TY - JOUR A1 - Aguzzi, Jacopo A1 - Costa, C. A1 - Ketmaier, V. A1 - Angelini, C. A1 - Antonucci, F. A1 - Menesatti, P. A1 - Company, J. B. T1 - Light-dependent genetic and phenotypic differences in the squat lobster Munida tenuimana (Crustacea: Decapoda) along deep continental margins JF - Progress in oceanography N2 - The levels of environmental light experienced by organisms during the behavioral activity phase deeply influence the performance of important ecological tasks. As a result, their shape and coloring may experience a light-driven selection process via the day-night rhythmic behavior. In this study, we tested the phenotypic and genetic variability of the western Mediterranean squat lobster (Munida tenuimana). We sampled at depths with different photic conditions and potentially, different burrow emergence rhythms. We performed day-night hauling at different depths, above and below the twilight zone end (i.e., 700 m, 1200 m, 1350 m, and 1500 m), to portray the occurrence of any burrow emergence rhythmicity. Collected animals were screened for shape and size (by geometric morphometry), spectrum and color variation (by photometric analysis), as well as for sequence variation at the mitochondria] DNA gene encoding for the NADH dehydrogenase subunit I. We found that a weak genetic structuring and shape homogeneity occurred together with significant variations in size, with the smaller individuals living at the twilight zone inferior limit and the larger individuals above and below. The infra-red wavelengths of spectral reflectance varied significantly with depth while the blue-green ones were size-dependent and expressed in smaller animals, which has a very small spectral reflectance. The effects of solar and bioluminescence lighting are discussed as depth-dependent evolutionary forces likely influencing the behavioral rhythms and coloring of M. tenuimana. Y1 - 2013 U6 - https://doi.org/10.1016/j.pocean.2013.07.011 SN - 0079-6611 VL - 118 IS - 4 SP - 199 EP - 209 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Allan, Eric A1 - Weisser, Wolfgang W. A1 - Fischer, Markus A1 - Schulze, Ernst-Detlef A1 - Weigelt, Alexandra A1 - Roscher, Christiane A1 - Baade, Jussi A1 - Barnard, Romain L. A1 - Bessler, Holger A1 - Buchmann, Nina A1 - Ebeling, Anne A1 - Eisenhauer, Nico A1 - Engels, Christof A1 - Fergus, Alexander J. F. A1 - Gleixner, Gerd A1 - Gubsch, Marlen A1 - Halle, Stefan A1 - Klein, Alexandra Maria A1 - Kertscher, Ilona A1 - Kuu, Annely A1 - Lange, Markus A1 - Le Roux, Xavier A1 - Meyer, Sebastian T. A1 - Migunova, Varvara D. A1 - Milcu, Alexandru A1 - Niklaus, Pascal A. A1 - Oelmann, Yvonne A1 - Pasalic, Esther A1 - Petermann, Jana S. A1 - Poly, Franck A1 - Rottstock, Tanja A1 - Sabais, Alexander C. W. A1 - Scherber, Christoph A1 - Scherer-Lorenzen, Michael A1 - Scheu, Stefan A1 - Steinbeiss, Sibylle A1 - Schwichtenberg, Guido A1 - Temperton, Vicky A1 - Tscharntke, Teja A1 - Voigt, Winfried A1 - Wilcke, Wolfgang A1 - Wirth, Christian A1 - Schmid, Bernhard T1 - A comparison of the strength of biodiversity effects across multiple functions JF - Oecologia N2 - In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination. KW - Bottom-up effects KW - Carbon cycling KW - Ecological synthesis KW - Ecosystem processes KW - Grasslands KW - Jena experiment KW - Nitrogen cycling Y1 - 2013 U6 - https://doi.org/10.1007/s00442-012-2589-0 SN - 0029-8549 VL - 173 IS - 1 SP - 223 EP - 237 PB - Springer CY - New York ER - TY - JOUR A1 - Andres, Dorothee A1 - Gohlke, Ulrich A1 - Bröker, Nina Kristin A1 - Schulze, Stefan A1 - Rabsch, Wolfgang A1 - Heinemann, Udo A1 - Barbirz, Stefanie A1 - Seckler, Robert T1 - An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers JF - Glycobiology N2 - Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose and paratose determine the specific serotype. P22 TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22 TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry showed that S. Paratyphi A octasaccharide binds P22 TSP less tightly, with a difference in binding free energy of similar to 7 kJ mol(-1) at 20 degrees C compared with S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable phi/epsilon glycosidic bond angle combination. In contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22 TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as nonsolution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites. KW - bacterial O-antigen KW - carbohydrate interaction KW - paratose KW - structural thermodynamics KW - tailspike protein Y1 - 2013 U6 - https://doi.org/10.1093/glycob/cws224 SN - 0959-6658 VL - 23 IS - 4 SP - 486 EP - 494 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Arnison, Paul G. A1 - Bibb, Mervyn J. A1 - Bierbaum, Gabriele A1 - Bowers, Albert A. A1 - Bugni, Tim S. A1 - Bulaj, Grzegorz A1 - Camarero, Julio A. A1 - Campopiano, Dominic J. A1 - Challis, Gregory L. A1 - Clardy, Jon A1 - Cotter, Paul D. A1 - Craik, David J. A1 - Dawson, Michael A1 - Dittmann-Thünemann, Elke A1 - Donadio, Stefano A1 - Dorrestein, Pieter C. A1 - Entian, Karl-Dieter A1 - Fischbach, Michael A. A1 - Garavelli, John S. A1 - Goeransson, Ulf A1 - Gruber, Christian W. A1 - Haft, Daniel H. A1 - Hemscheidt, Thomas K. A1 - Hertweck, Christian A1 - Hill, Colin A1 - Horswill, Alexander R. A1 - Jaspars, Marcel A1 - Kelly, Wendy L. A1 - Klinman, Judith P. A1 - Kuipers, Oscar P. A1 - Link, A. James A1 - Liu, Wen A1 - Marahiel, Mohamed A. A1 - Mitchell, Douglas A. A1 - Moll, Gert N. A1 - Moore, Bradley S. A1 - Mueller, Rolf A1 - Nair, Satish K. A1 - Nes, Ingolf F. A1 - Norris, Gillian E. A1 - Olivera, Baldomero M. A1 - Onaka, Hiroyasu A1 - Patchett, Mark L. A1 - Piel, Jörn A1 - Reaney, Martin J. T. A1 - Rebuffat, Sylvie A1 - Ross, R. Paul A1 - Sahl, Hans-Georg A1 - Schmidt, Eric W. A1 - Selsted, Michael E. A1 - Severinov, Konstantin A1 - Shen, Ben A1 - Sivonen, Kaarina A1 - Smith, Leif A1 - Stein, Torsten A1 - Suessmuth, Roderich D. A1 - Tagg, John R. A1 - Tang, Gong-Li A1 - Truman, Andrew W. A1 - Vederas, John C. A1 - Walsh, Christopher T. A1 - Walton, Jonathan D. A1 - Wenzel, Silke C. A1 - Willey, Joanne M. A1 - van der Donk, Wilfred A. T1 - Ribosomally synthesized and post-translationally modified peptide natural products overview and recommendations for a universal nomenclature JF - Natural product reports : a journal of current developments in bio-organic chemistry N2 - This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed. Y1 - 2013 U6 - https://doi.org/10.1039/c2np20085f SN - 0265-0568 VL - 30 IS - 1 SP - 108 EP - 160 PB - Royal Society of Chemistry CY - Cambridge ER - TY - THES A1 - Attermeyer, Katrin T1 - Effects of allochthonous organic carbon on bacterial metabolism and community structure, and consequences for carbon cycling in smal, shallow lakes Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Premke, Katrin A1 - Hornick, Thomas A1 - Hilt, Sabine A1 - Grossart, Hans-Peter T1 - Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats JF - Ecology : a publication of the Ecological Society of America N2 - In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using C-13-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POML and via benthic macroinvertebrates by shredding of t-POML. The latter pathway represents a benthic shortcut which efficiently transfers t-POML to higher trophic levels. KW - bacterial production KW - carbon turnover KW - community respiration KW - leaf litter KW - phospholipid-derived fatty acid KW - PLFA KW - Schulzensee KW - Germany KW - sediments KW - shallow lakes KW - stable isotopes KW - terrestrial subsidies Y1 - 2013 U6 - https://doi.org/10.1890/13-0420.1 SN - 0012-9658 SN - 1939-9170 VL - 94 IS - 12 SP - 2754 EP - 2766 PB - Wiley CY - Washington ER - TY - THES A1 - Badalyan, Artavazd T1 - Bioelectrochemistry of molybdenum hydroxylases : aldehyde oxidoreductase PaoABC from escherichia coli and xanthine dehydrogenase from rhodobacter capsulatus Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Neumann-Schaal, Meina A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A novel aldehyde oxidoreductase (PaoABC) from Escherichia coli was utilized for the development of an oxygen insensitive biosensor for benzaldehyde. The enzyme was immobilized in polyvinyl alcohol and currents were measured for aldehyde oxidation with different one and two electron mediators with the highest sensitivity for benzaldehyde in the presence of hexacyanoferrate(III). The benzaldehyde biosensor was optimized with respect to mediator concentration, enzyme loading and pH using potassium hexacyanoferrate(III). The linear measuring range is between 0.5200 mu M benzaldehyde. In correspondence with the substrate selectivity of the enzyme in solution the biosensor revealed a preference for aromatic aldehydes and less effective conversion of aliphatic aldehydes. The biosensor is oxygen independent, which is a particularly attractive feature for application. The biosensor can be applied to detect contaminations with benzaldehyde in solvents such as benzyl alcohol, where traces of benzaldehyde in benzyl alcohol down to 0.0042?% can be detected. KW - Aldehyde oxidoreductase KW - Benzaldehyde KW - Biosensor KW - Aromatic aldehydes KW - Molybdenum cofactor Y1 - 2013 U6 - https://doi.org/10.1002/elan.201200362 SN - 1040-0397 VL - 25 IS - 1 SP - 101 EP - 108 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Yoga, Etienne Galemou A1 - Schwuchow, Viola A1 - Pöller, Sascha A1 - Schuhmann, Wolfgang A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - Analysis of the interaction of the molybdenum hydroxylase PaoABC from Escherichia coli with positively and negatively charged metal complexes JF - Electrochemistry communications : an international journal dedicated to rapid publications in electrochemistry N2 - An unusual behavior of the periplasmic aldehyde oxidoreductase (PaoABC) from Escherichia coil has been observed from electrochemical investigations of the enzyme catalyzed oxidation of aromatic aldehydes with different mediators under different conditions of ionic strength. The enzyme has similarity to other molybdoenzymes of the xanthine oxidase family, but the catalytic behavior turned out to be very different. Under steady state conditions the turnover of PaoABC is maximal at pH 4 for the negatively charged ferricyanide and at pH 9 for a positively charged osmium complex. Stopped-flow kinetic measurements of the catalytic half reaction showed that oxidation of benzaldehyde proceeds also above pH 7. Thus, benzaldehyde oxidation can proceed under acidic and basic conditions using this enzyme, a property which has not been described before for molybdenum hydroxylases. It is also suggested that the electron transfer with artificial electron acceptors and PaoABC can proceed at different protein sites and depends on the nature of the electron acceptor in addition to the ionic strength. (C) 2013 Elsevier B.V. All rights reserved. KW - Electron transfer KW - Multi-cofactor enzymes KW - Molybdoenzymes KW - Aldehyde oxidoreductase Y1 - 2013 U6 - https://doi.org/10.1016/j.elecom.2013.09.017 SN - 1388-2481 SN - 1873-1902 VL - 37 SP - 5 EP - 7 PB - Elsevier CY - New York ER - TY - JOUR A1 - Bailleul, Frederic A1 - Grimm, Volker A1 - Chion, Clement A1 - Hammill, Mike T1 - Modeling implications of food resource aggregation on animal migration phenology JF - Ecology and evolution N2 - The distribution of poikilotherms is determined by the thermal structure of the marine environment that they are exposed to. Recent research has indicated that changes in migration phenology of beluga whales in the Arctic are triggered by changes in the thermal structure of the marine environment in their summering area. If sea temperatures reflect the spatial distribution of food resources, then changes in the thermal regime will affect how homogeneous or clumped food is distributed. We explore, by individual-based modelling, the hypothesis that changes in migration phenology are not necessarily or exclusively triggered by changes in food abundance, but also by changes in the spatial aggregation of food. We found that the level of food aggregation can significantly affect the relationship between the timing of the start of migration to the winter grounds and the total prey capture of individuals. Our approach strongly indicates that changes in the spatial distribution of food resources should be considered for understanding and quantitatively predicting changes in the phenology of animal migration. KW - Animal migration KW - food structuring KW - global change KW - individual-based model KW - polar environment Y1 - 2013 U6 - https://doi.org/10.1002/ece3.656 SN - 2045-7758 VL - 3 IS - 8 SP - 2535 EP - 2546 PB - Wiley-Blackwell CY - Hoboken ER -