TY - JOUR A1 - Chipman, Ariel D. A1 - Ferrier, David E. K. A1 - Brena, Carlo A1 - Qu, Jiaxin A1 - Hughes, Daniel S. T. A1 - Schroeder, Reinhard A1 - Torres-Oliva, Montserrat A1 - Znassi, Nadia A1 - Jiang, Huaiyang A1 - Almeida, Francisca C. A1 - Alonso, Claudio R. A1 - Apostolou, Zivkos A1 - Aqrawi, Peshtewani A1 - Arthur, Wallace A1 - Barna, Jennifer C. J. A1 - Blankenburg, Kerstin P. A1 - Brites, Daniela A1 - Capella-Gutierrez, Salvador A1 - Coyle, Marcus A1 - Dearden, Peter K. A1 - Du Pasquier, Louis A1 - Duncan, Elizabeth J. A1 - Ebert, Dieter A1 - Eibner, Cornelius A1 - Erikson, Galina A1 - Evans, Peter D. A1 - Extavour, Cassandra G. A1 - Francisco, Liezl A1 - Gabaldon, Toni A1 - Gillis, William J. A1 - Goodwin-Horn, Elizabeth A. A1 - Green, Jack E. A1 - Griffiths-Jones, Sam A1 - Grimmelikhuijzen, Cornelis J. P. A1 - Gubbala, Sai A1 - Guigo, Roderic A1 - Han, Yi A1 - Hauser, Frank A1 - Havlak, Paul A1 - Hayden, Luke A1 - Helbing, Sophie A1 - Holder, Michael A1 - Hui, Jerome H. L. A1 - Hunn, Julia P. A1 - Hunnekuhl, Vera S. A1 - Jackson, LaRonda A1 - Javaid, Mehwish A1 - Jhangiani, Shalini N. A1 - Jiggins, Francis M. A1 - Jones, Tamsin E. A1 - Kaiser, Tobias S. A1 - Kalra, Divya A1 - Kenny, Nathan J. A1 - Korchina, Viktoriya A1 - Kovar, Christie L. A1 - Kraus, F. Bernhard A1 - Lapraz, Francois A1 - Lee, Sandra L. A1 - Lv, Jie A1 - Mandapat, Christigale A1 - Manning, Gerard A1 - Mariotti, Marco A1 - Mata, Robert A1 - Mathew, Tittu A1 - Neumann, Tobias A1 - Newsham, Irene A1 - Ngo, Dinh N. A1 - Ninova, Maria A1 - Okwuonu, Geoffrey A1 - Ongeri, Fiona A1 - Palmer, William J. A1 - Patil, Shobha A1 - Patraquim, Pedro A1 - Pham, Christopher A1 - Pu, Ling-Ling A1 - Putman, Nicholas H. A1 - Rabouille, Catherine A1 - Ramos, Olivia Mendivil A1 - Rhodes, Adelaide C. A1 - Robertson, Helen E. A1 - Robertson, Hugh M. A1 - Ronshaugen, Matthew A1 - Rozas, Julio A1 - Saada, Nehad A1 - Sanchez-Gracia, Alejandro A1 - Scherer, Steven E. A1 - Schurko, Andrew M. A1 - Siggens, Kenneth W. A1 - Simmons, DeNard A1 - Stief, Anna A1 - Stolle, Eckart A1 - Telford, Maximilian J. A1 - Tessmar-Raible, Kristin A1 - Thornton, Rebecca A1 - van der Zee, Maurijn A1 - von Haeseler, Arndt A1 - Williams, James M. A1 - Willis, Judith H. A1 - Wu, Yuanqing A1 - Zou, Xiaoyan A1 - Lawson, Daniel A1 - Muzny, Donna M. A1 - Worley, Kim C. A1 - Gibbs, Richard A. A1 - Akam, Michael A1 - Richards, Stephen T1 - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima JF - PLoS biology N2 - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pbio.1002005 SN - 1545-7885 VL - 12 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Kaiser, M. A1 - Ellerbrock, Ruth H. A1 - Wulf, M. A1 - Dultz, S. A1 - Hierath, C. A1 - Sommer, M. T1 - The influence of mineral characteristics on organic matter content, composition, and stability of topsoils under long-term arable and forest land use JF - Journal of geophysical research : Biogeosciences N2 - In this study, we analyzed the influence of soil mineral characteristics (e. g., clay concentration and mineralogical composition, iron and aluminum oxide concentration and crystallinity, specific surface area, and exchangeable cation concentration) on (i) organic carbon (OC) content (kg m(-2)) and (ii) the concentration (g kg(-1)), composition, and stability of the mineral-associated organic matter (OM) of arable and forest topsoils. We selected seven soil types with different mineral characteristics for this study. For each soil type, samples were taken from topsoils of a deciduous forest and an adjacent arable site. The arable and forest sites have been used continuously for more than 100 years. Na-pyrophosphate soluble OM fractions (OM(PY)), representing mineral-associated OM, were extracted, analyzed for OC and C-14 concentrations, and characterized by FTIR spectroscopy. For the forest and arable topsoils, a linear relationship was found between the OC content and exchangeable Ca. For the arable topsoils (pH 6.7-7.5), correlation analyses indicated that the OCPY concentration increased with an increase in oxalate soluble Fe and Al, exchangeable Ca, and Na-pyrophosphate soluble Mg and Fe concentrations. The stability of OM(PY) determined by the C-14 measurements of the near-neutral arable topsoils was shown to increase with the specific surface area and the concentration of exchangeable Ca. For the acidic forest topsoils (pH < 5), the stability of OM(PY) was found to increase as the pH, and the concentration of C=O groups and Na-pyrophosphate soluble Mg increase. Y1 - 2012 U6 - https://doi.org/10.1029/2011JG001712 SN - 0148-0227 VL - 117 IS - 4 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Simons, Nadja K. A1 - Lewinsohn, Thomas A1 - Bluethgen, Nico A1 - Buscot, Francois A1 - Boch, Steffen A1 - Daniel, Rolf A1 - Gossner, Martin M. A1 - Jung, Kirsten A1 - Kaiser, Kristin A1 - Müller, Jörg A1 - Prati, Daniel A1 - Renner, Swen C. A1 - Socher, Stephanie A. A1 - Sonnemann, Ilja A1 - Weiner, Christiane N. A1 - Werner, Michael A1 - Wubet, Tesfaye A1 - Wurst, Susanne A1 - Weisser, Wolfgang W. T1 - Contrasting effects of grassland management modes on species-abundance distributions of multiple groups JF - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere N2 - Intensive land use is a major cause of biodiversity loss, but most studies comparing the response of multiple taxa rely on simple diversity measures while analyses of other community attributes are only recently gaining attention. Species-abundance distributions (SADs) are a community attribute that can be used to study changes in the overall abundance structure of species groups, and whether these changes are driven by abundant or rare species. We evaluated the effect of grassland management intensity for three land-use modes (fertilization, mowing, grazing) and their combination on species richness and SADs for three belowground (arbuscular mycorrhizal fungi, prokaryotes and insect larvae) and seven aboveground groups (vascular plants, bryophytes and lichens; arthropod herbivores; arthropod pollinators; bats and birds). Three descriptors of SADs were evaluated: general shape (abundance decay rate), proportion of rare species (rarity) and proportional abundance of the commonest species (dominance). Across groups, taxonomic richness was largely unaffected by land-use intensity and only decreased with increasing mowing intensity. Of the three SAD descriptors, abundance decay rate became steeper with increasing combined land-use intensity across groups. This reflected a decrease in rarity among plants, herbivores and vertebrates. Effects of fertilization on the three descriptors were similar to the combined land-use intensity effects. Mowing intensity only affected the SAD descriptors of insect larvae and vertebrates, while grazing intensity produced a range of effects on different descriptors in distinct groups. Overall, belowground groups had more even abundance distribtitions than aboveground groups. Strong differences among aboveground groups and between above- and belowground groups indicate that no single taxonomic group can serve as an indicator for effects in other groups. In the past, the use of SADs has been hampered by concerns over theoretical models underlying specific forms of SADs. Our study shows that SAD descriptors that are not connected to a particular model are suitable to assess the effect of land use on community structure. KW - Biodiversity KW - Cutting frequency KW - Management intensity KW - Rank-abundance KW - Species loss KW - Rarity Y1 - 2017 U6 - https://doi.org/10.1016/j.agee.2016.12.022 SN - 0167-8809 SN - 1873-2305 VL - 237 SP - 143 EP - 153 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schall, Peter A1 - Gossner, Martin M. A1 - Heinrichs, Steffi A1 - Fischer, Markus A1 - Boch, Steffen A1 - Prati, Daniel A1 - Jung, Kirsten A1 - Baumgartner, Vanessa A1 - Blaser, Stefan A1 - Böhm, Stefan A1 - Buscot, Francois A1 - Daniel, Rolf A1 - Goldmann, Kezia A1 - Kaiser, Kristin A1 - Kahl, Tiemo A1 - Lange, Markus A1 - Müller, Jörg Hans A1 - Overmann, Jörg A1 - Renner, Swen C. A1 - Schulze, Ernst-Detlef A1 - Sikorski, Johannes A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Weisser, Wolfgang W. A1 - Wemheuer, Bernd A1 - Wubet, Tesfaye A1 - Ammer, Christian T1 - The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests JF - Journal of applied ecology : an official journal of the British Ecological Society N2 - 1. For managed temperate forests, conservationists and policymakers favour fine-grained uneven-aged (UEA) management over more traditional coarse-grained even-aged (EA) management, based on the assumption that within-stand habitat heterogeneity enhances biodiversity. There is, however, little empirical evidence to support this assumption. We investigated for the first time how differently grained forest management systems affect the biodiversity of multiple above- and below-ground taxa across spatial scales. 2. We sampled 15 taxa of animals, plants, fungi and bacteria within the largest contiguous beech forest landscape of Germany and classified them into functional groups. Selected forest stands have been managed for more than a century at different spatial grains. The EA (coarse-grained management) and UEA (fine-grained) forests are comparable in spatial arrangement, climate and soil conditions. These were compared to forests of a nearby national park that have been unmanaged for at least 20years. We used diversity accumulation curves to compare -diversity for Hill numbers D-0 (species richness), D-1 (Shannon diversity) and D-2 (Simpson diversity) between the management systems. Beta diversity was quantified as multiple-site dissimilarity. 3. Gamma diversity was higher in EA than in UEA forests for at least one of the three Hill numbers for six taxa (up to 77%), while eight showed no difference. Only bacteria showed the opposite pattern. Higher -diversity in EA forests was also found for forest specialists and saproxylic beetles. 4. Between-stand -diversity was higher in EA than in UEA forests for one-third (all species) and half (forest specialists) of all taxa, driven by environmental heterogeneity between age-classes, while -diversity showed no directional response across taxa or for forest specialists. 5. Synthesis and applications. Comparing EA and uneven-aged forest management in Central European beech forests, our results show that a mosaic of different age-classes is more important for regional biodiversity than high within-stand heterogeneity. We suggest reconsidering the current trend of replacing even-aged management in temperate forests. Instead, the variability of stages and stand structures should be increased to promote landscape-scale biodiversity. KW - beta diversity KW - forest specialists KW - gamma diversity KW - heterogeneity KW - Hill numbers KW - saproxylic beetles KW - spatial grain KW - species accumulation curve KW - species richness KW - species turnover Y1 - 2017 U6 - https://doi.org/10.1111/1365-2664.12950 SN - 0021-8901 SN - 1365-2664 VL - 55 IS - 1 SP - 267 EP - 278 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Henkel, Carsten A1 - Steane, Andrew M. A1 - Kaiser, Robin A1 - Dalibard, Jean T1 - A modulated mirror for atomic interferometry N2 - A novel atomic beam splitter, using reflection of atoms off an evanescent light wave, is investigated theoretically. The intensity or frequency of the light is modulated in order to create sidebands on the reflected de Broglie wave. The weights and phases of the various sidevands are calculated using three different approaches: the Born approximation, a semiclassical path integral approach, and a numerical solution of the time-dependent Schrdinger equation. We show how this modulated mirror could be used to build practical atomic interferometers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 102 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-42279 ER - TY - JOUR A1 - Kubin, Markus A1 - Kern, Jan A1 - Gul, Sheraz A1 - Kroll, Thomas A1 - Chatterjee, Ruchira A1 - Loechel, Heike A1 - Fuller, Franklin D. A1 - Sierra, Raymond G. A1 - Quevedo, Wilson A1 - Weniger, Christian A1 - Rehanek, Jens A1 - Firsov, Anatoly A1 - Laksmono, Hartawan A1 - Weninger, Clemens A1 - Alonso-Mori, Roberto A1 - Nordlund, Dennis L. A1 - Lassalle-Kaiser, Benedikt A1 - Glownia, James M. A1 - Krzywinski, Jacek A1 - Moeller, Stefan A1 - Turner, Joshua J. A1 - Minitti, Michael P. A1 - Dakovski, Georgi L. A1 - Koroidov, Sergey A1 - Kawde, Anurag A1 - Kanady, Jacob S. A1 - Tsui, Emily Y. A1 - Suseno, Sandy A1 - Han, Zhiji A1 - Hill, Ethan A1 - Taguchi, Taketo A1 - Borovik, Andrew S. A1 - Agapie, Theodor A1 - Messinger, Johannes A1 - Erko, Alexei A1 - Föhlisch, Alexander A1 - Bergmann, Uwe A1 - Mitzner, Rolf A1 - Yachandra, Vittal K. A1 - Yano, Junko A1 - Wernet, Philippe T1 - Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers JF - Structural dynamics N2 - X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn similar to 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions. (C) 2017 Author(s). Y1 - 2017 U6 - https://doi.org/10.1063/1.4986627 SN - 2329-7778 VL - 4 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Mitzner, Rolf A1 - Rehanek, Jens A1 - Kern, Jan A1 - Gul, Sheraz A1 - Hattne, Johan A1 - Taguchi, Taketo A1 - Alonso-Mori, Roberto A1 - Tran, Rosalie A1 - Weniger, Christian A1 - Schröder, Henning A1 - Quevedo, Wilson A1 - Laksmono, Hartawan A1 - Sierra, Raymond G. A1 - Han, Guangye A1 - Lassalle-Kaiser, Benedikt A1 - Koroidov, Sergey A1 - Kubicek, Katharina A1 - Schreck, Simon A1 - Kunnus, Kristjan A1 - Brzhezinskaya, Maria A1 - Firsov, Alexander A1 - Minitti, Michael P. A1 - Turner, Joshua J. A1 - Möller, Stefan A1 - Sauter, Nicholas K. A1 - Bogan, Michael J. A1 - Nordlund, Dennis A1 - Schlotter, William F. A1 - Messinger, Johannes A1 - Borovik, Andrew S. A1 - Techert, Simone A1 - de Groot, Frank M. F. A1 - Föhlisch, Alexander A1 - Erko, Alexei A1 - Bergmann, Uwe A1 - Yachandra, Vittal K. A1 - Wernet, Philippe A1 - Yano, Junko T1 - L-edge x-ray absorption spectroscopy of dilute systems relevant to metalloproteins using an X-ray free-electron laser JF - The journal of physical chemistry letters N2 - L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming 0 K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples. Y1 - 2013 U6 - https://doi.org/10.1021/jz401837f SN - 1948-7185 VL - 4 IS - 21 SP - 3641 EP - 3647 PB - American Chemical Society CY - Washington ER -