@article{AllanWeisserFischeretal.2013, author = {Allan, Eric and Weisser, Wolfgang W. and Fischer, Markus and Schulze, Ernst-Detlef and Weigelt, Alexandra and Roscher, Christiane and Baade, Jussi and Barnard, Romain L. and Bessler, Holger and Buchmann, Nina and Ebeling, Anne and Eisenhauer, Nico and Engels, Christof and Fergus, Alexander J. F. and Gleixner, Gerd and Gubsch, Marlen and Halle, Stefan and Klein, Alexandra Maria and Kertscher, Ilona and Kuu, Annely and Lange, Markus and Le Roux, Xavier and Meyer, Sebastian T. and Migunova, Varvara D. and Milcu, Alexandru and Niklaus, Pascal A. and Oelmann, Yvonne and Pasalic, Esther and Petermann, Jana S. and Poly, Franck and Rottstock, Tanja and Sabais, Alexander C. W. and Scherber, Christoph and Scherer-Lorenzen, Michael and Scheu, Stefan and Steinbeiss, Sibylle and Schwichtenberg, Guido and Temperton, Vicky and Tscharntke, Teja and Voigt, Winfried and Wilcke, Wolfgang and Wirth, Christian and Schmid, Bernhard}, title = {A comparison of the strength of biodiversity effects across multiple functions}, series = {Oecologia}, volume = {173}, journal = {Oecologia}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-012-2589-0}, pages = {223 -- 237}, year = {2013}, abstract = {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.}, language = {en} } @article{AndresGohlkeBroekeretal.2013, author = {Andres, Dorothee and Gohlke, Ulrich and Br{\"o}ker, Nina Kristin and Schulze, Stefan and Rabsch, Wolfgang and Heinemann, Udo and Barbirz, Stefanie and Seckler, Robert}, title = {An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers}, series = {Glycobiology}, volume = {23}, journal = {Glycobiology}, number = {4}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {0959-6658}, doi = {10.1093/glycob/cws224}, pages = {486 -- 494}, year = {2013}, abstract = {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.}, language = {en} } @article{AttermeyerPremkeHornicketal.2013, author = {Attermeyer, Katrin and Premke, Katrin and Hornick, Thomas and Hilt, Sabine and Grossart, Hans-Peter}, title = {Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats}, series = {Ecology : a publication of the Ecological Society of America}, volume = {94}, journal = {Ecology : a publication of the Ecological Society of America}, number = {12}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, doi = {10.1890/13-0420.1}, pages = {2754 -- 2766}, year = {2013}, abstract = {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.}, language = {en} } @article{BadalyanNeumannSchaalLeimkuehleretal.2013, author = {Badalyan, Artavazd and Neumann-Schaal, Meina and Leimk{\"u}hler, Silke and Wollenberger, Ursula}, title = {A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {25}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {1}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201200362}, pages = {101 -- 108}, year = {2013}, abstract = {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.}, language = {en} } @article{BadalyanYogaSchwuchowetal.2013, author = {Badalyan, Artavazd and Yoga, Etienne Galemou and Schwuchow, Viola and P{\"o}ller, Sascha and Schuhmann, Wolfgang and Leimk{\"u}hler, Silke and Wollenberger, Ursula}, title = {Analysis of the interaction of the molybdenum hydroxylase PaoABC from Escherichia coli with positively and negatively charged metal complexes}, series = {Electrochemistry communications : an international journal dedicated to rapid publications in electrochemistry}, volume = {37}, journal = {Electrochemistry communications : an international journal dedicated to rapid publications in electrochemistry}, publisher = {Elsevier}, address = {New York}, issn = {1388-2481}, doi = {10.1016/j.elecom.2013.09.017}, pages = {5 -- 7}, year = {2013}, abstract = {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.}, language = {en} } @article{BailleulGrimmChionetal.2013, author = {Bailleul, Frederic and Grimm, Volker and Chion, Clement and Hammill, Mike}, title = {Modeling implications of food resource aggregation on animal migration phenology}, series = {Ecology and evolution}, volume = {3}, journal = {Ecology and evolution}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.656}, pages = {2535 -- 2546}, year = {2013}, abstract = {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.}, language = {en} } @article{BaselHarmsPrechtl2013, author = {Basel, Nicolai and Harms, Ute and Prechtl, Helmut}, title = {Analysis of students' arguments on evolutionary theory}, series = {Journal of biological education}, volume = {47}, journal = {Journal of biological education}, number = {4}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0021-9266}, doi = {10.1080/00219266.2013.799078}, pages = {192 -- 199}, year = {2013}, abstract = {A qualitative exploratory study was conducted to reveal students' argumentation skills in the context of the topic of evolution. Transcripts from problem-centred interviews on secondary students' beliefs about evolutionary processes of adaptation were analysed using a content analysis approach. For this purpose two categorical systems were deductively developed: one addressing the complexity of students' arguments, the other focusing on students' use of argumentation schemes. Subsequently, the categorical systems were inductively elaborated upon the basis of the analysed material showing a satisfactory inter-rater reliability. Regarding the arguments' complexity, students produced mainly single claims or claims with a single justification consisting of either data or warrants. With regard to argumentation schemes students drew their arguments mainly using causal schemes, analogies, or illustrative examples. Results are discussed in light of possible implications for teaching evolutionary theory using classroom argumentation.}, language = {en} } @article{BauerSommerGaedke2013, author = {Bauer, Barbara and Sommer, Ulrich and Gaedke, Ursula}, title = {High predictability of spring phytoplankton biomass in mesocosms at the species, functional group and community level}, series = {Freshwater biology}, volume = {58}, journal = {Freshwater biology}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/j.1365-2427.2012.02780.x}, pages = {588 -- 596}, year = {2013}, abstract = {1. Models aim to predict phytoplankton dynamics based on observed initial conditions and a set of equations and parameters. However, our knowledge about initial conditions in nature is never perfect. Thus, if phytoplankton dynamics are sensitive to small variations in initial conditions, they are difficult to predict. 2. We used time-series data from indoor mesocosm experiments with natural phyto- and zooplankton communities to quantify the extent to which small initial differences in the species, functional group and community biomass in parallel treatments were amplified or buffered over time. We compared the differences in dynamics between replicates and among all mesocosms of 1year. 3. Temperature-sensitive grazing during the exponential growth phase of phytoplankton caused divergence. In contrast, negative density dependence caused convergence. 4. Mean differences in biomass between replicates were similar for all hierarchical levels. This indicates that differences in their initial conditions were amplified to the same extent. Even though large differences in biomass occasionally occurred between replicates for a short time, dynamics returned to the same path at all hierarchical levels. This suggests that internal feedback mechanisms make the spring development of phytoplankton highly predictable.}, language = {en} } @article{BaumannBauer2013, author = {Baumann, Otto and Bauer, Alexandra}, title = {Development of apical membrane organization and V-ATPase regulation in blowfly salivary glands}, series = {The journal of experimental biology}, volume = {216}, journal = {The journal of experimental biology}, number = {7}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0022-0949}, doi = {10.1242/jeb.077420}, pages = {1225 -- 1234}, year = {2013}, abstract = {Secretory cells in blowfly salivary gland are specialized via morphological and physiological attributes in order to serve their main function, i.e. the transport of solutes at a high rate in response to a hormonal stimulus, namely serotonin (5-HT). This study examines the way that 5-HT-insensitive precursor cells differentiate into morphologically complex 5-HT-responsive secretory cells. By means of immunofluorescence microscopy, immunoblotting and measurements of the transepithelial potential changes, we show the following. (1) The apical membrane of the secretory cells becomes organized into an elaborate system of canaliculi and is folded into pleats during the last pupal day and the first day of adulthood. (2) The structural reorganization of the apical membrane is accompanied by an enrichment of actin filaments and phosphorylated ERM protein (phospho-moesin) at this membrane domain and by the deployment of the membrane-integral part of vacuolar-type H+-ATPase (V-ATPase). These findings suggest a role for phospho-moesin, a linker between actin filaments and membrane components, in apical membrane morphogenesis. (3) The assembly and activation of V-ATPase can be induced immediately after eclosion by way of 8-CPT-cAMP, a membrane-permeant cAMP analogue. (4) 5-HT, however, produces the assembly and activation of V-ATPase only in flies aged for at least 2 h after eclosion, indicating that, at eclosion, the 5-HT receptor/adenylyl cyclase/cAMP signalling pathway is inoperative upstream of cAMP. (5) 5-HT activates both the Ca2+ signalling pathway and the cAMP signalling cascade in fully differentiated secretory cells. However, the functionality of these signalling cascades does not seem to be established in a tightly coordinated manner during cell differentation.}, language = {en} } @article{BaumannArndtMueller2013, author = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V}, series = {BMC biotechnology}, volume = {13}, journal = {BMC biotechnology}, number = {10}, publisher = {BioMed Central}, address = {London}, issn = {1472-6750}, doi = {10.1186/1472-6750-13-81}, pages = {11}, year = {2013}, abstract = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.}, language = {en} }