of nonspecific binding. This paradox, that nature solved by evolution for biological receptors, needs to be addressed by the implementation of new concepts in molecular imprinting of proteins. Additionally, the structural variability, large size and incompatibility with a range of monomers made the development of protein MIPs to take a slow start. While the majority of MIP preparation methods are variants of chemical polymerization, the polymerization of electroactive functional monomers emerged as a particularly advantageous approach for chemical sensing application. Electropolymerization can be performed from aqueous solutions to preserve the natural conformation of the protein templates, with high spatial resolution and electrochemical control of the polymerization process. This review compiles the latest results, identifying major trends and providing an outlook on the perspectives of electrosynthesised protein-imprinted MIPs for chemical sensing. (C) 2016 Elsevier B.V. All rights reserved. KW - Molecularly imprinted polymers KW - Proteins KW - Surface imprinting KW - Electropolymerization KW - Nanostructuring KW - Hybrid nanofilms Y1 - 2016 U6 - https://doi.org/10.1016/j.trac.2015.12.018 SN - 0165-9936 SN - 1879-3142 VL - 79 SP - 179 EP - 190 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Pinyou, Piyanut A1 - Ruff, Adrian A1 - Poeller, Sascha A1 - Alsaoub, Sabine A1 - Leimkühler, Silke A1 - Wollenberger, Ursula A1 - Schuhmann, Wolfgang T1 - Wiring of the aldehyde oxidoreductase PaoABC to electrode surfaces via entrapment in low potential phenothiazine-modified redox polymers JF - Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society N2 - Phenothiazine-modified redox hydrogels were synthesized and used for the wiring of the aldehyde oxidoreductase PaoABC to electrode surfaces. The effects of the pH value and electrode surface modification on the biocatalytic activity of the layers were studied in the presence of vanillin as the substrate. The enzyme electrodes were successfully employed as bioanodes in vanillin/O-2 biofuel cells in combination with a high potential bilirubin oxidase biocathode. Open circuit voltages of around 700 mV could be obtained in a two compartment biofuel cell setup. Moreover, the use of a rather hydrophobic polymer with a high degree of crosslinking sites ensures the formation of stable polymer/enzyme films which were successfully used as bioanode in membrane-less biofuel cells. (C) 2015 Elsevier B.V. All rights reserved. KW - Aldehyde oxidoreductase KW - Enzyme electrode KW - Redox polymer KW - Phenothiazine KW - Biosensor KW - Biofuel cell Y1 - 2016 U6 - https://doi.org/10.1016/j.bioelechem.2015.12.005 SN - 1567-5394 SN - 1878-562X VL - 109 SP - 24 EP - 30 PB - Elsevier CY - Lausanne ER - TY - GEN A1 - Lechon, Tamara A1 - Sanz, Luis A1 - Pollmann, Stephan A1 - Sauer, Michael A1 - Sandalio, Luisa A1 - Lorenzo, Oscar T1 - Nitric oxide modification of plant endocytosis and PIN1 localization T2 - New biotechnology Y1 - 2016 U6 - https://doi.org/10.1016/j.nbt.2015.10.028 SN - 1871-6784 SN - 1876-4347 VL - 33 SP - 424 EP - 424 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Hartmann, Tobias A1 - Schrapers, Peer A1 - Utesch, Tillmann A1 - Nimtz, Manfred A1 - Rippers, Yvonne A1 - Dau, Holger A1 - Mroginski, Maria Andrea A1 - Haumann, Michael A1 - Leimkühler, Silke T1 - The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions JF - Biochemistry N2 - Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pK(a) of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase. Y1 - 2016 U6 - https://doi.org/10.1021/acs.biochem.6b00002 SN - 0006-2960 VL - 55 SP - 2381 EP - 2389 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Stein, F. A1 - Doering-Arjes, P. A1 - Fladung, Erik A1 - Brämick, Uwe A1 - Bendall, B. A1 - Schroeder, B. T1 - Downstream Migration of the European Eel (Anguilla Anguilla) in the Elbe River, Germany: Movement Patterns and the Potential Impact of Environmental Factors JF - River Research and Applications N2 - Recruitment of European eels (Anguilla anguilla) has declined to the extent that they have been added to the IUCN Red List of Threatened Species. Therefore, it is critical to ensure that eels complete their outward river migration in order to contribute to the available spawning stock. We conducted a 4-year (2007-2011) telemetry study to understand the migratory behaviour and potential impact of environmental factors on the eel during this critical life stage. Out of 399 female eels tagged with acoustic transmitters, only 28% demonstrated clear downstream migratory behaviour. Fifty-five percent were detected exhibiting no downstream migration behaviour and 17% were not detected at any monitoring station. Movement patterns of downstream-migrating (silver) eels were characterized by nocturnal activity and seasonal migration, with distinct peaks in autumn and spring. Migration was often discontinuous and exhibited phases of active locomotion and expanded stopovers. The most important determinants of movement activity were water temperature, cumulative precipitation and moonlight, although the significance varied by season and location in the river basin. Our results evidence a discontinuous, stepwise migration over an extended period. Furthermore, our findings indicate that migration success depends on holding duration prior to tagging and environmental predictors with varying importance depending on the season, as well as the locations of capture, tagging and release. Copyright (c) 2015 John Wiley & Sons, Ltd. KW - acoustic telemetry KW - fish migration KW - environmental trigger KW - generalized linear model KW - handling effect KW - discontinuous migration KW - Anguilla anguilla KW - seasonal migration Y1 - 2016 U6 - https://doi.org/10.1002/rra.2881 SN - 1535-1459 SN - 1535-1467 VL - 32 SP - 666 EP - 676 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - van de Weijer, Steve A1 - Bijleveld, Catrien A1 - Huschek, Doreen T1 - Offending and mortality JF - Advances in life course research N2 - Background: Previous research has shown that offenders are at increased risk to die prematurely, but the etiology of this association is still unknown. Moreover, most previous studies use relatively short follow-up periods and do not take into account variation within the offender population with respect to frequency, timing and types of offenses. Method: Using conviction data for a number of families at high-risk of offending born on average in 1932, we study mortality in both offenders and non-offenders, from a similar socio-economic background, until 2007. We condition on life expectancy of the parents, age, gender, year of birth and marital status. We investigate associations between mortality and offending for different types of offenses: violent offenses, property offenses, weapons offenses, drugs offenses and driving under influence. Results: In general, offending sample members were not significantly more likely to have died than non offending sample members. Compared to the general population, however, both the offending and non offending sample members were at increased risk to die. Sample members who were convicted for driving under the influence of alcohol or weapons offenses were at increased risk to die prematurely compared to non-offending sample members. Conclusions: The relationship between offending in general and mortality is largely spurious. Limitations: The use of official conviction data might have influenced the results. (C) 2015 Elsevier Ltd. All rights reserved. KW - Mortality KW - Offending KW - Mechanisms KW - Survival KW - The Netherlands Y1 - 2016 U6 - https://doi.org/10.1016/j.alcr.2015.11.004 SN - 1569-4909 SN - 1879-6974 VL - 28 SP - 91 EP - 99 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Fer, Istem A1 - Tietjen, Britta A1 - Jeltsch, Florian T1 - High-resolution modelling closes the gap between data and model simulations for Mid-Holocene and present-day biomes of East Africa JF - Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences N2 - East Africa hosts a striking diversity of terrestrial ecosystems, which vary both in space and time due to complex regional topography and a dynamic climate. The structure and functioning of these ecosystems under this environmental setting can be studied with dynamic vegetation models (DVMs) in a spatially explicit way. Yet, regional applications of DVMs to East Africa are rare and a comprehensive validation of such applications is missing. Here, we simulated the present-day and mid-Holocene vegetation of East Africa with the DVM, LPJ-GUESS and we conducted an exhaustive comparison of model outputs with maps of potential modern vegetation distribution, and with pollen records of local change through time. Overall, the model was able to reproduce the observed spatial patterns of East African vegetation. To see whether running the model at higher spatial resolutions (10′ × 10′) contribute to resolve the vegetation distribution better and have a better comparison scale with the observational data (i.e. pollen data), we run the model with coarser spatial resolution (0.5° × 0.5°) for the present-day as well. Both the area- and point-wise comparison showed that a higher spatial resolution allows to better describe spatial vegetation changes induced by the complex topography of East Africa. Our analysis of the difference between modelled mid-Holocene and modern-day vegetation showed that whether a biome shifts to another is best explained by both the amount of change in precipitation it experiences and the amount of precipitation it received originally. We also confirmed that tropical forest biomes were more sensitive to a decrease in precipitation compared to woodland and savanna biomes and that Holocene vegetation changes in East Africa were driven not only by changes in annual precipitation but also by changes in its seasonality. KW - Dynamic vegetation models KW - Biome KW - Mid-Holocene KW - Leaf area index KW - Climate change KW - East Africa Y1 - 2016 U6 - https://doi.org/10.1016/j.palaeo.2015.12.001 SN - 0031-0182 SN - 1872-616X VL - 444 SP - 144 EP - 151 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Orawetz, Tom A1 - Malinova, Irina A1 - Orzechowski, Slawomir A1 - Fettke, Jörg T1 - Reduction of the plastidial phosphorylase in potato (Solanum tuberosum L.) reveals impact on storage starch structure during growth at low temperature JF - Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology N2 - Tubers of potato (Solanum tuberosum L.), one of the most important crops, are a prominent example for an efficient production of storage starch. Nevertheless, the synthesis of this storage starch is not completely understood. The plastidial phosphorylase (Phol; EC 2.4.11) catalyzes the reversible transfer of glucosyl residues from glucose-1-phosphate to the non-reducing end of alpha-glucans with the release of orthophosphate. Thus, the enzyme is in principle able to act during starch synthesis. However, so far under normal growth conditions no alterations in tuber starch metabolism were observed. Based on analyses of other species and also from in vitro experiments with potato tuber slices it was supposed, that Phol has a stronger impact on starch metabolism, when plants grow under low temperature conditions. Therefore, we analyzed the starch content, granule size, as well as the internal structure of starch granules isolated from potato plants grown under low temperatures. Besides wild type, transgenic potato plants with a strong reduction in the Phol activity were analyzed. No significant alterations in starch content and granule size were detected. In contrast, when plants were cultivated at low temperatures the chain length distributions of the starch granules were altered. Thus, the granules contained more short glucan chains. That was not observed in the transgenic plants, revealing that Pho1 in wild type is involved in the formation of the short glucan chains, at least at low temperatures. (C) 2016 Elsevier Masson SAS. All rights reserved. KW - Potato KW - Solanum tuberosum L. KW - Plastidial phosphorylase KW - Starch synthase KW - Starch metabolism KW - Starch granule Y1 - 2016 U6 - https://doi.org/10.1016/j.plaphy.2016.01.013 SN - 0981-9428 VL - 100 SP - 141 EP - 149 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Pfestorf, Hans A1 - Körner, Katrin A1 - Sonnemann, Ilja A1 - Wurst, Susanne A1 - Jeltsch, Florian T1 - Coupling experimental data with individual-based modelling reveals differential effects of root herbivory on grassland plant co-existence along a resource gradient JF - Journal of vegetation science N2 - QuestionThe empirical evidence of root herbivory effects on plant community composition and co-existence is contradictory. This originates from difficulties connected to below-ground research and confinement of experimental studies to a small range of environmental conditions. Here we suggest coupling experimental data with an individual-based model to overcome the limitations inherent in either approach. To demonstrate this, we investigated the consequences of root herbivory, as experimentally observed on individual plants, on plant competition and co-existence in a population and community context under different root herbivory intensities (RHI), fluctuating and constant root herbivore activity and grazing along a resource gradient. LocationBerlin, Germany, glasshouse; Potsdam, Germany, high performance cluster computer. MethodsThe well-established community model IBC-Grass was adapted to allow for a flexible species parameterization and to include annual species. Experimentally observed root herbivory effects on performance of eight common grassland plant species were incorporated into the model by altering plant growth rates. We then determined root herbivore effects on plant populations, competitive hierarchy and consequences for co-existence and community diversity. ResultsRoot herbivory reduced individual biomass, but temporal fluctuation allowed for compensation of herbivore effects. Reducing resource availability strongly shifted competitive hierarchies, with, however, more similar hierarchies along the gradient under root herbivory, pointing to reduced ecological species differences. Consequently, negative effects on co-existence and diversity prevailed, with the exception of a few positive effects on co-existence of selected species pairs. Temporal fluctuation alleviated but did not remove negative root herbivore effects, despite of the stronger influence of intra- compared to interspecific competition. Grazing in general augmented co-existence. Most interestingly, grazing interacted with RHI and resource availability by promoting positive effects of root herbivory. ConclusionsThrough integrating experimental data on the scale of individual plants with a simulation model we verified that root herbivory could affect plant competition with consequences for species co-existence. Our approach demonstrates the benefit that accrues when empirical and modelling approaches are brought more closely together, and that gathering data on distinct processes and under specific conditions, combined with appropriate models, can be used to answer challenging research questions in a more general way. KW - Above-/below-ground interactions KW - Below-ground resources KW - Competitive hierarchies KW - Grassland KW - Greenhouse experiment KW - Simulation experiment KW - Species co-existence KW - Wireworms Y1 - 2016 U6 - https://doi.org/10.1111/jvs.12357 SN - 1100-9233 SN - 1654-1103 VL - 27 SP - 269 EP - 282 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Jargosch, M. A1 - Kroeger, S. A1 - Gralinska, E. A1 - Klotz, Ulrike A1 - Fang, Z. A1 - Chen, W. A1 - Leser, U. A1 - Selbig, Joachim A1 - Groth, Detlef A1 - Baumgrass, Ria T1 - Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions JF - Genetics and molecular research N2 - Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation. We focused on transcription factors (TFs), cytokines, and cytokine receptors and delineated 59 positively and 41 negatively STAT6-regulated genes, which were used to construct a transcriptional network around STAT6. The network illustrates that important and well-known TFs for Th2 cell differentiation are positively regulated by STAT6 and act either as activators for Th2 cells (e.g., Gata3, Atf3, Satb1, Nfil3, Maf, and Pparg) or as suppressors for other Th cell subpopulations such as Th1 (e.g., Ar), Th17 (e.g., Etv6), or iTreg (e.g., Stat3 and Hifla) cells. Moreover, our approach reveals 11 TFs (e.g., Atf5, Creb3l2, and Asb2) with unknown functions in Th cell differentiation. This fact together with the observed enrichment of asthma risk genes among those regulated by STAT6 underlines the potential value of the data integration strategy used here. Thus, our results clearly support the opinion that data integration is a useful tool to delineate complex physiological processes. KW - Data integration KW - Th2 cells KW - Gene regulatory network KW - STAT6 KW - Transcription factors Y1 - 2016 U6 - https://doi.org/10.4238/gmr.15028493 SN - 1676-5680 VL - 15 PB - FUNPEC CY - Ribeirao Preto ER - TY - JOUR A1 - Ud-Din, Aziz A1 - Rauf, Mamoona A1 - Ghafoor, S. A1 - Khattak, M. N. K. A1 - Hameed, M. W. A1 - Shah, H. A1 - Jan, S. A1 - Muhammad, K. A1 - Rehman, A. A1 - Inamullah, T1 - Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana JF - Genetics and molecular research N2 - Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative realtime polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant. KW - Artificial micro-RNA KW - Arabidopsis thaliana KW - qRT-PCR KW - AtExpA8 KW - AHL25 Y1 - 2016 U6 - https://doi.org/10.4238/gmr.15027439 SN - 1676-5680 VL - 15 PB - FUNPEC CY - Ribeirao Preto ER - TY - JOUR A1 - Kruse, Michaela A1 - Stein-Bachinger, Karin A1 - Gottwald, Frank A1 - Schmidt, Elisabeth A1 - Heinken, Thilo T1 - Influence of grassland management on the biodiversity of plants and butterflies on organic suckler cow farms JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - The intensification of agricultural practices has led to a severe decrease in grassland biodiversity. Although there is strong evidence that organic farming can reduce the negative impacts of land use, knowledge regarding the most beneficial management system for species richness on organic grasslands is still scarce. This study examines differences in the biodiversity of plants and butterflies on rotationally and continuously grazed pastures as well as on meadows cut twice per year on two large organic suckler cow farms in NE Germany. Vegetation and flower abundance, as factors likely to influence butterfly abundance and diversity, were compared and used to explain the differences. The data attained by vegetation assessments and monthly transect inspections from May to August were analyzed using descriptive statistics and nonparametric methods. The abiotic site conditions of the studied plots had more influence on plant species numbers than the management method. Dry and nutrient-poor areas (mainly poor types of Cynosurion) and undrained wet fens (Calthion) were important for phytodiversity, measured by the absolute number of species, indicator species for ecologically valuable grasslands and the Shannon Index. Meadows tended to have more indicator species than pastures, where small-scale special sites such as wet depressions were crucial for plant diversity. Butterfly diversity was very low, and 90% of the recorded butterflies were individuals of the generalist species Pieris napi. Butterfly abundance depended mainly on occurrence of specific habitat types and specific larval host plants. Supply of flowers was crucial only in certain time periods. Differences in butterfly abundance between the management systems could be explained by the site conditions of the studied grasslands. We conclude that meadows are more favorable to support ecologically valuable plant species; however, their extension is contradictory to the organic farming method of suckler cows maintained outside of stables. Rotationally grazed pastures could be a compromise that would enhance the temporal heterogeneity of flower abundance and vegetation structure. The plant diversity on pastures should be improved by less intensive grazing on special sites and plant species enrichment by means of hay transfer. For enhancing butterfly diversity we suggest to reduce land use intensity especially on poor soils. Considering the economic perspective of the farms, small parts of the agricultural area could be sufficient if connectivity to other suitable habitats is assured. Flower abundance and diversity of larval host plants could be promoted by high diversity of farming practices as well as preserving small uncut strips of meadows. KW - cattle grazing KW - continuous pasture KW - land use impact KW - lowland fen KW - meadow KW - organic farming KW - plant community KW - rotational pasture KW - species diversity KW - wet grassland Y1 - 2016 U6 - https://doi.org/10.14471/2016.56.006 SN - 0722-494X VL - 37 SP - 97 EP - 119 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Mao, Hailiang A1 - Nakamura, Moritaka A1 - Viotti, Corrado A1 - Grebe, Markus T1 - A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.01252 SN - 0032-0889 SN - 1532-2548 VL - 172 SP - 2245 EP - 2260 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Reinecke, J. A1 - Wulf, M. A1 - Baeten, Lander A1 - Brunet, J. A1 - Decocq, G. A1 - De Frenne, G. A1 - Diekmann, M. A1 - Graae, B. J. A1 - Heinken, Thilo A1 - Hermy, M. A1 - Jamoneau, A. A1 - Lenoir, J. A1 - Plue, J. A1 - Orczewska, A. A1 - Van Calster, H. A1 - Verheyen, Kris A1 - Naaf, T. T1 - Acido- and neutrophilic temperate forest plants display distinct shifts in ecological pH niche across north-western Europe JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - Ecological niches of organisms vary across geographical space, but niche shift patterns between regions and the underlying mechanisms remain largely unexplored. We studied shifts in the pH niche of 42 temperate forest plant species across a latitudinal gradient from northern France to boreo-nemoral Sweden. We asked 1) whether species restrict their niches with increasing latitude as they reach their northern range margin (environmental constraints); 2) whether species expand their niches with increasing latitude as regional plant species richness decreases (competitive release); and 3) whether species shift their niche position toward more acidic sites with increasing latitude as the relative proportion of acidic soils increases (local adaptation). Based on 1458 vegetation plots and corresponding soil pH values, we modelled species response curves using Huisman-Olff-Fresco models. Four niche measures (width, position, left and right border) were compared among regions by randomization tests. We found that with increasing latitude, neutrophilic species tended to retreat from acidic sites, indicating that these species retreat to more favorable sites when approaching their range margin. Alternatively, these species might benefit from enhanced nitrogen deposition on formerly nutrient-poor, acidic sites in southern regions or lag behind in post-glacial recolonization of potential habitats in northern regions. Most acidophilic species extended their niche toward more base-rich sites with increasing latitude, indicating competitive release from neutrophilic species. Alternatively, acidophilic species might benefit from optimal climatic conditions in the north where some have their core distribution area. Shifts in the niche position suggested that local adaptation is of minor importance. We conclude that shifts in the pH niche of temperate forest plants are the rule, but the directions of the niche shifts and possible explanations vary. Our study demonstrates that differentiating between acidophilic and neutrophilic species is crucial to identify general patterns and underlying mechanisms. Y1 - 2016 U6 - https://doi.org/10.1111/ecog.02051 SN - 0906-7590 SN - 1600-0587 VL - 39 SP - 1164 EP - 1175 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Procter, Duncan S. A1 - Cottrell, Joan E. A1 - Watts, Kevin A1 - Hofreiter, Michael A1 - Robinson, Elva J. H. T1 - Does cooperation mean kinship between spatially discrete ant nests? JF - Ecology and evolution N2 - Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation. KW - colony organization KW - eusociality KW - Formica lugubris KW - kin selection KW - polydomy KW - social organization Y1 - 2016 U6 - https://doi.org/10.1002/ece3.2590 SN - 2045-7758 VL - 6 SP - 8846 EP - 8856 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wutke, Saskia A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez Soto, Javier Esteban A1 - Hallsson, Jon Hallsteinn A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Spotted phenotypes in horses lost attractiveness in the Middle Ages JF - Scientific reports N2 - Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population. Y1 - 2016 U6 - https://doi.org/10.1038/srep38548 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Coutinho, Renato Mendes A1 - Klauschies, Toni A1 - Gaedke, Ursula T1 - Bimodal trait distributions with large variances question the reliability of trait-based aggregate models JF - Theoretical ecology N2 - Functionally diverse communities can adjust their species composition to altered environmental conditions, which may influence food web dynamics. Trait-based aggregate models cope with this complexity by ignoring details about species identities and focusing on their functional characteristics (traits). They describe the temporal changes of the aggregate properties of entire communities, including their total biomasses, mean trait values, and trait variances. The applicability of aggregate models depends on the validity of their underlying assumptions that trait distributions are normal and exhibit small variances. We investigated to what extent this can be expected to work by comparing an innovative model that accounts for the full trait distributions of predator and prey communities to a corresponding aggregate model. We used a food web structure with well-established trade-offs among traits promoting mutual adjustments between prey edibility and predator selectivity in response to selection. We altered the shape of the trade-offs to compare the outcome of the two models under different selection regimes, leading to trait distributions increasingly deviating from normality. Their biomass and trait dynamics agreed very well for stabilizing selection and reasonably well for directional selection, under which different trait values are favored at different times. However, for disruptive selection, the results of the aggregate model strongly deviated from the full trait distribution model that showed bimodal trait distributions with large variances. Hence, the outcome of aggregate models is reliable under ideal conditions but has to be questioned when confronted with more complex selection regimes and trait distributions, which are commonly observed in nature. KW - Fitness gradient KW - Communities as complex adaptive systems KW - Moment closure for trait-based aggregate model approaches KW - Multimodal trait distributions KW - Lumpiness in pattern formation and self-organization KW - Shape of trade-offs and stabilizing and disruptive selection Y1 - 2016 U6 - https://doi.org/10.1007/s12080-016-0297-9 SN - 1874-1738 SN - 1874-1746 VL - 9 SP - 389 EP - 408 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Lukoszek, Radoslaw A1 - Feist, Peter A1 - Ignatova, Zoya T1 - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq JF - BMC plant biology N2 - Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure. KW - Translation KW - Ribosome profiling KW - Transcription KW - RNA-Seq KW - Secondary structure KW - G-quadruplexes KW - Heat stress response Y1 - 2016 U6 - https://doi.org/10.1186/s12870-016-0915-0 SN - 1471-2229 VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, Andre A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites JF - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2016 U6 - https://doi.org/10.3389/fpls.2016.01560 SN - 1664-462X VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Navarro-Retamal, Carlos A1 - Bremer, Anne A1 - Alzate-Morales, Jans H. A1 - Caballero, Julio A1 - Hincha, Dirk K. A1 - Gonzalez, Wendy A1 - Thalhammer, Anja T1 - Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain alpha-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state. Y1 - 2016 U6 - https://doi.org/10.1039/c6cp02272c SN - 1463-9076 SN - 1463-9084 VL - 18 SP - 25806 EP - 25816 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schneider, Florian D. A1 - Brose, Ulrich A1 - Rall, Björn C. A1 - Guill, Christian T1 - Animal diversity and ecosystem functioning in dynamic food webs JF - Nature Communications N2 - Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity. Y1 - 2016 U6 - https://doi.org/10.1038/ncomms12718 SN - 2041-1723 VL - 7 SP - 3129 EP - 3138 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Han, Xiao Xia A1 - Li, Junbo A1 - Öner, Ibrahim Halil A1 - Zhao, Bing A1 - Leimkühler, Silke A1 - Hildebrandt, Peter A1 - Weidinger, Inez M. T1 - Nickel electrodes as a cheap and versatile platform for studying structure and function of immobilized redox proteins JF - Analytica chimica acta : an international journal devoted to all branches of analytical chemistry N2 - Practical use of many bioelectronic and bioanalytical devices is limited by the need of expensive materials and time consuming fabrication. Here we demonstrate the use of nickel electrodes as a simple and cheap solid support material for bioelectronic applications. The naturally nanostructured electrodes showed a surprisingly high electromagnetic surface enhancement upon light illumination such that immobilization and electron transfer reactions of the model redox proteins cytochrome b(5) (Cyt b(5)) and cytochrome c (Cyt c) could be followed via surface enhanced resonance Raman spectroscopy. It could be shown that the nickel surface, when used as received, promotes a very efficient binding of the proteins upon preservation of their native structure. The immobilized redox proteins could efficiently exchange electrons with the electrode and could even act as an electron relay between the electrode and solubilized myoglobin. Our results open up new possibility for nickel electrodes as an exceptional good support for bioelectronic devices and biosensors on the one hand and for surface enhanced spectroscopic investigations on the other hand. (C) 2016 Elsevier B.V. All rights reserved. KW - Ni electrodes KW - Redox proteins KW - Surface enhanced Raman spectroscopy KW - Electron relay KW - Biocompatibility KW - Electron transfer Y1 - 2016 U6 - https://doi.org/10.1016/j.aca.2016.08.053 SN - 0003-2670 SN - 1873-4324 VL - 941 SP - 35 EP - 40 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zeng, Ting A1 - Frasca, Stefano A1 - Rumschöttel, Jens A1 - Koetz, Joachim A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - Role of Conductive Nanoparticles in the Direct Unmediated Bioelectrocatalysis of Immobilized Sulfite Oxidase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis KW - Direct electron transfer KW - Protein voltammetry KW - Human sulfite oxidase KW - Bioelectrocatalysis KW - Nanoparticles Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600246 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2303 EP - 2310 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Dongmo, Saustin A1 - Leyk, Janina A1 - Dosche, Carsten A1 - Richter-Landsberg, Christiane A1 - Wollenberger, Ursula A1 - Wittstock, Gunther T1 - Electrogeneration of O-2(center dot-) and H2O2 Using Polymer-modified Microelectrodes in the Environment of Living Cells JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - Microelectrodes modified with electropolymerized plumbagin (PLG) were used for the generation of superoxide radical (O-2(center dot-)) and hydrogen peroxide (H2O2) during oxygen reduction reaction (ORR) in an aqueous medium, specifically in serum-free cell culture media. This is enabled by the specific design of a polymer film on the microelectrode. The generation and diffusion of O-2(center dot-) during electrocatalytic ORR at a positionable PLG polymer-modified microelectrode was followed by fluorescence microscopy with the selective dye 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) and by amperometric detection using a cytochrome c-modified electrode at + 0.13 V. H2O2 production, either by direct oxygen reduction or as product of O-2(center dot-) disproportionation, was monitored by the reaction with Amplex UltraRed. The PLG polymer-modified microelectrodes were used to expose mammalian B6-RPE07 retinal cells to defined local fluxes of reactive oxygen species (ROS), and cellular responses and morphological alterations were observed. The use of a controllable source of ROS opens many possibilities to study how living cells respond to the presence of a certain flux of specific ROS. KW - reactive oxygen species KW - microelectrode KW - scanning electrochemical microscopy KW - biosensor KW - polymer-modified electrode KW - oxygen reduction reaction Y1 - 2016 U6 - https://doi.org/10.1002/elan.201600267 SN - 1040-0397 SN - 1521-4109 VL - 28 SP - 2400 EP - 2407 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Guardado-Calvo, Pablo A1 - Bignon, Eduardo A. A1 - Stettner, Eva A1 - Jeffers, Scott Allen A1 - Perez-Vargas, Jimena A1 - Pehau-Arnaudet, Gerard A1 - Tortoric, M. Alejandra A1 - Jestin, Jean-Luc A1 - England, Patrick A1 - Tischler, Nicole D. A1 - Rey, Felix A. T1 - Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc JF - PLoS Pathogens N2 - Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic beta-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha-and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens. Y1 - 2016 U6 - https://doi.org/10.1371/journal.ppat.1005813 SN - 1553-7366 SN - 1553-7374 VL - 12 SP - 153 EP - 166 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Gietler, Marta A1 - Nykiel, Malgorzata A1 - Orzechowski, Slawomir A1 - Zagdanska, Barbara A1 - Fettke, Jörg T1 - Proteomic analysis of S-nitrosylated and S-glutathionylated proteins in wheat seedlings with different dehydration tolerances JF - Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology N2 - A loss of dehydration tolerance in wheat seedlings on the fifth day following imbibition is associated with a disturbance in cellular redox homeostasis, as documented by a shift of the reduced/oxidized glutathione ratio to a more oxidized state and a significant increase in the ratio of protein thiols to the total thiol group content. Therefore, the identification and characterization of redox-sensitive proteins are important steps toward understanding the molecular mechanisms of the loss of dehydration tolerance. In the present study, proteins that were differentially expressed between fully turgid (control), dehydrated tolerant (four-day-old) and dehydrated sensitive (six-day-old) wheat seedlings were analysed. Protein spots having at least a significant (p < 0.05) two-fold change in protein abundance were selected by Delta2D as differentially expressed, identified by MALDI-TOF and LC-MS/MS, and classified according to their function. The observed changes in the proteomic patterns of the differentially S-nitrosylated and S-glutathionylated proteins were highly specific in dehydration-tolerant and-sensitive wheat seedlings. The metabolic function of these proteins indicates that dehydration tolerance is mainly related to nucleic acids, protein metabolism, and energy metabolism. It has been proven that leaf-specific thionins BTH6 and DB4, chloroplastic 50S ribosomal protein L16, phospholipase A1-II delta, and chloroplastic thioredoxin M2 are both S-nitrosylated and S-glutathionylated upon water deficiency. Our results revealed the existence of interplay between S-nitrosylation and S-glutathionylation, two redox-regulated protein posttranslational modifications that could enhance plant defence mechanisms and/or facilitate the acclimation of plants to unfavourable environmental conditions. (C) 2016 Elsevier Masson SAS. All rights reserved. KW - Dehydration tolerance KW - Proteomics KW - Redox sensitive proteins KW - S-glutathionylation KW - S-nitrosylation KW - Triticum aestivum L. Y1 - 2016 U6 - https://doi.org/10.1016/j.plaphy.2016.08.017 SN - 0981-9428 VL - 108 SP - 507 EP - 518 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Nukarinen, Ella A1 - Nägele, Thomas A1 - Pedrotti, Lorenzo A1 - Wurzinger, Bernhard A1 - Mair, Andrea A1 - Landgraf, Ramona A1 - Börnke, Frederik A1 - Hanson, Johannes A1 - Teige, Markus A1 - Baena-Gonzalez, Elena A1 - Dröge-Laser, Wolfgang A1 - Weckwerth, Wolfram T1 - Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation JF - Scientific reports N2 - Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA:: SnRK1 alpha 2 in a snrk1 alpha 1 knock out background (snrk1 alpha 1/alpha 2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1 alpha 1/alpha 2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1 alpha 1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1 alpha 1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1 alpha 1/alpha 2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants. Y1 - 2016 U6 - https://doi.org/10.1038/srep31697 SN - 2045-2322 VL - 6 SP - 10248 EP - 10252 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Périllon, Cécile A1 - Hilt, Sabine T1 - Groundwater influence differentially affects periphyton and macrophyte production in lakes JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Groundwater influx can significantly contribute to nutrient and carbon budgets of lakes, and its influence is the strongest in littoral areas dominated by macrophytes and periphyton. We have reviewed the effects of groundwater-borne nitrogen and phosphorus and dissolved inorganic and organic carbon (DIC, DOC) on these benthic primary producers in lakes. We develop a hypothesis for groundwater effects including the less studied impacts of periphyton shading on macrophytes. Groundwater-borne nutrients and DIC promote both macrophytes and periphyton. Direct studies on groundwater-borne DOC effects are lacking, but coloured DOC contributes to light attenuation and thus can restrict the growth of benthic primary producers. We predict that above certain threshold levels of nutrient influx by groundwater, periphyton and macrophyte biomass should decline owing to shading by phytoplankton and periphyton, respectively. However, because of their higher light requirements, those thresholds should be lower for macrophytes. For macrophytes, a threshold level is also predicted for a shift from DIC limitation to light limitation. Differences in light requirements are expected to result in lower thresholds of DOC loading for declines of macrophytes than periphyton. KW - Dissolved inorganic carbon KW - Dissolved organic carbon KW - Light KW - Macrophytes KW - Nutrients KW - Periphyton Y1 - 2016 U6 - https://doi.org/10.1007/s10750-015-2485-9 SN - 0018-8158 SN - 1573-5117 VL - 778 SP - 91 EP - 103 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Saffert, Paul A1 - Adamla, Frauke A1 - Schieweck, Rico A1 - Atkins, John F. A1 - Ignatova, Zoya T1 - An Expanded CAG Repeat in Huntingtin Causes+1 Frameshifting JF - The journal of biological chemistry N2 - Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5 end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1. KW - aggregation KW - Huntington disease KW - translation KW - translation regulation KW - trinucleotide repeat disease KW - frameshifting KW - seeding Y1 - 2016 U6 - https://doi.org/10.1074/jbc.M116.744326 SN - 0021-9258 SN - 1083-351X VL - 291 SP - 18505 EP - 18513 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Soliveres, Santiago A1 - van der Plas, Fons A1 - Manning, Peter A1 - Prati, Daniel A1 - Gossner, Martin M. A1 - Renner, Swen C. A1 - Alt, Fabian A1 - Arndt, Hartmut A1 - Baumgartner, Vanessa A1 - Binkenstein, Julia A1 - Birkhofer, Klaus A1 - Blaser, Stefan A1 - Blüthgen, Nico A1 - Boch, Steffen A1 - Böhm, Stefan A1 - Börschig, Carmen A1 - Buscot, Francois A1 - Diekötter, Tim A1 - Heinze, Johannes A1 - Hölzel, Norbert A1 - Jung, Kirsten A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Klemmer, Sandra A1 - Krauss, Jochen A1 - Lange, Markus A1 - Morris, E. Kathryn A1 - Müller, Jörg A1 - Oelmann, Yvonne A1 - Overmann, Jörg A1 - Pasalic, Esther A1 - Rillig, Matthias C. A1 - Schaefer, H. Martin A1 - Schloter, Michael A1 - Schmitt, Barbara A1 - Schöning, Ingo A1 - Schrumpf, Marion A1 - Sikorski, Johannes A1 - Socher, Stephanie A. A1 - Solly, Emily F. A1 - Sonnemann, Ilja A1 - Sorkau, Elisabeth A1 - Steckel, Juliane A1 - Steffan-Dewenter, Ingolf A1 - Stempfhuber, Barbara A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Venter, Paul C. A1 - Weiner, Christiane N. A1 - Weisser, Wolfgang W. A1 - Werner, Michael A1 - Westphal, Catrin A1 - Wilcke, Wolfgang A1 - Wolters, Volkmar A1 - Wubet, Tesfaye A1 - Wurst, Susanne A1 - Fischer, Markus A1 - Allan, Eric T1 - Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality JF - Nature : the international weekly journal of science Y1 - 2016 U6 - https://doi.org/10.1038/nature19092 SN - 0028-0836 SN - 1476-4687 VL - 536 SP - 456 EP - + PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Wutke, Saskia A1 - Andersson, Leif A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Gonzalez, Javier A1 - Hallsson, Jon Hallsteinn A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Munoz-Rodriguez, Mariana B. A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Hofreiter, Michael A1 - Ludwig, Arne T1 - The origin of ambling horses T2 - Current biology N2 - Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called ‘gaited’ horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th–11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date. Y1 - 2016 U6 - https://doi.org/10.1016/j.cub.2016.07.001 SN - 0960-9822 SN - 1879-0445 VL - 26 SP - R697 EP - R699 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Turjeman, Sondra Feldman A1 - Centeno-Cuadros, Alejandro A1 - Eggers, Ute A1 - Rotics, Shay A1 - Blas, Julio A1 - Fiedler, Wolfgang A1 - Kaatz, Michael A1 - Jeltsch, Florian A1 - Wikelski, Martin A1 - Nathan, Ran T1 - Extra-pair paternity in the socially monogamous white stork (Ciconia ciconia) is fairly common and independent of local density JF - Scientific reports N2 - Although many birds are socially monogamous, most (>75%) studied species are not strictly genetically monogamous, especially under high breeding density. We used molecular tools to reevaluate the reproductive strategy of the socially monogamous white stork (Ciconia ciconia) and examined local density effects. DNA samples of nestlings (Germany, Spain) were genotyped and assigned relationships using a two-program maximum likelihood classification. Relationships were successfully classified in 79.2% of German (n = 120) and 84.8% of Spanish (n = 59) nests. For each population respectively, 76.8% (n = 73) and 66.0% (n = 33) of nests contained only full-siblings, 10.5% (n = 10) and 18.0% (n = 9) had half-siblings (at least one nestling with a different parent), 3.2% (n = 3) and 10.0% (n = 5) had unrelated nestlings (at least two nestlings, each with different parents), and 9.5% (n = 9) and 6.0% (n = 3) had “not full-siblings” (could not differentiate between latter two cases). These deviations from strict monogamy place the white stork in the 59th percentile for extra-pair paternity among studied bird species. Although high breeding density generally increases extra-pair paternity, we found no significant association with this species’ mating strategies. Thus although genetic monogamy is indeed prominent in the white stork, extra-pair paternity is fairly common compared to other bird species and cannot be explained by breeding density. Y1 - 2016 U6 - https://doi.org/10.1038/srep27976 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wettstein, Christoph A1 - Kano, Kenji A1 - Schaefer, Daniel A1 - Wollenberger, Ursula A1 - Lisdat, Fred T1 - Interaction of Flavin-Dependent Fructose Dehydrogenase with Cytochrome c as Basis for the Construction of Biomacromolecular Architectures on Electrodes JF - Analytical chemistry N2 - The creation of electron transfer (ET) chains based on the defined arrangement of enzymes and redox proteins on electrode surfaces represents an interesting approach within the field of bioelectrocatalysis. In this study, we investigated the ET reaction of the flavin-dependent enzyme fructose dehydrogenase (FDH) with the redox protein cytochrome c (cyt c). Two different pH optima were found for the reaction in acidic and neutral solutions. When cyt c was adsorbed on an electrode surface while the enzyme remained in solution, ET proceeded efficiently in media of neutral pH. Interprotein ET was also observed in acidic media; however, it appeared to be less efficient. These findings suggest that two different ET pathways between the enzyme and cyt c may occur. Moreover, cyt c and FDH were immobilized in multiple layers on an electrode surface by means of another biomacromolecule: DNA (double stranded) using the layer -by -layer technique. The biprotein multilayer architecture showed a catalytic response in dependence on the fructose concentration, indicating that the ET reaction between both proteins is feasible even in the immobilized state. The electrode showed a defined response to fructose and a good storage stability. Our results contribute to the better understanding of the ET reaction between FDH and cyt c and provide the basis for the creation of all-biomolecule based fructose sensors the sensitivity of which can be controlled by the layer preparation. Y1 - 2016 U6 - https://doi.org/10.1021/acs.analchem.6b00815 SN - 0003-2700 SN - 1520-6882 VL - 88 SP - 6382 EP - 6389 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Almathen, Faisal A1 - Charruau, Pauline A1 - Mohandesan, Elmira A1 - Mwacharo, Joram M. A1 - Orozco-terWengel, Pablo A1 - Pitt, Daniel A1 - Abdussamad, Abdussamad M. A1 - Uerpmann, Margarethe A1 - Uerpmann, Hans-Peter A1 - De Cupere, Bea A1 - Magee, Peter A1 - Alnaqeeb, Majed A. A1 - Salim, Bashir A1 - Raziq, Abdul A1 - Dessie, Tadelle A1 - Abdelhadi, Omer M. A1 - Banabazi, Mohammad H. A1 - Al-Eknah, Marzook A1 - Walzer, Chris A1 - Fayer, Bernard A1 - Hofreiter, Michael A1 - Peters, Joris A1 - Hanotte, Olivier A1 - Burger, Pamela A. T1 - Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. KW - anthropogenic admixture KW - Camelus dromedarius KW - demographic history KW - paleogenetics KW - wild dromedary Y1 - 2016 U6 - https://doi.org/10.1073/pnas.1519508113 SN - 0027-8424 VL - 113 SP - 6707 EP - 6712 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Hoffmann, Stefan A. A1 - Kruse, Sabrina M. A1 - Arndt, Katja Maren T1 - Long-range transcriptional interference in E-coli used to construct a dual positive selection system for genetic switches JF - Nucleic acids research N2 - We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong σ70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw125 SN - 0305-1048 SN - 1362-4962 VL - 44 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Mahlow, Sebastian A1 - Orzechowski, Slawomir A1 - Fettke, Jörg T1 - Starch phosphorylation: insights and perspectives JF - Cellular and molecular life sciences N2 - During starch metabolism, the phosphorylation of glucosyl residues of starch, to be more precise of amylopectin, is a repeatedly observed process. This phosphorylation is mediated by dikinases, the glucan, water dikinase (GWD) and the phosphoglucan, water dikinase (PWD). The starch-related dikinases utilize ATP as dual phosphate donor transferring the terminal gamma-phosphate group to water and the beta-phosphate group selectively to either C6 position or C3 position of a glucosyl residue within amylopectin. By the collaborative action of both enzymes, the initiation of a transition of alpha-glucans from highly ordered, water-insoluble state to a less order state is realized and thus the initial process of starch degradation. Consequently, mutants lacking either GWD or PWD reveal a starch excess phenotype as well as growth retardation. In this review, we focus on the increased knowledge collected over the last years related to enzymatic properties, the precise definition of the substrates, the physiological implications, and discuss ongoing questions. KW - Starch metabolism KW - Glucan, water dikinase KW - Phosphoglucan, water dikinase KW - Starch phosphorylation KW - Starch degradation Y1 - 2016 U6 - https://doi.org/10.1007/s00018-016-2248-4 SN - 1420-682X SN - 1420-9071 VL - 73 SP - 2753 EP - 2764 PB - Springer CY - Basel ER - TY - JOUR A1 - Gorochowski, Thomas E. A1 - Aycilar-Kucukgoze, Irem A1 - Bovenberg, Roel A. L. A1 - Roubos, Johannes A. A1 - Ignatova, Zoya T1 - A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes JF - ACS synthetic biology N2 - Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources. KW - protein biosynthesis KW - translation KW - synthetic biology KW - systems biology Y1 - 2016 U6 - https://doi.org/10.1021/acssynbio.6b00040 SN - 2161-5063 VL - 5 SP - 710 EP - 720 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Beenken, Ludwig A1 - Sainge, Moses N. A1 - Kocyan, Alexander T1 - Lactarius megalopterus, a new angiocarpous species from a tropical rainforest in Central Africa, shows adaptations to endozoochorous spore dispersal JF - Mycological progress : international journal of the German Mycological Society N2 - A new sequestrate Lactarius species was found in a humid evergreen tropical rainforest dominated by Fabaceae of the subfamily Caesalpinioideae in Cameroon, Central Africa. It is described here as new to science and is named Lactarius megalopterus, referring to its spore ornamentation of extraordinarily high wings. Anatomical characters and molecular systematic analyses confirm its relationship to Lactarius subgenus Plinthogali. Phylogenetic analyses based on two nuclear DNA regions revealed its close relationship to Lactarius angiocarpus, which is also an angiocarpous species from Zambia in Africa. Molecular studies have shown that tuber-like, sequestrate sporocarps evolved independently in several lineages of Basidiomycota. The findings of sequestrate fungi in tropical rainforests raise questions regarding the evolutionary benefit of enclosing the spore-producing hymenium. The enclosure of spore-producing tissue has often been associated with the protection of the delicate hymenium against desiccation in arid habitats or against frost in cold habitats. However, these cannot be the selective factors in warm and humid areas like the tropics. This controversy is exemplarily studied and discussed in the family of Russulaceae, especially in the genus Lactarius. Characters shown by the angiocarpous sporocarp of the new Lactarius, such as thick-walled statismospores, an aromatic smell and mild taste, can be interpreted as adaptations to endozoochorous spore dispersal by mammals. Therefore, here we prefer the alternative hypothesis that sequestrate sporocarps are the result of adaptation to endozoochorous spore dispersal. KW - Russulaceae KW - Lactarius subgenus Plinthogali KW - Mycophagy KW - Endozoochory syndrome KW - Cameroon Y1 - 2016 U6 - https://doi.org/10.1007/s11557-016-1198-4 SN - 1617-416X SN - 1861-8952 VL - 15 SP - 158 EP - 173 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Wadke, Namita A1 - Kandasamy, Dineshkumar A1 - Vogel, Heiko A1 - Lah, Ljerka A1 - Wingfield, Brenda D. A1 - Paetz, Christian A1 - Wright, Louwrance P. A1 - Gershenzon, Jonathan A1 - Hammerbacher, Almuth T1 - The Bark-Beetle-Associated Fungus, Endoconidiophora polonica, Utilizes the Phenolic Defense Compounds of Its Host as a Carbon Source JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Norway spruce (Picea abies) is periodically attacked by the bark beetle Ips typographus and its fungal associate, Endoconidiophora polonica, whose infection is thought to be required for successful beetle attack. Norway spruce produces terpenoid resins and phenolics in response to fungal and bark beetle invasion. However, how the fungal associate copes with these chemical defenses is still unclear. In this study, we investigated changes in the phenolic content of Norway spruce bark upon E. polonica infection and the biochemical factors mediating these changes. Although genes encoding the rate-limiting enzymes in Norway spruce stilbene and flavonoid biosynthesis were actively transcribed during fungal infection, there was a significant time-dependent decline of the corresponding metabolites in fungal lesions. In vitro feeding experiments with pure phenolics revealed that E. polonica transforms both stilbenes and flavonoids to muconoid-type ring-cleavage products, which are likely the first steps in the degradation of spruce defenses to substrates that can enter the tricarboxylic acid cycle. Four genes were identified in E. polonica that encode catechol dioxygenases carrying out these reactions. These enzymes catalyze the cleavage of phenolic rings with a vicinal dihydroxyl group to muconoid products accepting a wide range of Norway spruce-produced phenolics as substrates. The expression of these genes and E. polonica utilization of the most abundant spruce phenolics as carbon sources both correlated positively with fungal virulence in several strains. Thus, the pathways for the degradation of phenolic compounds in E. polonica, initiated by catechol dioxygenase action, are important to the infection, growth, and survival of this bark beetle-vectored fungus and may play a major role in the ability of I. typographus to colonize spruce trees. Y1 - 2016 U6 - https://doi.org/10.1104/pp.15.01916 SN - 0032-0889 SN - 1532-2548 VL - 171 SP - 914 EP - 931 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Kocyan, Alexander A1 - Wiland-Szymanska, Justyna T1 - Friedmannia: a new genus from the Seychelles and the beginning of a generic realignment of Curculigo (Hypoxidaceae) JF - Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy N2 - Recent molecular phylogenetic reconstruction of the monocot Hypoxidaceae implies that the genus Curculigo is non-monophyletic. Curculigo seychellensis occurs on the Seychelles islands and is part of an isolated though geographically well-defined clade. However, Curculigo seychellensis differs in a wide range of character-states from other species of Curculigo and from the genus Hypoxidia, representing the sister clade of C. seychellensis. Therefore, we here propose a new-though monotypic-genus, endemic to the Seychelles: Friedmannia. A detailed reasoning combined with a whole set of new data is presented. A neotype for the genus and the species is designated here. KW - Curculigo KW - Asparagales KW - neotypification KW - taxonomy Y1 - 2016 U6 - https://doi.org/10.11646/phytotaxa.283.1.3 SN - 1179-3155 SN - 1179-3163 VL - 283 SP - 54 EP - 64 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Sander, Martha Maria A1 - Scheffler, Christiane T1 - Bilateral asymmetry in left handers increased concerning morphological laterality in a recent sample of young adults JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie KW - anthropometry KW - handedness KW - laterality KW - bilateral asymmetry KW - left handers KW - upper extremity KW - reskilling KW - elbow breadth Y1 - 2016 U6 - https://doi.org/10.1127/anthranz/2016/0663 SN - 0003-5548 VL - 73 SP - 335 EP - 342 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Ali, Tahir A1 - Runge, Fabian A1 - Dutbayev, Ayan A1 - Schmuker, Angelika A1 - Solovyeva, Irina A1 - Nigrelli, Lisa A1 - Buch, Ann-Katrin A1 - Xia, Xiaojuan A1 - Ploch, Sebastian A1 - Orren, Ouria A1 - Kummer, Volker A1 - Paule, Juraj A1 - Celik, Ali A1 - Vakhrusheva, Ljudmila A1 - Gabrielyan, Ivan A1 - Thines, Marco T1 - Microthlaspi erraticum (Jord.) T. Ali et Thines has a wide distribution, ranging from the Alps to the Tien Shan JF - Flora : morphology, distribution, functional ecology of plants N2 - Microthlaspi is a predominantly Eurasian genus which also occurs in the northernmost parts of Africa (Maghreb). The most widespread species of the genus is M. perfoliatum, which can be found from Sweden to Algeria and from Portugal to China. The other species are thought to have much more confined distribution ranges, often covering only a few hundred kilometres. This is also believed for the diploid M. erraticum, which was recently re-appraised as a taxon independent from the tetra- to hexaploid M. perfoliatum. Previously, M. erraticum was believed to be present only in Central Europe, from the East of France to Slovenia. In order to gain a deeper understanding of the ecology, evolution and migration history of Microthlaspi it was the focus of the current study to investigate, if M. erraticum is present in habitats outside Central Europe, but with microclimates similar to Central Europe. It is demonstrated that M. erraticum is much more widespread than previously thought, while other lineages apart from M. perfoliatum s.str. and M. erraticum seem to have restricted distribution ranges. The latter species was observed from the Alps and their foreland, the Balkans, the mountainous areas around the Black Sea, Southern Siberia, as well as the Altai and Tien Shan mountains. This demonstrates a widespread occurrence of this easily-overlooked species. (C) 2016 Elsevier GmbH. All rights reserved. KW - Biogeography KW - Coluteocarpeae KW - Noccaea KW - Phylogeny KW - Species complex KW - Thlaspi perfoliatum Y1 - 2016 U6 - https://doi.org/10.1016/j.flora.2016.09.008 SN - 0367-2530 SN - 1618-0585 VL - 225 SP - 76 EP - 81 PB - American Chemical Society CY - Jena ER - TY - JOUR A1 - Zwickel, Theresa A1 - Kahl, Sandra M. A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions JF - Toxins N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 degrees C, 25 degrees C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 degrees C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions. KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2016 U6 - https://doi.org/10.3390/toxins8110344 SN - 2072-6651 VL - 8 SP - 570 EP - 583 PB - MDPI CY - Basel ER - TY - JOUR A1 - Bergmann, Joana A1 - Verbruggen, Erik A1 - Heinze, Johannes A1 - Xiang, Dan A1 - Chen, Baodong A1 - Joshi, Jasmin Radha A1 - Rillig, Matthias C. T1 - The interplay between soil structure, roots, and microbiota as a determinant of plant-soil feedback JF - Ecology and evolution N2 - Plant-soil feedback (PSF) can influence plant community structure via changes in the soil microbiome. However, how these feedbacks depend on the soil environment remains poorly understood. We hypothesized that disintegrating a naturally aggregated soil may influence the outcome of PSF by affecting microbial communities. Furthermore, we expected plants to differentially interact with soil structure and the microbial communities due to varying root morphology. We carried out a feedback experiment with nine plant species (five forbs and four grasses) where the training phase consisted of aggregated versus disintegrated soil. In the feedback phase, a uniform soil was inoculated in a fully factorial design with soil washings from conspecific- versus heterospecific-trained soil that had been either disintegrated or aggregated. This way, the effects of prior soil structure on plant performance in terms of biomass production and allocation were examined. In the training phase, soil structure did not affect plant biomass. But on disintegrated soil, plants with lower specific root length (SRL) allocated more biomass aboveground. PSF in the feedback phase was negative overall. With training on disintegrated soil, conspecific feedback was positively correlated with SRL and significantly differed between grasses and forbs. Plants with higher SRL were likely able to easily explore the disintegrated soil with smaller pores, while plants with lower SRL invested in belowground biomass for soil exploration and seemed to be more susceptible to fungal pathogens. This suggests that plants with low SRL could be more limited by PSF on disintegrated soils of early successional stages. This study is the first to examine the influence of soil structure on PSF. Our results suggest that soil structure determines the outcome of PSF mediated by SRL. We recommend to further explore the effects of soil structure and propose to include root performance when working with PSF. KW - arbuscular mycorrhizal fungi KW - biomass allocation KW - plant functional traits KW - plant-soil (belowground) interactions KW - soil aggregation KW - specific root length KW - succession KW - water-stable aggregates Y1 - 2016 U6 - https://doi.org/10.1002/ece3.2456 SN - 2045-7758 VL - 6 SP - 7633 EP - 7644 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Sakschewski, Boris A1 - von Bloh, Werner A1 - Boit, Alice A1 - Poorter, Lourens A1 - Pe~na-Claros, Marielos A1 - Heinke, Jens A1 - Joshi, Jasmin Radha A1 - Thonicke, Kirsten T1 - Resilience of Amazon forests emerges from plant trait diversity JF - Nature climate change Y1 - 2016 U6 - https://doi.org/10.1038/NCLIMATE3109 SN - 1758-678X SN - 1758-6798 VL - 6 SP - 1032 EP - + PB - Nature Publ. Group CY - London ER -