TY - JOUR A1 - Breitkopf, Hendrik A1 - Schlüter, P. M. A1 - Xu, S. A1 - Schiestl, Florian P. A1 - Cozzolino, S. A1 - Scopece, G. T1 - Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence? JF - Journal of evolutionary biology N2 - Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic distance among populations with contrasting predominant pollinators. We analysed floral hydrocarbons as a proxy for floral divergence between populations. Floral adoption of pollinators and their fidelity was tested using pollinator choice experiments. Interpopulation gene flow and population differentiation levels were estimated using AFLP markers. The Tyrrhenian O.sphegodes population preferentially attracted the pollinator bee Andrena bimaculata, whereas the Adriatic O.sphegodes population exclusively attracted A.nigroaenea. Significant differences in scent component proportions were identified in O.sphegodes populations that attracted different preferred pollinators. High interpopulation gene flow was detected, but populations were genetically structured at species level. The high interpopulation gene flow levels independent of preferred pollinators suggest that local adaptation to different pollinators has not (yet) generated detectable genome-wide separation. Alternatively, despite extensive gene flow, few genes underlying floral isolation remain differentiated as a consequence of divergent selection. Different pollination ecotypes in O.sphegodes might represent a local selective response imposed by temporal variation in a geographical mosaic of pollinators as a consequence of the frequent disturbance regimes typical of Ophrys habitats. KW - adaptation KW - ecotypes KW - floral scent KW - gene flow KW - Ophrys KW - orchids KW - pollinator shift KW - sexual deception KW - speciation Y1 - 2013 U6 - https://doi.org/10.1111/jeb.12216 SN - 1010-061X SN - 1420-9101 VL - 26 IS - 10 SP - 2197 EP - 2208 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wang, Jing A1 - Fritzsch, Claire A1 - Bernarding, Johannes A1 - Krause, Thomas A1 - Mauritz, Karl-Heinz A1 - Brunetti, Maddalena A1 - Dohle, Christian T1 - Cerebral activation evoked by the mirror illusion of the hand in stroke patients compared to normal subjects JF - Neurorehabilitation : an interdisciplinary journal N2 - BACKGROUND: Mirror therapy (MT) was found to improve motor function after stroke, but its neural mechanisms remain unclear, especially in single stroke patients. OBJECTIVES: The following imaging study was designed to compare brain activation patterns evoked by the mirror illusion in single stroke patients with normal subjects. METHODS: Fifteen normal volunteers and five stroke patients with severe arm paresis were recruited. Cerebral activations during movement mirroring by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Single-subject analysis was performed using SPM 8. RESULTS: For normal subjects, ten and thirteen subjects displayed lateralized cerebral activations evoked by the mirror illusion while moving their right and left hand respectively. The magnitude of this effect in the precuneus contralateral to the seen hand was not dependent on movement speed or subjective experience. Negative correlation of activation strength with age was found for the right hand only. The activation pattern in stroke patients is comparable to that of normal subjects and present in four out of five patients. CONCLUSIONS: In summary, the mirror illusion can elicit cerebral activation contralateral to the perceived hand in the majority of single normal subjects, but not in all of them. This is similar even in stroke patients with severe hemiparesis. KW - Movement KW - mirror illusion KW - imaging KW - mirror therapy KW - stroke Y1 - 2013 U6 - https://doi.org/10.3233/NRE-130999 SN - 1053-8135 SN - 1878-6448 VL - 33 IS - 4 SP - 593 EP - 603 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Nahavandi, Nahid A1 - Ketmaier, Valerio A1 - Plath, Martin A1 - Tiedemann, Ralph T1 - Diversification of Ponto-Caspian aquatic fauna - morphology and molecules retrieve congruent evolutionary relationships in Pontogammarus maeoticus (Amphipoda: Pontogammaridae) JF - Molecular phylogenetics and evolution N2 - The geological history of the Ponto-Caspian region, with alternating cycles of isolation and reconnection among the three main basins (Black and Azov Seas, and the more distant Caspian Sea) as well as between them and the Mediterranean Sea, profoundly affected the diversification of its aquatic fauna, leading to a high degree of endemism. Two alternative hypotheses on the origin of this amazing biodiversity have been proposed, corresponding to phases of allopatric separation of aquatic fauna among sea basins: a Late Miocene origin (10-6 MYA) vs. a more recent Pleistocene ancestry (<2 MYA). Both hypotheses support a vicariant origin of (1) Black + Azov Sea lineages on the one hand, and (2) Caspian Sea lineages on the other. Here, we present a study on the Ponto-Caspian endemic amphipod Pontogammarus maeoticus. We assessed patterns of divergence based on (a) two mitochondrial and one nuclear gene, and (b) a morphometric analysis of 23 morphological traits in 16 populations from South and West Caspian Sea, South Azov Sea and North-West Black Sea. Genetic data indicate a long and independent evolutionary history, dating back from the late Miocene to early Pleistocene (6.6-1.6 MYA), for an unexpected, major split between (i) a Black Sea clade and (ii) a well-supported clade grouping individuals from the Caspian and Azov Seas. Absence of shared haplotypes argues against either recent or human-mediated exchanges between Caspian and Azov Seas. A mismatch distribution analysis supports more stable population demography in the Caspian than in the Black Sea populations. Morphological divergence largely followed patterns of genetic divergence: our analyses grouped samples according to the basin of origin and corroborated the close phylogenetic affinity between Caspian and Azov Sea lineages. Altogether, our results highlight the necessity of careful (group-specific) evaluation of evolutionary trajectories in marine taxa that should certainly not be inferred from the current geographical proximity of sea basins alone. (C) 2013 Elsevier Inc. All rights reserved. KW - Biodiversity hotspot KW - Black Sea KW - Caspian Sea KW - Paratethys KW - Sea of Azov KW - Vicariance Y1 - 2013 U6 - https://doi.org/10.1016/j.ympev.2013.05.021 SN - 1055-7903 SN - 1095-9513 VL - 69 IS - 3 SP - 1063 EP - 1076 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Pavesi, Laura A1 - Tiedemann, Ralph A1 - DeMatthaeis, Elvira A1 - Ketmaier, Valerio T1 - Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea Y1 - 2013 UR - 1960 = DOI: 10.1186/1742-9994-10-21 SN - 1742-9994 ER - TY - JOUR A1 - Fiorentino, V. A1 - Manganelli, Giuseppe A1 - Giusti, Folco A1 - Tiedemann, Ralph A1 - Ketmaier, Valerino T1 - A question of time the land snail Murella muralis (Gastropoda: Pulmonata) reveals constraints on past ecological speciation JF - Molecular ecology N2 - The lively debate about speciation currently focuses on the relative importance of factors driving population differentiation. While many studies are increasingly producing results on the importance of selection, little is known about the interaction between drift and selection. Moreover, there is still little knowledge on the spatial-temporal scales at which speciation occurs, that is, arrangement of habitat patches, abruptness of habitat transitions, climate and habitat changes interacting with selective forces. To investigate these questions, we quantified variation on a fine geographical scale analysing morphological (shell) and genetic data sets coupled with environmental data in the land snail Murella muralis, endemic to the Mediterranean island of Sicily. Analysis of a fragment of the mitochondrial DNA cytochrome oxidase I gene (COI) and eight nuclear microsatellite loci showed that genetic variation is highly structured at a very fine spatial scale by local palaeogeographical events and historical population dynamics. Molecular clock estimates, calibrated here specifically for Tyrrhenian land snails, provided a framework of palaeogeographical events responsible for the observed geographical variations and migration routes. Finally, we showed for the first time well-documented lines of evidence of selection in the past, which explains divergence of land snail shell shapes. We suggest that time and palaeogeographical history acted as constraints in the progress along the ecological speciation continuum. Our study shows that testing for correlation among palaeogeography, morphology and genetic data on a fine geographical scale provides information fundamental for a detailed understanding of ecological speciation processes. KW - allopatry KW - cytochrome oxidase I gene KW - ecological speciation KW - land snails KW - microsatellites KW - Murella Y1 - 2013 U6 - https://doi.org/10.1111/mec.12107 SN - 0962-1083 SN - 1365-294X VL - 22 IS - 1 SP - 170 EP - 186 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Pavesi, Laura A1 - Tiedemann, Ralph A1 - De Matthaeis, Elvira A1 - Ketmaier, Valerio T1 - Genetic connectivity between land and sea - the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea JF - Frontiers in zoology N2 - Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism. KW - Orchestia montagui KW - Talitrids KW - Mediterranean Sea KW - Phylogeography KW - Mitochondrial DNA KW - Microsatellites KW - Allozymes KW - Approximate Bayesian Computation Y1 - 2013 U6 - https://doi.org/10.1186/1742-9994-10-21 SN - 1742-9994 VL - 10 IS - 4-5 PB - BioMed Central CY - London ER - TY - JOUR A1 - Milinkovitch, Michel C. A1 - Kanitz, Ricardo A1 - Tiedemann, Ralph A1 - Tapia, Washington A1 - Llerena, Fausto A1 - Caccone, Adalgisa A1 - Gibbs, James P. A1 - Powell, Jeffrey R. T1 - Recovery of a nearly extinct Galapagos tortoise despite minimal genetic variation JF - Evolutionary applications N2 - A species of Galapagos tortoise endemic to Espanola Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size <8 due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity. These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population. Using simple morphological data scored on the sampled animals, we also show that a strongly heterogeneous distribution of tortoise sizes on Espanola Island observed today is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40years. Our study reveals that, at least in the short run, some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts. KW - captive populations KW - conservation biology KW - conservation genetics Y1 - 2013 U6 - https://doi.org/10.1111/eva.12014 SN - 1752-4571 VL - 6 IS - 2 SP - 377 EP - 383 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hechavarria, Julio C. A1 - Macias, Silvio A1 - Vater, Marianne A1 - Mora, Emanuel C. A1 - Kössl, Manfred T1 - Evolution of neuronal mechanisms for echolocation specializations for target-range computation in bats of the genus Pteronotus JF - The journal of the Acoustical Society of America N2 - Delay tuning was studied in the auditory cortex of Pteronotus quadridens. All the 136 delay-tuned units that were studied responded strongly to heteroharmonic pulse-echo pairs presented at specific delays. In the heteroharmonic pairs, the first sonar call harmonic marks the timing of pulse emission while one of the higher harmonics (second or third) indicates the timing of the echo. Delay-tuned units are organized chronotopically along a rostrocaudal axis according to their characteristic delay. There is no obvious indication of multiple cortical axes specialized in the processing of different harmonic combinations of pulse and echo. Results of this study serve for a straight comparison of cortical delay-tuning between P. quadridens and the well-studied mustached bat, Pteronotus parnellii. These two species stem from the most recent and most basal nodes in the Pteronotus lineage, respectively. P. quadridens and P. parnellii use comparable heteroharmonic target-range computation strategies even though they do not use biosonar calls of a similar design. P. quadridens uses short constant-frequency (CF)/frequency-modulated (FM) echolocation calls, while P. parnellii uses long CF/FM calls. The ability to perform "heteroharmonic" target-range computations might be an ancestral neuronal specialization of the genus Pteronotus that was subjected to positive Darwinian selection in the evolution. Y1 - 2013 U6 - https://doi.org/10.1121/1.4768794 SN - 0001-4966 VL - 133 IS - 1 SP - 570 EP - 578 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Hechavarria, Julio C. A1 - Macias, Silvio A1 - Vater, Marianne A1 - Voss, Cornelia A1 - Mora, Emanuel C. A1 - Kossl, Manfred T1 - Blurry topography for precise target-distance computations in the auditory cortex of echolocating bats JF - Nature Communications N2 - Echolocating bats use the time from biosonar pulse emission to the arrival of echo (defined as echo delay) to calculate the space depth of targets. In the dorsal auditory cortex of several species, neurons that encode increasing echo delays are organized rostrocaudally in a topographic arrangement defined as chronotopy. Precise chronotopy could be important for precise target-distance computations. Here we show that in the cortex of three echolocating bat species (Pteronotus quadridens, Pteronotus parnellii and Carollia perspicillata), chronotopy is not precise but blurry. In all three species, neurons throughout the chronotopic map are driven by short echo delays that indicate the presence of close targets and the robustness of map organization depends on the parameter of the receptive field used to characterize neuronal tuning. The timing of cortical responses (latency and duration) provides a binding code that could be important for assembling acoustic scenes using echo delay information from objects with different space depths. Y1 - 2013 U6 - https://doi.org/10.1038/ncomms3587 SN - 2041-1723 VL - 4 IS - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Tikhonenko, Irina A1 - Magidson, Valentin A1 - Gräf, Ralph A1 - Khodjakov, Alexey A1 - Koonce, Michael P. T1 - A kinesin-mediated mechanism that couples centrosomes to nuclei JF - Cellular and molecular life sciences N2 - The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment. KW - Centrosome KW - Kinesin KW - Microtubule KW - Dictyostelium Y1 - 2013 U6 - https://doi.org/10.1007/s00018-012-1205-0 SN - 1420-682X VL - 70 IS - 7 SP - 1285 EP - 1296 PB - Springer CY - Basel ER - TY - JOUR A1 - Junemann, Alexander A1 - Winterhoff, Moritz A1 - Nordholz, Benjamin A1 - Rottner, Klemens A1 - Eichinger, Ludwig A1 - Gräf, Ralph A1 - Faix, Jan T1 - ForC lacks canonical formin activity but bundles actin filaments and is required for multicellular development of Dictyostelium cells JF - European journal of cell biology N2 - Diaphanous-related formins (DRFs) drive the nucleation and elongation of linear actin filaments downstream of Rho GTPase signalling pathways. Dictyostelium formin C (ForC) resembles a DRF, except that it lacks a genuine formin homology domain 1 (FH1), raising the questions whether or not ForC can nucleate and elongate actin filaments. We found that a recombinant ForC-FH2 fragment does not nucleate actin polymerization, but moderately decreases the rate of spontaneous actin assembly and disassembly, although the barbed-end elongation rate in the presence of the formin was not markedly changed. However, the protein bound to and crosslinked actin filaments into loose bundles of mixed polarity. Furthermore, ForC is an important regulator of morphogenesis since ForC-null cells are severely impaired in development resulting in the formation of aberrant fruiting bodies. Immunoblotting revealed that ForC is absent during growth, but becomes detectable at the onset of early aggregation when cells chemotactically stream together to form a multicellular organism, and peaks around the culmination stage. Fluorescence microscopy of cells ectopically expressing a GFP-tagged, N-terminal ForC fragment showed its prominent accumulation in the leading edge, suggesting that ForC may play a role in cell migration. In agreement with its expression profile, no defects were observed in random migration of vegetative mutant cells. Notably, chemotaxis of starved cells towards a source of cAMP was severely impaired as opposed to control. This was, however, largely due to a marked developmental delay of the mutant, as evidenced by the expression profile of the early developmental marker csA. In line with this, chemotaxis was almost restored to wild type levels after prolonged starvation. Finally, we observed a complete failure of phototaxis due to abolished slug formation and a massive reduction of spores consistent with forC promoter-driven expression of beta-galactosidase in prespore cells. Together, these findings demonstrate ForC to be critically involved in signalling of the cytoskeleton during various stages of development. KW - Actin bundles KW - Cell migration KW - Chemotaxis KW - Development KW - Dictyostelium KW - Formin KW - Morphogenesis KW - Phototaxis KW - Spore formation Y1 - 2013 U6 - https://doi.org/10.1016/j.ejcb.2013.07.001 SN - 0171-9335 VL - 92 IS - 6-7 SP - 201 EP - 212 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Müller, Sara A1 - Windhof, Indra M. A1 - Maximov, Vladimir A1 - Jurkowski, Tomasz A1 - Jeltsch, Albert A1 - Förstner, Konrad U. A1 - Sharma, Cynthia M. A1 - Gräf, Ralph A1 - Nellen, Wolfgang T1 - Target recognition, RNA methylation activity and transcriptional regulation of the dictyostelium discoideum Dnmt2-homologue (DnmA) JF - Nucleic acids research N2 - Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNA(Asp(GUC)) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNA(Glu(CUC/UUC)) and tRNA(Gly(GCC)) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation. Y1 - 2013 U6 - https://doi.org/10.1093/nar/gkt634 SN - 0305-1048 SN - 1362-4962 VL - 41 IS - 18 SP - 8615 EP - 8627 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Benina, Maria A1 - Obata, Toshihiro A1 - Mehterov, Nikolay A1 - Ivanov, Ivan A1 - Petrov, Veselin A1 - Toneva, Valentina A1 - Fernie, Alisdair R. A1 - Gechev, Tsanko S. T1 - Comparative metabolic profiling of Haberlea rhodopensis, Thellungiella halophyla, and Arabidopsis thaliana exposed to low temperature JF - Frontiers in plant science N2 - Haberlea rhodopensis is a resurrection species with extreme resistance to drought stress and desiccation but also with ability to withstand low temperatures and freezing stress. In order to identify biochemical strategies which contribute to Haberlea's remarkable stress tolerance, the metabolic reconfiguration of H. rhodopensis during low temperature (4 degrees C) and subsequent return to optimal temperatures (21 degrees C) was investigated and compared with that of the stress tolerant Thellungiella halophyla and the stress sensitive Arabidopsis thaliana. Metabolic analysis by GC-MS revealed intrinsic differences in the metabolite levels of the three species even at 21 degrees C. H. rhodopensis had significantly more raffinose, melibiose, trehalose, rhamnose, myo-inositol, sorbitol, galactinol, erythronate, threonate, 2-oxoglutarate, citrate, and glycerol than the other two species. A. thaliana had the highest levels of putrescine and fumarate, while T halophila had much higher levels of several amino acids, including alanine, asparagine, beta-alanine, histidine, isoleucine, phenylalanine, serine, threonine, and valine. In addition, the three species responded differently to the low temperature treatment and the subsequent recovery, especially with regard to the sugar metabolism. Chilling induced accumulation of maltose in H. rhodopensis and raffinose in A. thaliana but the raffinose levels in low temperature exposed Arabidopsis were still much lower than these in unstressed Haberlea. While all species accumulated sucrose during chilling, that accumulation was transient in H. rhodopensis and A. thaliana but sustained in T halophila after the return to optimal temperature. Thus, Haberlea's metabolome appeared primed for chilling stress but the low temperature acclimation induced additional stress-protective mechanisms. A diverse array of sugars, organic acids, and polyols constitute Haberlea's main metabolic defence mechanisms against chilling, while accumulation of amino acids and amino acid derivatives contribute to the low temperature acclimation in Arabidopsis and Thellungiella. Collectively, these results show inherent differences in the metabolomes under the ambient temperature and the strategies to respond to low temperature in the three species. KW - Arabidopsis thaliana KW - Haberlea rhodopensis KW - low temperature stress KW - metabolite profiling KW - Thellungiella halophila Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00499 SN - 1664-462X VL - 4 IS - 1 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - May, Felix A1 - Giladi, Itamar A1 - Ristow, Michael A1 - Ziv, Yaron A1 - Jeltsch, Florian T1 - Metacommunity, mainland-island system or island communities? : assessing the regional dynamics of plant communities in a fragmented landscape JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - Understanding the regional dynamics of plant communities is crucial for predicting the response of plant diversity to habitat fragmentation. However, for fragmented landscapes the importance of regional processes, such as seed dispersal among isolated habitat patches, has been controversially debated. Due to the stochasticity and rarity of among-patch dispersal and colonization events, we still lack a quantitative understanding of the consequences of these processes at the landscape-scale. In this study, we used extensive field data from a fragmented, semi-arid landscape in Israel to parameterize a multi-species incidence-function model. This model simulates species occupancy pattern based on patch areas and habitat configuration and explicitly considers the locations and the shapes of habitat patches for the derivation of patch connectivity. We implemented an approximate Bayesian computation approach for parameter inference and uncertainty assessment. We tested which of the three types of regional dynamics - the metacommunity, the mainland-island, or the island communities type - best represents the community dynamics in the study area and applied the simulation model to estimate the extinction debt in the investigated landscape. We found that the regional dynamics in the patch-matrix study landscape is best represented as a system of highly isolated island' communities with low rates of propagule exchange among habitat patches and consequently low colonization rates in local communities. Accordingly, the extinction rates in the local communities are the main drivers of community dynamics. Our findings indicate that the landscape carries a significant extinction debt and in model projections 33-60% of all species went extinct within 1000 yr. Our study demonstrates that the combination of dynamic simulation models with field data provides a promising approach for understanding regional community dynamics and for projecting community responses to habitat fragmentation. The approach bears the potential for efficient tests of conservation activities aimed at mitigating future losses of biodiversity. Y1 - 2013 U6 - https://doi.org/10.1111/j.1600-0587.2012.07793.x SN - 0906-7590 VL - 36 IS - 7 SP - 842 EP - 853 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - May, Felix A1 - Giladi, Itamar A1 - Ristow, Michael A1 - Ziv, Yaron A1 - Jeltsch, Florian T1 - Plant functional traits and community assembly along interacting gradients of productivity and fragmentation JF - Perspectives in plant ecology, evolution and systematics N2 - Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes. In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south-north productivity gradient. We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m x 0.25 m). All traits varied significantly along the S-N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S-N gradient. Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass). Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits. KW - Connectivity KW - Drought-stress KW - Habitat filtering KW - Limiting similarity KW - Null models KW - Plant height KW - Seed mass KW - Seed number KW - Specific leaf area (SLA) Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.08.002 SN - 1433-8319 VL - 15 IS - 6 SP - 304 EP - 318 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Martins, Marina Camara Mattos A1 - Hejazi, Mahdi A1 - Fettke, Jörg A1 - Steup, Martin A1 - Feil, Regina A1 - Krause, Ursula A1 - Arrivault, Stephanie A1 - Vosloh, Daniel A1 - Figueroa, Carlos Maria A1 - Ivakov, Alexander A1 - Yadav, Umesh Prasad A1 - Piques, Maria A1 - Metzner, Daniela A1 - Stitt, Mark A1 - Lunn, John Edward T1 - Feedback inhibition of starch degradation in arabidopsis leaves mediated by trehalose 6-phosphate JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by beta-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 mu M in the cytosol, 0.2 to 0.5 mu M in the chloroplasts, and 0.05 mu M in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night. Y1 - 2013 U6 - https://doi.org/10.1104/pp.113.226787 SN - 0032-0889 SN - 1532-2548 VL - 163 IS - 3 SP - 1142 EP - 1163 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Ruzanski, Christian A1 - Smirnova, Julia A1 - Rejzek, Martin A1 - Cockburn, Darrell A1 - Pedersen, Henriette L. A1 - Pike, Marilyn A1 - Willats, William G. T. A1 - Svensson, Birte A1 - Steup, Martin A1 - Ebenhöh, Oliver A1 - Smith, Alison M. A1 - Field, Robert A. T1 - A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night JF - The journal of biological chemistry N2 - Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway. KW - Carbohydrate Metabolism KW - Computer Modeling KW - Metabolic Regulation KW - Oligosaccharide KW - Plant Biochemistry KW - Glucanotransferase KW - Leaf Cell KW - Maltose Metabolism KW - Starch Degradation Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M113.497867 SN - 0021-9258 SN - 1083-351X VL - 288 IS - 40 SP - 28581 EP - 28598 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Schwarte, Sandra A1 - Brust, Henrike A1 - Steup, Martin A1 - Tiedemann, Ralph T1 - Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana Y1 - 2013 UR - http://www.biomedcentral.com/content/pdf/1756-0500-6-84.pdf U6 - https://doi.org/10.1186/1756-0500-6-84 ER - TY - JOUR A1 - Malinova, Irina A1 - Steup, Martin A1 - Fettke, Jörg T1 - Carbon transitions from either Calvin cycle or transitory starch to heteroglycans as revealed by 14-C-labeling experiments using protoplasts from Arabidopsis JF - Physiologia plantarum N2 - Plants metabolize transitory starch by precisely coordinated plastidial and cytosolic processes. The latter appear to include the action of water-soluble heteroglycans (SHG(in)) whose monosaccharide pattern is similar to that of apoplastic glycans (SHG(ex)) but, unlike SHG(ex), SHG(in) strongly interacts with glucosyl transferases. In this study, we analyzed starch metabolism using mesophyll protoplasts from wild-type plants and two knock-out mutants [deficient in the cytosolic transglucosidase, disproportionating isoenzyme 2 (DPE2) or the plastidial phosphoglucomutase (PGM1)] from Arabidopsis thaliana. Protoplasts prelabeled by photosynthetic (CO2)-C-14 fixation were transferred to an unlabeled medium and were darkened or illuminated. Carbon transitions from the Calvin cycle or from starch to both SHG(in) and SHG(ex) were analyzed. In illuminated protoplasts, starch turn-over was undetectable but darkened protoplasts continuously degraded starch. During illumination, neither the total C-14 content nor the labeling patterns of the sugar residues of SHG(in) were significantly altered but both the total amount and the labeling of the constituents of SHG(ex) increased with time. In darkened protoplasts, the C-14-content of most of the sugar residues of SHG(in) transiently and strongly increased and then declined. This effect was not observed in any SHG(ex) constituent. In darkened DPE2-deficient protoplasts, none of the SHG(in) constituents exhibited an essential transient increase in labeling. In contrast, some residues of SHG(in) from the PGM1 mutant exhibited a transient increase in label but this effect significantly differed from that of the wild type. Two conclusions are reached: first, SHG(in) and SHG(ex) exert different metabolic functions and second, SHG(in) is directly involved in starch degradation. Y1 - 2013 U6 - https://doi.org/10.1111/ppl.12033 SN - 0031-9317 VL - 149 IS - 1 SP - 25 EP - 44 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schmieder, Peter A1 - Nitschke, Felix A1 - Steup, Martin A1 - Mallow, Keven A1 - Specker, Edgar T1 - Determination of glucan phosphorylation using heteronuclear H-1,C-13 double and H-1,C-13,P-31 triple-resonance NMR spectra JF - Magnetic resonance in chemistry N2 - Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear H-1,C-13 and H-1,C-13,P-31 techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples. KW - heteronuclear NMR KW - triple resonance KW - phosphorylation KW - starch Y1 - 2013 U6 - https://doi.org/10.1002/mrc.3996 SN - 0749-1581 VL - 51 IS - 10 SP - 655 EP - 661 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Lukas, Marcus A1 - Frost, Paul C. A1 - Wacker, Alexander T1 - The neonate nutrition hypothesis - early feeding affects the body stoichiometry of Daphnia offspring JF - Freshwater biology N2 - Aquatic herbivores consume variable quantities and qualities of food. In freshwater systems, where phosphorus (P) is often a primary limiting element, inadequate dietary P can slow maternal growth and reduce body P content. There remains uncertainty about whether and how dietary effects on mothers are transferred to offspring by way of egg provisioning. Using the keystone herbivore Daphnia, we tested a novel explanation (the neonate nutrition hypothesis') to determine whether the early nutrition of newborns affects their elemental composition and whether the indications of differences in maternal P nutrition found previously might be overestimated. We thus examined the P content of mothers and their eggs from deposition through development to the birth of neonates. We examined further whether very short periods of ingestion (3h) by the offspring alter the overall P content of juvenile Daphnia. We showed that strong dietary P effects on mothers were not directly transferred to their eggs. Irrespective of the supply of P in the maternal diet, the P content of eggs in different developmental stages and in (unfed) neonates did not differ. This indicates that Daphnia mothers do not reduce the quality (in terms of P) of newly produced offspring after intermittent periods (i.e. several days) of poor nutrition. In contrast, the P content of neonates reflected that of their food after brief periods of feeding, indicating that even temporary exposure to nutrient poor food immediately after birth may strongly affect the elemental composition of neonates. Our results thus support the neonate nutrition hypothesis, which, like differential maternal provisioning, is a possible explanation for the variable elemental quality of young Daphnia. KW - ecological stoichiometry KW - food quality KW - maternal effects KW - nutrient limitation KW - zooplankton Y1 - 2013 U6 - https://doi.org/10.1111/fwb.12213 SN - 0046-5070 VL - 58 IS - 11 SP - 2333 EP - 2344 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hartwich, Melanie A1 - Martin-Creuzburg, Dominik A1 - Wacker, Alexander T1 - Seasonal changes in the accumulation of polyunsaturated fatty acids in zooplankton JF - Journal of plankton research N2 - In aquatic food webs, consumers, such as daphnids and copepods, differ regarding their accumulation of polyunsaturated fatty acids (PUFAs). We tested if the accumulation of PUFAs in a seston size fraction containing different consumers and in Daphnia as a separate consumer is subject to seasonal changes in a large deep lake due to changes in the dietary PUFA supply and specific demands of different consumers. We found that the accumulation of arachidonic acid (ARA) in Daphnia increased from early summer to late summer and autumn. However, ARA requirements of Daphnia appeared to be constant throughout the year, because the accumulation of ARA increased when the dietary ARA supply decreased. In the size fraction 140 m, we found an increased accumulation of docosahexaenoic acid (DHA) during late summer and autumn. These seasonal changes in DHA accumulation were linked to changes in the proportion of copepods in this size fraction, which may have increasingly accumulated DHA for active overwintering. We show that consumer-specific PUFA demands can result in seasonal changes in PUFA accumulation, which may influence the trophic transfer of PUFAs within the food web. KW - accumulation KW - Daphnia KW - copepods KW - ARA KW - DHA Y1 - 2013 U6 - https://doi.org/10.1093/plankt/fbs078 SN - 0142-7873 VL - 35 IS - 1 SP - 121 EP - 134 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schmitz-Hertzberg, Sebastian-Tim A1 - Mak, Wing Cheung A1 - Lai, Kwok Kei A1 - Teller, Carsten A1 - Bier, Frank Fabian T1 - Multifactorial design of Poly(D, L-lactic-co-glycolic acid) capsules with various release properties for differently sized filling agents JF - Journal of applied polymer science N2 - The hydrolytic degradation and corresponding content release of capsules made of poly(d,l-lactic-co-glycolic acid) (PLGA) strongly depends on the composition and material properties of the initially applied copolymer. Consecutive or simultaneous release from capsule batches of combinable material compositions, therefore, offers high control over the bioavailability of an encapsulated drug. The keynote of this study was the creation of a superordinated database that addressed the correlation between the release kinetics of filling agents with different molecular weights from PLGA capsules of alternating composition. Fluorescein isothiocyanate (FITC)-dextran (with molecular weights of 4, 40, and 2000 kDa) was chosen as a model analyte, whereas the copolymers were taken from various 50:50 PLGA, 75:25 PLGA, and polylactide blends. With reference to recent publications, the capsule properties, such as the size, morphology, and encapsulation efficiency, were further modified during production. Hence, uniform microdisperse and polydisperse submicrometer nanocapsules were prepared by two different water-in-oil-in-water emulsification techniques, and additional effects on the size and morphology were achieved by capsule solidification in two different sodium salt buffers. The qualitative and quantitative examination of the physical capsule properties was performed by confocal laser scanning microscopy, scanning electron microscopy, and Coulter counting techniques to evaluate the capsule size distribution and the morphological appearance of the different batches. The corresponding agent release was quantified by fluorescence measurement of the FITC-dextran in the incubation media and by the direct measurement of the capsule brightness via fluorescence microscopy. In summary, the observed agent release showed a highly controllable flexibility depending on the PLGA blends, preparation methods, and molecular weight of the used filling substances. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 4219-4228, 2013 KW - biodegradable copolymers (PLGA) KW - microcapsules KW - submicrometer KW - nanocapsules KW - FITC-dextran release KW - drug delivery system KW - biomedical applications Y1 - 2013 U6 - https://doi.org/10.1002/app.39537 SN - 0021-8995 SN - 1097-4628 VL - 130 IS - 6 SP - 4219 EP - 4228 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Sauter, Tilman A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Pore-size distribution controls shape-memory properties on the macro- and microscale of polymeric foams JF - Macromolecular chemistry and physics N2 - Open porous foams with identical foam density but different pore-size distributions (bimodal or monomodal) are prepared from a shape-memory polyetherurethane (PEU) by thermally induced phase separation. The shape-memory effect of the two PEU foams is explored by cyclic thermomechanical compression tests and microstructural analysis. The obtained results reveal that the PEU foam with a bimodal pore-size distribution exhibits an increased shape-recovery under stress-free conditions, both on the macro- (foam level) as well as the microscale (pore level). While bimodal pore-size distributions induce microscale bending during compression, buckling occurs in foams with monomodal pore-size distributions, leading to both a reduced and delayed shape recovery. KW - microstructure KW - morphology KW - polymer foams KW - pore-size distribution KW - shape-memory polymers Y1 - 2013 U6 - https://doi.org/10.1002/macp.201300062 SN - 1022-1352 VL - 214 IS - 11 SP - 1184 EP - 1188 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Rüder, Constantin A1 - Sauter, Tilman A1 - Kratz, Karl A1 - Haase, Tobias A1 - Peter, Jan A1 - Jung, Friedrich A1 - Lendlein, Andreas A1 - Zohlnhöfer, Dietlind T1 - Influence of fibre diameter and orientation of electrospun copolyetheresterurethanes on smooth muscle and endothelial cell behaviour JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Polymers exhibiting cell-selective effects represent an extensive research field with high relevance for biomedical applications e.g. in the cardiovascular field supporting re-endothelialization while suppressing smooth muscle cell overgrowth. Such an endothelial cell-selective effect could be recently demonstrated for a copolyetheresterurethane (PDC) containing biodegradable poly(p-dioxanone) and poly(epsilon-caprolactone) segments, which selectively enhanced the adhesion of human umbilical vein endothelial cells (HUVEC) while suppressing the attachment of smooth muscle cells (SMC). In this study we investigated the influence of the fibre orientation (random and aligned) and fibre diameter (2 mu m and 500 nm) of electrospun PDC scaffolds on the adhesion, proliferation and apoptosis of HUVEC and SMC. Adhesion, viability and proliferation of HUVEC was diminished when the fibre diameter was reduced to a submicron scale, while the orientation of the microfibres did only slightly influence the cellular behaviour. In contrast, a submicron fibre diameter improved SMC viability. In conclusion, PDC scaffolds with micron-sized single fibres could be promising candidate materials for cell-selective stent coatings. KW - Endothelialization KW - drug eluting stent KW - degradable polymer KW - electrospinning KW - cell selectivity Y1 - 2013 U6 - https://doi.org/10.3233/CH-131787 SN - 1386-0291 SN - 1875-8622 VL - 55 IS - 4 SP - 513 EP - 522 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Burgold, Julia A1 - Rolfes, Manfred T1 - Of voyeuristic safari tours and responsible tourism with educational value observing moral communication in slum and township tourism in Cape Town and Mumbai JF - Die Erde : journal of the Geographical Society of Berlin ; Zeitschrift der Gesellschaft für Erdkunde zu Berlin N2 - Sightseeing in the poorest quarters of southern hemisphere cities has been observed occurring in Cape Town, Rio de Janeiro, Mumbai and many other cities. The increasing global interest in touring poor urban environments is accompanied by a strong morally charged debate; so far, this debate has not been critically addressed. This article avoids asking if slum tourism is good or bad, but instead seeks a second-order observation, i.e. to investigate under what conditions the social praxis of slum tourism is considered as good or bad, by processing information on esteem or dis-esteem among tourists and tour providers. Special attention is given to any relation between morality and place, and the thesis posited is that the moral charging of slum tourism is dependent on the presence of specific preconceived notions of slums and poverty. This shall be clarified by means of references to two empirical case studies carried out in (1) Cape Town in 2007 and 2008 and (2) Mumbai in 2009. KW - Slum tourism KW - township tourism KW - morality KW - place Y1 - 2013 SN - 0013-9998 VL - 144 IS - 2 SP - 161 EP - 174 PB - Gesellschaft für Erdkunde CY - Berlin ER - TY - JOUR A1 - Basel, Nicolai A1 - Harms, Ute A1 - Prechtl, Helmut T1 - Analysis of students' arguments on evolutionary theory JF - Journal of biological education N2 - 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. KW - evolutionary theory KW - reasoning KW - argumentation KW - argumentation schemes Y1 - 2013 U6 - https://doi.org/10.1080/00219266.2013.799078 SN - 0021-9266 SN - 2157-6009 VL - 47 IS - 4 SP - 192 EP - 199 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Hoppe, Sebastian A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of campylobacter jejuni JF - PLoS one N2 - Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium's pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C. jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0065837 SN - 1932-6203 VL - 8 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Hüttl, Christine A1 - Hettrich, Cornelia A1 - Miller, Reinhard A1 - Paulke, Bernd-Reiner A1 - Henklein, Petra A1 - Rawel, Harshadrai Manilal A1 - Bier, Frank Fabian T1 - Self-assembled peptide amphiphiles function as multivalent binder with increased hemagglutinin affinity JF - BMC biotechnology N2 - Background: A promising way in diagnostic and therapeutic applications is the development of peptide amphiphiles (PAs). Peptides with a palmitic acid alkylchain were designed and characterized to study the effect of the structure modifications on self-assembling capabilities and the multiple binding capacity to hemagglutinin (HA), the surface protein of influenza virus type A. The peptide amphiphiles consists of a hydrophilic headgroup with a biological functionality of the peptide sequence and a chemically conjugated hydrophobic tail. In solution they self-assemble easily to micelles with a hydrophobic core surrounded by a closely packed peptide-shell. Results: In this study the effect of a multiple peptide binding partner to the receptor binding site of HA could be determined with surface plasmon resonance measurements. The applied modification of the peptides causes signal amplification in relationship to the unmodified peptide wherein the high constant specificity persists. The molecular assembly of the peptides was characterized by the determination of critical micelle concentration (CMC) with concentration of 10(-5) M and the colloidal size distribution. Conclusion: The modification of the physico-chemical parameters by producing peptide amphiphiles form monomeric structures which enhances the binding affinity and allows a better examination of the interaction with the virus surface protein hemagglutinin. KW - CMC KW - Influenza virus detection KW - Micelle KW - PAs KW - Surface plasmon resonance Y1 - 2013 U6 - https://doi.org/10.1186/1472-6750-13-51 SN - 1472-6750 VL - 13 IS - 22 PB - BioMed Central CY - London ER - TY - JOUR A1 - Sachse, Rita A1 - Wüstenhagen, Doreen Anja A1 - Samalikova, Maria A1 - Gerrits, Michael A1 - Bier, Frank Fabian A1 - Kubick, Stefan T1 - Synthesis of membrane proteins in eukaryotic cell-free systems JF - Engineering in life sciences : Industry, Environment, Plant, Food N2 - Cell-free protein synthesis (CFPS) is a valuable method for the fast expression of difficult-to-express proteins as well as posttranslationally modified proteins. Since cell-free systems circumvent possible cytotoxic effects caused by protein overexpression in living cells, they significantly enlarge the scale and variety of proteins that can be characterized. We demonstrate the high potential of eukaryotic CFPS to express various types of membrane proteins covering a broad range of structurally and functionally diverse proteins. Our eukaryotic cell-free translation systems are capable to provide high molecular weight membrane proteins, fluorescent-labeled membrane proteins, as well as posttranslationally modified proteins for further downstream analysis. KW - Cell-free protein expression KW - In vitro protein synthesis KW - Labeled membrane proteins KW - Synthetic glycoprotein Y1 - 2013 U6 - https://doi.org/10.1002/elsc.201100235 SN - 1618-0240 VL - 13 IS - 1 SP - 39 EP - 48 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hill, Natascha A1 - Leow, Alexander A1 - Bleidorn, Christoph A1 - Groth, Detlef A1 - Tiedemann, Ralph A1 - Selbig, Joachim A1 - Hartmann, Stefanie T1 - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information JF - Theory in biosciences N2 - Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary. KW - Mutual Information KW - Evolution KW - Gene structure Y1 - 2013 U6 - https://doi.org/10.1007/s12064-012-0173-0 SN - 1431-7613 VL - 132 IS - 2 SP - 93 EP - 104 PB - Springer CY - New York ER - TY - JOUR A1 - Zhang, Hucai A1 - Paijmans, Johanna L. A. A1 - Chang, Fengqin A1 - Wu, Xiaohong A1 - Chen, Guangjie A1 - Lei, Chuzhao A1 - Yang, Xiujuan A1 - Wei, Zhenyi A1 - Bradley, Daniel G. A1 - Orlando, Ludovic A1 - O'Connor, Terry A1 - Hofreiter, Michael T1 - Morphological and genetic evidence for early Holocene cattle management in northeastern China JF - Nature Communications N2 - The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years. Y1 - 2013 U6 - https://doi.org/10.1038/ncomms3755 SN - 2041-1723 VL - 4 IS - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Scheffler, Christiane T1 - Types of Body Shape JF - Auxology : Studying Human Growth and Development Y1 - 2013 SN - 978-3-510-65278-5 SP - 28 EP - 29 PB - Schweizerbart Science Publishers CY - Stuttgart ER - TY - JOUR A1 - Buchmann, Carsten M. A1 - Schurr, Frank Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - Habitat loss and fragmentation affecting mammal and bird communities-The role of interspecific competition and individual space use JF - Ecological informatics : an international journal on ecoinformatics and computational ecolog N2 - Fragmentation and loss of habitat are major threats to animal communities and are therefore important to conservation. Due to the complexity of the interplay of spatial effects and community processes, our mechanistic understanding of how communities respond to such landscape changes is still poor. Modelling studies have mostly focused on elucidating the principles of community response to fragmentation and habitat loss at relatively large spatial and temporal scales relevant to metacommunity dynamics. Yet, it has been shown that also small scale processes, like foraging behaviour, space use by individuals and local resource competition are also important factors. However, most studies that consider these smaller scales are designed for single species and are characterized by high model complexity. Hence, they are not easily applicable to ecological communities of interacting individuals. To fill this gap, we apply an allometric model of individual home range formation to investigate the effects of habitat loss and fragmentation on mammal and bird communities, and, in this context, to investigate the role of interspecific competition and individual space use. Results show a similar response of both taxa to habitat loss. Community composition is shifted towards higher frequency of relatively small animals. The exponent and the 95%-quantile of the individual size distribution (ISD, described as a power law distribution) of the emerging communities show threshold behaviour with decreasing habitat area. Fragmentation per se has a similar and strong effect on mammals, but not on birds. The ISDs of bird communities were insensitive to fragmentation at the small scales considered here. These patterns can be explained by competitive release taking place in interacting animal communities, with the exception of bird's buffering response to fragmentation, presumably by adjusting the size of their home ranges. These results reflect consequences of higher mobility of birds compared to mammals of the same size and the importance of considering competitive interaction, particularly for mammal communities, in response to landscape fragmentation. Our allometric approach enables scaling up from individual physiology and foraging behaviour to terrestrial communities, and disentangling the role of individual space use and interspecific competition in controlling the response of mammal and bird communities to landscape changes. KW - Allometry KW - Body size KW - Fractal landscapes KW - Foraging movement KW - Individual-based model KW - Locomotion costs Y1 - 2013 U6 - https://doi.org/10.1016/j.ecoinf.2012.11.015 SN - 1574-9541 VL - 14 SP - 90 EP - 98 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Seifan, Merav A1 - Seifan, Tal A1 - Schiffers, Katja A1 - Jeltsch, Florian A1 - Tielboerger, Katja T1 - Beyond the competition-colonization trade-off - linking multiple trait response to disturbance characteristics JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Disturbances' role in shaping communities is well documented but highly disputed. We suggest replacing the overused two-trait trade-off approach with a functional group scheme, constructed from combinations of four key traits that represent four classes of species' responses to disturbances. Using model results and field observations from sites affected by two highly different disturbances, we demonstrated that popular dichotomous trade-offs are not sufficient to explain community dynamics, even if some emerge under certain conditions. Without disturbances, competition was only sufficient to predict species survival but not relative success, which required some escape mechanism (e.g., long-term dormancy). With highly predictable and large-scale disturbances, successful species showed a combination of high individual tolerance to disturbance and, more surprisingly, high competitive ability. When disturbances were less predictable, high individual tolerance and long-term seed dormancy were favored, due to higher environmental uncertainty. Our study demonstrates that theories relying on a small number of predefined trade-offs among traits (e.g., competition-colonization trade-off) may lead to unrealistic results. We suggest that the understanding of disturbance-community relationships can be significantly improved by employing sets of relevant trait assemblies instead of the currently common approach in which trade-offs are assumed in advance. KW - competition resistance trade-off KW - functional types KW - intermediate disturbance hypothesis KW - plant communities KW - species assemblies Y1 - 2013 U6 - https://doi.org/10.1086/668844 SN - 0003-0147 VL - 181 IS - 2 SP - 151 EP - 160 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Fechner, Lennart A1 - Baumann, Otto A1 - Walz, Bernd T1 - Activation of the cyclic AMP pathway promotes serotonin-induced Ca2+ oscillations in salivary glands of the blowfly Calliphora vicina JF - Cell calcium N2 - Ca2+ and cAMP signalling pathways interact in a complex manner at multiple sites. This crosstalk fine-tunes the spatiotemporal patterns of Ca2+ and cAMP signals. In salivary glands of the blowfly Calliphora vicina fluid secretion is stimulated by serotonin (5-hydroxytryptamine, 5-HT) via activation of two different 5-HT receptors coupled to the InsP(3)/Ca2+ (Cv5-HT2 alpha) or the cAMP pathway (Cv5-HT7), respectively. We have shown recently in permeabilized gland cells that cAMP sensitizes InsP(3)-induced Ca2+ release to InsP(3). Here we study the effects of the CAMP signalling pathway on 5-HT-induced oscillations in transepithelial potential (TEP) and in intracellular [Ca2+]. We show: (1) Blocking the activation of the cAMP pathway by cinanserin suppresses the generation of TEP and Ca2+ oscillations, (2) application of 8-CPT-cAMP in the presence of cinanserin restores 5-HT-induced TEP and Ca2+ oscillations, (3) 8-CPT-cAMP sensitizes the InsP(3)/Ca2+ signalling pathway to 5-HT and the Cv5-HT2 alpha, receptor agonist 5-MeOT, (4) 8-CPT-cAMP induces Ca2+ oscillations in cells loaded with subthreshold concentrations of InsP(3), (5) inhibition of protein kinase A by H-89 abolishes 5-HT-induced TEP and Ca2+ spiking and mimics the effect of cinanserin. These results suggest that activation of the cyclic AMP pathway promotes the generation of 5-HT-induced Ca2+ oscillations in blowfly salivary glands. KW - Calcium KW - Ca2+ KW - Calcium oscillations KW - cAMP KW - Signalling KW - Crosstalk KW - Salivary gland KW - Calliphora KW - Blowfly KW - Insect Y1 - 2013 U6 - https://doi.org/10.1016/j.ceca.2012.10.004 SN - 0143-4160 VL - 53 IS - 2 SP - 94 EP - 101 PB - Churchill Livingstone CY - Edinburgh ER - TY - JOUR A1 - Socher, Stephanie A. A1 - Prati, Daniel A1 - Boch, Steffen A1 - Müller, Jörg A1 - Baumbach, Henryk A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Schöning, Ingo A1 - Wells, Konstans A1 - Buscot, Francois A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, Karl Eduard A1 - Schulze, Ernst-Detlef A1 - Weisser, Wolfgang W. A1 - Fischer, Markus T1 - Interacting effects of fertilization, mowing and grazing on plant species diversity of 1500 grasslands in Germany differ between regions JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - The relationship of different types of grassland use with plant species richness and composition ( functional groups of herbs, legumes, and grasses) has so far been studied at small regional scales or comprising only few components of land use. We comprehensively studied the relationship between abandonment, fertilization, mowing intensity, and grazing by different livestock types on plant diversity and composition of 1514 grassland sites in three regions in North-East, Central and South-West Germany. We further considered environmental site conditions including soil type and topographical situation. Fertilized grasslands showed clearly reduced plant species diversity (-15% plant species richness, -0.1 Shannon diversity on fertilized grasslands plots of 16m(2)) and changed composition (-3% proportion of herb species), grazing had the second largest effects and mowing the smallest ones. Among the grazed sites, the ones grazed by sheep had higher than average species richness (+27%), and the cattle grazed ones lower (-42%). Further, these general results were strongly modulated by interactions between the different components of land use and by regional context: land-use effects differed largely in size and sometimes even in direction between regions. This highlights the importance of comparing different regions and to involve a large number of plots KW - Biodiversity exploratories KW - Functional groups KW - Land use type KW - Livestock type KW - Shannon diversity Y1 - 2013 U6 - https://doi.org/10.1016/j.baae.2012.12.003 SN - 1439-1791 VL - 14 IS - 2 SP - 126 EP - 136 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Caliendo, Marco A1 - Lee, Wang-Sheng T1 - Fat chance! - Obesity and the transition from unemployment to employment JF - Economics and human biology N2 - This paper focuses on estimating the magnitude of any potential weight discrimination by examining whether obese job applicants in Germany get treated or behave differently from non-obese applicants. Based on two waves of rich survey data from the IZA Evaluation dataset, which includes measures that control for education, demographic characteristics, labor market history, psychological factors and health, we estimate differences in job search behavior and labor market outcomes between obese/overweight and normal weight individuals. Unlike other observational studies which are generally based on obese and non-obese individuals who might already be at different points in the job ladder (e.g., household surveys), in our data, individuals are newly unemployed and all start from the same point. The only subgroup we find in our data experiencing any possible form of negative labor market outcomes is obese women. Despite making more job applications and engaging more in job training programs, we find some indications that they experienced worse (or at best similar) employment outcomes than normal weight women. Obese women who found a job also had significantly lower wages than normal weight women. KW - Obesity KW - Discrimination KW - Employment KW - Labor demand Y1 - 2013 U6 - https://doi.org/10.1016/j.ehb.2012.02.002 SN - 1570-677X VL - 11 IS - 2 SP - 121 EP - 133 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bhabak, Krishna P. A1 - Kleuser, Burkhard A1 - Huwiler, Andrea A1 - Arenz, Christoph T1 - Effective inhibition of acid and neutral ceramidases by novel B-13 and LCL-464 analogues JF - Bioorganic & medicinal chemistry : a Tetrahedron publication for the rapid dissemination of full original research papers and critical reviews on biomolecular chemistry, medicinal chemistry and related disciplines N2 - Induction of apoptosis mediated by the inhibition of ceramidases has been shown to enhance the efficacy of conventional chemotherapy in several cancer models. Among the inhibitors of ceramidases reported in the literature, B-13 is considered as a lead compound having good in vitro potency towards acid ceramidase. Furthermore, owing to the poor activity of B-13 on lysosoamal acid ceramidase in living cells, LCL-464 a modified derivative of B-13 containing a basic omega-amino group at the fatty acid was reported to have higher potency towards lysosomal acid ceramidase in living cells. In a search for more potent inhibitors of ceramidases, we have designed a series of compounds with structural modifications of B-13 and LCL-464. In this study, we show that the efficacy of B-13 in vitro as well as in intact cells can be enhanced by suitable modification of functional groups. Furthermore, a detailed SAR investigation on LCL-464 analogues revealed novel promising inhibitors of aCDase and nCDase. In cell culture studies using the breast cancer cell line MDA-MB-231, some of the newly developed compounds elevated endogenous ceramide levels and in parallel, also induced apoptotic cell death. In summary, this study shows that structural modification of the known ceramidase inhibitors B-13 and LCL-464 generates more potent ceramidase inhibitors that are active in intact cells and not only elevates the cellular ceramide levels, but also enhances cell death. KW - Sphingolipids KW - Ceramide KW - Ceramidase inhibitors KW - Structure-activity-relationship Y1 - 2013 U6 - https://doi.org/10.1016/j.bmc.2012.12.014 SN - 0968-0896 VL - 21 IS - 4 SP - 874 EP - 882 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Linklater, Wayne L. A1 - Mayer, Katharina A1 - Swaisgood, Ronald R. T1 - Chemical signals of age, sex and identity in black rhinoceros JF - Animal behaviour N2 - Olfactory communication may be particularly important to black rhinoceros, Diceros bicornis, because they are solitary living and have comparatively poor eyesight but their populations are structured by inter-and intrasexual relationships. Understanding olfactory functions and processes might achieve better conservation management but their study in rhinoceros remains anecdotal or descriptive. Experimental approaches are required but rarely possible as rhinoceros are difficult to observe and manipulate. We measured the olfactory investigation behaviour (duration and frequency of sniffing) of black rhinoceros in four experiments designed to determine the function of chemosignals in dung and urine. A habituationedishabituation trial demonstrated that black rhinoceros discriminated individually distinctive odours from faecal signals (experiment 1). When adults (>6 years old) were presented with dung from conspecifics of different sex and age classes (adult, and subadult from 2 to 4 years old), male dung was investigated more by both sexes, and females investigated subadult dung more (experiment 2). Both dung and urine from the same adult donors were investigated by both sexes, but male dung was investigated more than female dung and female urine more than male urine, although differences were statistically weak (experiment 3). Lastly, fresh faecal samples and those aged 1, 2, 4, 16 and 32 days were similarly investigated, indicating that they still function as olfactory signals. Together the results indicate that dung or urine signalled age, sex and identity to conspecifics and signals may persist as dung decays. Chemosignals are likely to be important to the social and spatial organization of black rhinoceros. KW - black rhinoceros KW - Diceros bicornis var. minor KW - dung KW - faeces KW - hook-lipped rhinoceros KW - individual discrimination KW - olfactory communication KW - signal KW - urine Y1 - 2013 U6 - https://doi.org/10.1016/j.anbehav.2012.12.034 SN - 0003-3472 VL - 85 IS - 3 SP - 671 EP - 677 PB - Elsevier CY - London ER - TY - JOUR A1 - Speck, Janina A1 - Räuber, Christina A1 - Kükenshöner, Tim A1 - Niemöller, Christoph A1 - Mueller, Katelyn J. A1 - Schleberger, Paula A1 - Dondapati, Padmarupa A1 - Hecky, Jochen A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation JF - Protein engineering design & selection N2 - The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections. KW - HiT selection KW - NHR2 KW - TAT selection KW - three hybrid KW - two hybrid Y1 - 2013 U6 - https://doi.org/10.1093/protein/gzs098 SN - 1741-0126 VL - 26 IS - 3 SP - 225 EP - 242 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Bauer, Barbara A1 - Sommer, Ulrich A1 - Gaedke, Ursula T1 - High predictability of spring phytoplankton biomass in mesocosms at the species, functional group and community level JF - Freshwater biology N2 - 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. KW - divergence KW - hierarchical level KW - mesocosms KW - predictability KW - replicates Y1 - 2013 U6 - https://doi.org/10.1111/j.1365-2427.2012.02780.x SN - 0046-5070 VL - 58 IS - 3 SP - 588 EP - 596 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Lin, Yue A1 - Berger, Uta A1 - Grimm, Volker A1 - Huth, Franka A1 - Weiner, Jacob T1 - Plant interactions alter the predictions of metabolic scaling theory JF - PLoS one N2 - Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0057612 SN - 1932-6203 VL - 8 IS - 2 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Boch, Steffen A1 - Müller, Jörg A1 - Pratil, Daniel A1 - Blaser, Stefan A1 - Fischer, Markus T1 - Up in the tree - the overlooked richness of bryophytes and lichens in Tree Crowns JF - PLoS one N2 - Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m x 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0084913 SN - 1932-6203 VL - 8 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Mahro, Martin A1 - Bras, Natercia F. A1 - Cerqueira, Nuno M. F. S. A. A1 - Teutloff, Christian A1 - Coelho, Catarina A1 - Romao, Maria Joao A1 - Leimkühler, Silke T1 - Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity JF - PLoS one N2 - In order to elucidate factors that determine substrate specificity and activity of mammalian molybdo-flavoproteins we performed site directed mutagenesis of mouse aldehyde oxidase 3 (mAOX3). The sequence alignment of different aldehyde oxidase (AOX) isoforms identified variations in the active site of mAOX3 in comparison to other AOX proteins and xanthine oxidoreductases (XOR). Based on the structural alignment of mAOX3 and bovine XOR, differences in amino acid residues involved in substrate binding in XORs in comparison to AOXs were identified. We exchanged several residues in the active site to the ones found in other AOX homologues in mouse or to residues present in bovine XOR in order to examine their influence on substrate selectivity and catalytic activity. Additionally we analyzed the influence of the [2Fe-2S] domains of mAOX3 on its kinetic properties and cofactor saturation. We applied UV-VIS and EPR monitored redox-titrations to determine the redox potentials of wild type mAOX3 and mAOX3 variants containing the iron-sulfur centers of mAOX1. In addition, a combination of molecular docking and molecular dynamic simulations (MD) was used to investigate factors that modulate the substrate specificity and activity of wild type and AOX variants. The successful conversion of an AOX enzyme to an XOR enzyme was achieved exchanging eight residues in the active site of mAOX3. It was observed that the absence of the K889H exchange substantially decreased the activity of the enzyme towards all substrates analyzed, revealing that this residue has an important role in catalysis. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0082285 SN - 1932-6203 VL - 8 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Leuschner, Christoph A1 - Wulf, Monika A1 - Bäuchler, Patricia A1 - Hertel, Dietrich T1 - Soil C and nutrient stores under Scots pine afforestations compared to ancient beech forests in the German Pleistocene - the role of tree species and forest history JF - Forest ecology and management N2 - In the diluvial lowlands of northern Germany, the Netherlands and northern Poland, an estimated similar to 5 Mio ha of Scots pine plantations (Pinus sylvestris) has been established on sandy soil in the last 250 years replacing the former temperate broad-leaved forests after extended periods of cultivation in the Middle Ages. We examined the effect of variable stand continuity of pine plantations (recent vs. ancient: 51-128 vs. >230 years) on the soil organic carbon (SOC) store and soil nutrient capital in comparison to ancient beech forests (>230 years of continuity) which represent the potential natural forest vegetation. Recent and ancient pine stands had c. 75% larger organic layer C stores than ancient beech forests, while the total C stock in the soil (organic layer and mineral soil to 100 cm) was similar to 25% larger in the beech forests due to higher C concentrations in 0-50 cm depth of the mineral soil. The soil stores of N-tot were similar to 50% and the exchangeable Ca, K and Mg pools about three times larger under beech than under the pine stands. Resin-exchangeable P was enriched in the soils under ancient pine stands probably due to manuring in the past. After clear-cut and long cultivation, it may take >230 years of forest presence to restore the greatly reduced mineral soil C and N pools. The C and N sequestration potential of the soils appeared to be particularly small under pine indicating a pronounced tree species (pine vs. beech) effect on soil C and N dynamics. We conclude that, in the face of rising greenhouse gas emissions, the limited soil C and nutrient storage potential of Scots pine plantations on sandy soils needs consideration when selecting suitable tree species for future forestry. (C) 2013 Elsevier B.V. All rights reserved. KW - Sandy soil KW - Pinus sylvestris KW - Fagus sylvatica KW - Forest continuity KW - Historic land use KW - Nitrogen Y1 - 2013 U6 - https://doi.org/10.1016/j.foreco.2013.08.043 SN - 0378-1127 SN - 1872-7042 VL - 310 IS - 6 SP - 405 EP - 415 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Thamm, Markus A1 - Rolke, Daniel A1 - Jordan, Nadine A1 - Balfanz, Sabine A1 - Schiffer, Christian A1 - Baumann, Arnd A1 - Blenau, Wolfgang T1 - Function and distribution of 5-HT2 receptors in the honeybee (apis mellifera) JF - PLoS one N2 - Background: Serotonin plays a pivotal role in regulating and modulating physiological and behavioral processes in both vertebrates and invertebrates. In the honeybee (Apis mellifera), serotonin has been implicated in division of labor, visual processing, and learning processes. Here, we present the cloning, heterologous expression, and detailed functional and pharmacological characterization of two honeybee 5-HT2 receptors. Methods: Honeybee 5-HT2 receptor cDNAs were amplified from brain cDNA. Recombinant cell lines were established constitutively expressing receptor variants. Pharmacological properties of the receptors were investigated by Ca2+ imaging experiments. Quantitative PCR was applied to explore the expression patterns of receptor mRNAs. Results: The honeybee 5-HT2 receptor class consists of two subtypes, Am5-HT2 alpha and Am5-HT2 beta. Each receptor gene also gives rise to alternatively spliced mRNAs that possibly code for truncated receptors. Only activation of the full-length receptors with serotonin caused an increase in the intracellular Ca2+ concentration. The effect was mimicked by the agonists 5-methoxytryptamine and 8-OH-DPAT at low micromolar concentrations. Receptor activities were blocked by established 5-HT receptor antagonists such as clozapine, methiothepin, or mianserin. High transcript numbers were detected in exocrine glands suggesting that 5-HT2 receptors participate in secretory processes in the honeybee. Conclusions: This study marks the first molecular and pharmacological characterization of two 5-HT2 receptor subtypes in the same insect species. The results presented should facilitate further attempts to unravel central and peripheral effects of serotonin mediated by these receptors. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0082407 SN - 1932-6203 VL - 8 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Klingstrom, Tomas A1 - Soldatova, Larissa A1 - Stevens, Robert A1 - Roos, T. Erik A1 - Swertz, Morris A. A1 - Müller, Kristian M. A1 - Kalas, Matus A1 - Lambrix, Patrick A1 - Taussig, Michael J. A1 - Litton, Jan-Eric A1 - Landegren, Ulf A1 - Bongcam-Rudloff, Erik T1 - Workshop on laboratory protocol standards for the molecular methods database JF - New biotechnology N2 - Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point. Y1 - 2013 U6 - https://doi.org/10.1016/j.nbt.2012.05.019 SN - 1871-6784 VL - 30 IS - 2 SP - 109 EP - 113 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - von der Lippe, Moritz A1 - Bullock, James M. A1 - Kowarik, Ingo A1 - Knopp, Tatjana A1 - Wichmann, Matthias T1 - Human-mediated dispersal of seeds by the airflow of vehicles JF - PLoS one N2 - Human-mediated dispersal is known as an important driver of long-distance dispersal for plants but underlying mechanisms have rarely been assessed. Road corridors function as routes of secondary dispersal for many plant species but the extent to which vehicles support this process remains unclear. In this paper we quantify dispersal distances and seed deposition of plant species moved over the ground by the slipstream of passing cars. We exposed marked seeds of four species on a section of road and drove a car along the road at a speed of 48 km/h. By tracking seeds we quantified movement parallel as well as lateral to the road, resulting dispersal kernels, and the effect of repeated vehicle passes. Median distances travelled by seeds along the road were about eight meters for species with wind dispersal morphologies and one meter for species without such adaptations. Airflow created by the car lifted seeds and resulted in longitudinal dispersal. Single seeds reached our maximum measuring distance of 45 m and for some species exceeded distances under primary dispersal. Mathematical models were fit to dispersal kernels. The incremental effect of passing vehicles on longitudinal dispersal decreased with increasing number of passes as seeds accumulated at road verges. We conclude that dispersal by vehicle airflow facilitates seed movement along roads and accumulation of seeds in roadside habitats. Dispersal by vehicle airflow can aid the spread of plant species and thus has wide implications for roadside ecology, invasion biology and nature conservation. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0052733 SN - 1932-6203 VL - 8 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Hocher, Berthold A1 - Oberthür, Dominik A1 - Slowinski, Torsten A1 - Querfeld, Uwe A1 - Schäfer, Franz A1 - Doyon, Anke A1 - Tepel, Martin A1 - Roth, Heinz J. A1 - Grön, Hans J. A1 - Reichetzeder, Christoph A1 - Betzel, Christian A1 - Armbruster, Franz Paul T1 - Modeling of Oxidized PTH (oxPTH) and Non-oxidized PTH (n-oxPTH) Receptor Binding and Relationship of Oxidized to Non-Oxidized PTH in Children with Chronic Renal Failure, Adult Patients on Hemodialysis and Kidney Transplant Recipients JF - Kidney & blood pressure research : official organ of the Gesellschaft für Nephrologie N2 - Background: The biological properties of oxidized and non-oxidized PTH are substantially different. Oxidized PTH (oxPTH) loses its PTH receptor-stimulating properties, whereas non-oxidized PTH (n-oxPTH) is a full agonist of the receptor. This was described in more than 20 well published studies in the 1970(s) and 80(s). However, PTH oxidation has been ignored during the development of PTH assays for clinical use so far. Even the nowadays used third generation assay systems do not consider oxidation of PTH. We recently developed an assay to differentiate between oxPTH and n-oxPTH. In the current study we established normal values for this assay system. Furthermore, we compare the ratio of oxPTH to n-oxPTH in different population with chronic renal failure: 620 children with renal failure stage 2-4 of the 4C study, 342 adult patients on dialysis, and 602 kidney transplant recipients. In addition, we performed modeling of the interaction of either oxPTH or n-oxPTH with the PTH receptor using biophysical structure approaches. Results: The children had the highest mean as well as maximum n-oxPTH concentrations as compared to adult patients (both patients on dialysis as well as kidney transplant recipients). The relationship between oxPTH and n-oxPTH of individual patients varied substantially in all three populations with renal impairment. The analysis of n-oxPTH in 89 healthy control subjects revealed that n-oxPTH concentrations in patient with renal failure were higher as compared to healthy adult controls (2.25-fold in children with renal failure, 1.53-fold in adult patients on dialysis, and 1.56-fold in kidney transplant recipients, respectively). Computer assisted biophysical structure modeling demonstrated, however, minor sterical- and/or electrostatic changes in oxPTH and n-oxPTH. This indicated that PTH oxidation may induce refolding of PTH and hence alters PTH-PTH receptor interaction via oxidation induced three-dimensional structure alteration of PTH. Conclusion: A huge proportion of circulating PTH measured by current state-of-the-art assay systems is oxidized and thus not biologically active. The relationship between oxPTH and n-oxPTH of individual patients varied substantially. Non-oxidized PTH concentrations are 1.5 - 2.25 fold higher in patients with renal failure as compared to health controls. Measurements of n-oxPTH may reflect the hormone status more precise. The iPTH measures describes most likely oxidative stress in patients with renal failure rather than the PTH hormone status. This, however, needs to be demonstrated in further clinical studies. KW - n-oxPTH KW - Chronic Renal Failure KW - Kidney Transplantation KW - Hemodialysis KW - Oxidation KW - PTH KW - Chronic Renal Failure in Children Y1 - 2013 U6 - https://doi.org/10.1159/000350149 SN - 1420-4096 SN - 1423-0143 VL - 37 IS - 4-5 SP - 240 EP - 251 PB - Karger CY - Basel ER - TY - JOUR A1 - Feger, Martina A1 - Fajol, Abul A1 - Lebedeva, Aleksandra A1 - Meissner, Adrian A1 - Michael, Diana A1 - Völkl, Jakob A1 - Alesutan, Ioana A1 - Schleicher, Erwin A1 - Reichetzeder, Christoph A1 - Hocher, Berthold A1 - Qadri, Syed M. A1 - Lang, Florian T1 - Effect of Carbon Monoxide Donor CORM-2 on Vitamin D-3 Metabolism JF - Kidney & blood pressure research : official organ of the Gesellschaft für Nephrologie N2 - Background/Aims: Carbon monoxide (CO) interferes with cytochrome-dependent cellular functions and acts as gaseous transmitter. CO is released from CO-releasing molecules (CORM) including tricarbonyl-dichlororuthenium (II) dimer (CORM-2), molecules considered for the treatment of several disorders including vascular dysfunction, inflammation, tissue ischemia and organ rejection. Cytochrome P450-sensitive function include formation of 1,25-dihydroxyvitamin D-3 (1,25(OH)(2)D-3) by renal 25-hydroxyvitamin D-3 1-alpha-hydroxylase (Cyp27b1). The enzyme is regulated by PTH, FGF23 and klotho. 1,25(OH)(2)D-3 regulates Ca2+ and phosphate transport as well as klotho expression. The present study explored, whether CORM-2 influences 1,25(OH)(2)D-3 formation and klotho expression. Methods: Mice were treated with intravenous CORM-2 (20 mg/kg body weight). Plasma 1,25(OH)(2)D-3 and FGF23 concentrations were determined by ELISA, phosphate, calcium and creatinine concentrations by colorimetric methods, transcript levels by quantitative RT-PCR and protein expression by western blotting. Fgf23 mRNA transcript levels were further determined in rat osteosarcoma UMR106 cells without or with prior treatment for 24 hours with 20 mu M CORM-2. Results: CORM-2 injection within 24 hours significantly increased FGF23 plasma levels and decreased 1,25(OH)(2)D-3 plasma levels, renal Cyp27b1 gene expression as well as renal klotho protein abundance and transcript levels. Moreover, treatment of UMR106 cells with CORM-2 significantly increased Fgf23 transcript levels. Conclusion: CO-releasing molecule CORM-2 enhances FGF23 expression and release and decreases klotho expression and 1,25(OH)(2)D-3 synthesis. KW - CORM-2 KW - 1,25-Dihydroxyvitamin D-3 KW - Klotho KW - FGF23 KW - Phosphate KW - Calcium Y1 - 2013 U6 - https://doi.org/10.1159/000355730 SN - 1420-4096 SN - 1423-0143 VL - 37 IS - 4-5 SP - 496 EP - 505 PB - Karger CY - Basel ER - TY - JOUR A1 - Schrade, Lisa A1 - Scheffler, Christiane T1 - Assessing the applicability of the digital laser rangefinder GLM Professional (R) Bosch 250 VF for anthropometric field studies JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - The digital laser rangefinder GLM Professional (R) BOSCH 250 VF was tested as a modified preproduction model with regard to its applicability of quantifying humans' height. The aim of this investigation was to determine and evaluate the instrument's precision, as well as its manageability within anthropometric field studies. Data collected by the digital laser rangefinder did not show a significant difference to data of control by an anthropometer. Furthermore, more than 96% of the difference values are located within area of agreement. Nevertheless, the GLM Professional (R) is a highly sensitive instrument and mean SD within threefold data acquisition is twice as high as SD resulting from data collection by an anthropometer. However, due to the minimal percentage differences within data acquisition and compared to the standard method, the GLM Professional (R) is proved to be a reliable instrument and to be highly applicable for anthropometric field studies. Furthermore, due to its excellent manageability and compact size, the GLM Professional (R) shows a very good applicability even for less trained anthropometrists and thus ameliorates the possibilities of collecting reliable data within anthropometric field studies. KW - anthropometric field studies KW - height KW - measuring instrument KW - digital laser range finder Y1 - 2013 U6 - https://doi.org/10.1127/0003-5548/2013/0223 SN - 0003-5548 VL - 70 IS - 2 SP - 137 EP - 145 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Heinken, Thilo A1 - Weber, Ewald T1 - Consequences of habitat fragmentation for plant species do we know enough? JF - Perspectives in plant ecology, evolution and systematics N2 - Habitat fragmentation is one of the most important causes for the decline of plant species. However, plants differing in phylogeny, habitat requirements and biology are likely to respond differently to habitat fragmentation. We ask whether case studies on the effects of habitat fragmentation conducted so far allow generalizations about its effects on the fitness and genetic diversity of populations of endangered plant species. We compared the characteristics of plant species endangered in Germany whose sensitivity to habitat fragmentation had been studied with those of the endangered species that had not been studied. We found strong discrepancies between the two groups with regard to their taxonomy and traits relevant to their sensitivity to habitat fragmentation. Monocots, graminoids, clonal, abiotically pollinated and self compatible species were underrepresented among the studied species, and most study species were from a few habitat types, in particular grasslands. We conclude that our current knowledge of the effects of habitat fragmentation on plant populations is not sufficient to provide widely applicable guidelines for species management. The selection of species studied so far has been biased toward species from certain habitats and species exhibiting traits that probably make them vulnerable to habitat fragmentation. Future studies should include community-wide approaches in different habitats, e.g. re-visitation studies in which the species pool is assessed at different time intervals, and population-biological studies of species from a wide range of habitats, and of different life forms and growth strategies. A more representative picture of the effects of habitat fragmentation would allow a better assessment of threats and more specific recommendations for optimally managing populations of endangered plants. KW - CSR-strategies KW - Naturally rare species KW - Plant conservation KW - Recently rare species KW - Species traits KW - Taxonomic position Y1 - 2013 U6 - https://doi.org/10.1016/j.ppees.2013.05.003 SN - 1433-8319 VL - 15 IS - 4 SP - 205 EP - 216 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Girstmair, Hannah A1 - Saffert, Paul A1 - Rode, Sascha A1 - Czech, Andreas A1 - Holland, Gudrun A1 - Bannert, Norbert A1 - Ignatova, Zoya T1 - Depletion of Cognate Charged Transfer RNA Causes Translational Frameshifting within the Expanded CAG Stretch in Huntingtin JF - Cell reports N2 - Huntington disease (HD), a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG-encoded polyglutamine (polyQ) repeat in huntingtin (Htt), displays a highly heterogeneous etiopathology and disease onset. Here, we show that the translation of expanded CAG repeats in mutant Htt exon 1 leads to a depletion of charged glutaminyl-transfer RNA (tRNA) Gln-CUG that pairs exclusively to the CAG codon. This results in translational frameshifting and the generation of various transframe-encoded species that differently modulate the conformational switch to nucleate fibrillization of the parental polyQ protein. Intriguingly, the frameshifting frequency varies strongly among different cell lines and is higher in cells with intrinsically lower concentrations of tRNA Gln-CUG. The concentration of tRNA Gln-CUG also differs among different brain areas in the mouse. We propose that translational frameshifting may act as a significant disease modifier that contributes to the cell-selective neurotoxicity and disease course heterogeneity of HD on both cellular and individual levels. Y1 - 2013 U6 - https://doi.org/10.1016/j.celrep.2012.12.019 SN - 2211-1247 VL - 3 IS - 1 SP - 148 EP - 159 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Drygala, Frank A1 - Werner, Ulrike A1 - Zoller, Hinrich T1 - Diet composition of the invasive raccoon dog (Nyctereutes procyonoides) and the native red fox (Vulpes vulpes) in north-east Germany JF - Hystrix : the Italian journal of mammalogy N2 - Invasive alien species pose a great threat to the integrity of natural communities by competition with and predation on native species. In Germany the invasive raccoon dog (Nyctereutes procyonoides) and the native red fox (Vulpes vulpes) occupy a similar ecological niche. Therefore, the aim of our study was to discover the extent of exploitative diet competition between these two generalist carnivores. Carcasses of red foxes (n=256) and raccoon dogs (n=253) were collected throughout Mecklenburg Western-Pomerania (north-east Germany) and stomachs contains were analysed. Frequency of occurrence and biomass share indicate that both canids are omnivorous and pursue opportunistic feeding strategies. Small mammals and edible plant material were the most important food resources for red foxes and raccoon dogs. Nonetheless, interspecies differences were recorded for edible plant material, small mammals and insects. While red foxes mostly feed on voles, raccoon dogs consumed mice and shrews as often as voles. Only raccoon dogs preyed on amphibians. There were no differences in carrion consumption, both species scavenged on wild boar and we found clear competition for carrion year-round. Moreover, there was evidence that two red foxes foraged on raccoon dogs and vice versa. The mean annual interspecies diet overlap index was relatively high. The diets determined for raccoon dogs and red foxes were quite similar and a similar food niche breadth was recorded. However, only minor competition is assumed to take place since differences in feeding habits do exist. KW - Nyctereutes procyonoides KW - Vulpes vulpes KW - invasive species KW - diet competition KW - feeding strategies Y1 - 2013 U6 - https://doi.org/10.4404/hystrix.-24.2-8867 SN - 0394-1914 SN - 1825-5272 VL - 24 IS - 2 SP - 190 EP - 194 PB - Associazione Teriologica Romana CY - Roma ER - TY - JOUR A1 - Scheffler, Christiane T1 - Variable and Invariable Proportions in the Ontogenesis of the Human Face Y1 - 2013 ER - TY - JOUR A1 - Rietsch, Katrin A1 - Godina, Elena A1 - Scheffler, Christiane T1 - Decreased external skeletal robustness in schoolchildren : a global trend? Ten year comparison of Russian and German data Y1 - 2013 UR - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0068195 ER - TY - JOUR A1 - Schrade, Lisa A1 - Scheffler, Christiane T1 - Assessing the applicability of the digital laser rangefinder GLM Professional Bosch 250 VF for anthropometric field studies Y1 - 2013 ER - TY - JOUR A1 - Neumann-Schaal, Meina A1 - Messerschmidt, Katrin A1 - Grenz, Nicole A1 - Heilmann, Katja T1 - Use of antibody gene library for the isolation of specific single chain antibodies. by ampicillin-antigen conjugates JF - Immunology letters : an international journal providing for the rapid publication of short reports in immunology N2 - Isolation of recombinant antibodies from antibody libraries is commonly performed by different molecular display formats including phage display and ribosome display or different cell-surface display formats. We describe a new method which allows the selection of Escherichia coil cells producing the required single chain antibody by cultivation in presence of ampicillin conjugated to the antigen of interest. The method utilizes the neutralization of the conjugate by the produced single chain antibody which is secreted to the periplasm. Therefore, a new expression system based on the pET26b vector was designed and a library was constructed. The method was successfully established first for the selection of E. coli BL21 Star (DE3) cells expressing a model single chain antibody (anti-fluorescein) by a simple selection assay on LB-agar plates. Using this selection assay, we could identify a new single chain antibody binding biotin by growing E. coil BL21 Star (DE3) containing the library in presence of a biotin-ampicillin conjugate. In contrast to methods as molecular or cell surface display our selection system applies the soluble single chain antibody molecule and thereby avoids undesired effects, e.g. by the phage particle or the yeast fusion protein. By selecting directly in an expression strain, production and characterization of the selected single chain antibody is possible without any further cloning or transformation steps. KW - Single chain antibody KW - Selection method KW - Anti-biotin antibody KW - Naive single chain library Y1 - 2013 U6 - https://doi.org/10.1016/j.imlet.2013.02.005 SN - 0165-2478 VL - 151 IS - 1-2 SP - 39 EP - 43 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Baumann, Otto A1 - Bauer, Alexandra T1 - Development of apical membrane organization and V-ATPase regulation in blowfly salivary glands JF - The journal of experimental biology N2 - 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. KW - secretory cell KW - moesin KW - morphogenesis KW - serotonin KW - vacuolar ATPase KW - cAMP Y1 - 2013 U6 - https://doi.org/10.1242/jeb.077420 SN - 0022-0949 VL - 216 IS - 7 SP - 1225 EP - 1234 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Hancock, Christine A1 - Wäschke, Nicole A1 - Schumacher, Uta A1 - Linsenmair, Karl Eduard A1 - Meiners, Torsten A1 - Obermaier, Elisabeth T1 - Fertilizer application decreases insect abundance on Plantago lanceolata - a large-scale experiment in three geographic regions JF - Arthropod-plant interactions : an international journal devoted to studies on interactions of insects, mites, and other arthropods with plants N2 - Humans have substantially altered the nitrogen cycle of ecosystems through the application of agricultural fertilizer. Fertilization may not only affect plant species diversity, but also insect dynamics by altering plant nitrogen supplies. We investigated the effect of experimental fertilization on the vegetation, with the ribwort plantain as the focal plant, and on higher trophic levels on differently managed grasslands throughout Germany. Over a period of 2 years, we examined two specialist herbivores and their parasitoid on Plantago lanceolata L., and the composition and structure of the surrounding vegetation. Over 70 sites in three geographic regions, within the large-scale project "German Biodiversity Exploratories", were included in the study. The model system consisted of the host plant P. lanceolata L., the monophagous weevils Mecinus labilis Herbst and M. pascuorum Gyllenhal, and their parasitoid Mesopolobus incultus Walker. Fertilization decreased plant species richness and host plant abundance, whereas it enhanced the total vegetation growth. The increased size and heigher leaf nitrogen content did not improve herbivore performance. On the contrary, the abundance of the two herbivores was decreased by fertilization. The parasitoid depended on the abundance of one of its hosts, M. pascuorum (positively density-dependent). Reduced herbivore abundance due to fertilization might be explained by a lower abundance of the host plant, a lower stalk number, and by changed patterns of host localization within higher vegetation. Fertilization negatively affected the third trophic level by cascading up via host abundance. The relationships between fertilization, surrounding vegetation and the tritrophic system were measured throughout the three regions and over the 2-year period. Our findings present consequences of intensification for a plant-herbivore-parasitoid system, and may have significant implications for the conservation of multitrophic systems in managed grasslands. KW - Fertilization KW - Nitrogen KW - Tritrophic interaction KW - Plant species richness KW - Grassland management KW - Vegetation structure Y1 - 2013 U6 - https://doi.org/10.1007/s11829-012-9237-9 SN - 1872-8855 SN - 1872-8847 VL - 7 IS - 2 SP - 147 EP - 158 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Sarmento, Juliano Sarmento A1 - Jeltsch, Florian A1 - Thuiller, Wilfried A1 - Higgins, Steven A1 - Midgley, Guy F. A1 - Rebelo, Anthony G. A1 - Rouget, Mathieu A1 - Schurr, Frank Martin T1 - Impacts of past habitat loss and future climate change on the range dynamics of South African Proteaceae JF - Diversity & distributions : a journal of biological invasions and biodiversity N2 - Aim To assess how habitat loss and climate change interact in affecting the range dynamics of species and to quantify how predicted range dynamics depend on demographic properties of species and the severity of environmental change. Location South African Cape Floristic Region. Methods We use data-driven demographic models to assess the impacts of past habitat loss and future climate change on range size, range filing and abundances of eight species of woody plants (Proteaceae). The species-specific models employ a hybrid approach that simulates population dynamics and long-distance dispersal on top of expected spatio-temporal dynamics of suitable habitat. Results Climate change was mainly predicted to reduce range size and range filling (because of a combination of strong habitat shifts with low migration ability). In contrast, habitat loss mostly decreased mean local abundance. For most species and response measures, the combination of habitat loss and climate change had the most severe effect. Yet, this combined effect was mostly smaller than expected from adding or multiplying effects of the individual environmental drivers. This seems to be because climate change shifts suitable habitats to regions less affected by habitat loss. Interspecific variation in range size responses depended mostly on the severity of environmental change, whereas responses in range filling and local abundance depended mostly on demographic properties of species. While most surviving populations concentrated in areas that remain climatically suitable, refugia for multiple species were overestimated by simply overlying habitat models and ignoring demography. Main conclusions Demographic models of range dynamics can simultaneously predict the response of range size, abundance and range filling to multiple drivers of environmental change. Demographic knowledge is particularly needed to predict abundance responses and to identify areas that can serve as biodiversity refugia under climate change. These findings highlight the need for data-driven, demographic assessments in conservation biogeography. KW - biodiversity refugia KW - CFR Proteaceae KW - climate change KW - demographic properties KW - habitat loss KW - local abundances KW - process-based range models KW - range filling KW - range size KW - species distribution models Y1 - 2013 U6 - https://doi.org/10.1111/ddi.12011 SN - 1366-9516 VL - 19 IS - 4 SP - 363 EP - 376 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Voss, Björn A1 - Bolhuis, Henk A1 - Fewer, David P. A1 - Kopf, Matthias A1 - Möke, Fred A1 - Haas, Fabian A1 - El-Shehawy, Rehab A1 - Hayes, Paul A1 - Bergman, Birgitta A1 - Sivonen, Kaarina A1 - Dittmann-Thünemann, Elke A1 - Scanlan, Dave J. A1 - Hagemann, Martin A1 - Stal, Lucas J. A1 - Hess, Wolfgang R. T1 - Insights into the physiology and ecology of the brackish-water-adapted cyanobacterium nodularia spumigena CCY9414 based on a genome-transcriptome analysis JF - PLoS one N2 - Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0060224 SN - 1932-6203 VL - 8 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Marelja, Zvonimir A1 - Chowdhury, Mita Mullick A1 - Dosche, Carsten A1 - Hille, Carsten A1 - Baumann, Otto A1 - Löhmannsröben, Hans-Gerd A1 - Leimkühler, Silke T1 - The L-cysteine desulfurase NFS1 is localized in the cytosol where it provides the sulfur for molybdenum cofactor biosynthesis in humans JF - PLoS one N2 - In humans, the L-cysteine desulfurase NFS1 plays a crucial role in the mitochondrial iron-sulfur cluster biosynthesis and in the thiomodification of mitochondrial and cytosolic tRNAs. We have previously demonstrated that purified NFS1 is able to transfer sulfur to the C-terminal domain of MOCS3, a cytosolic protein involved in molybdenum cofactor biosynthesis and tRNA thiolation. However, no direct evidence existed so far for the interaction of NFS1 and MOCS3 in the cytosol of human cells. Here, we present direct data to show the interaction of NFS1 and MOCS3 in the cytosol of human cells using Forster resonance energy transfer and a split-EGFP system. The colocalization of NFS1 and MOCS3 in the cytosol was confirmed by immunodetection of fractionated cells and localization studies using confocal fluorescence microscopy. Purified NFS1 was used to reconstitute the lacking molybdoenzyme activity of the Neurospora crassa nit-1 mutant, giving additional evidence that NFS1 is the sulfur donor for Moco biosynthesis in eukaryotes in general. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0060869 SN - 1932-6203 VL - 8 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Scheffler, Ingo A1 - Bego, Ferdinand A1 - Theou, Philippe A1 - Podany, Milan A1 - Pospischil, Reiner A1 - Hübner, Sven T1 - Ectoparasites of Bats in Albania Species Range and Host Preference Ektoparasiten der Fledermaeuse in Albanien - Artenspektren und Wirtsbindung N2 - 279 bat specimens of 14 species were examined for ectoparasites during the autumnal swarming period in different cave roosts in Albania. A total of 550 ectoparasites were identified belonging to 19 species. The structure of the ectoparasite fauna and the influence of body mass index and body surface area on the parasite load were discussed for the most common bat species (Miniopterus schreibersii, Myotis myotis, M. capaccinii and Rhinolophus ferrumequinum). The ectoparasite fauna of the studied bats in Albania is qualitatively similar to northern Bulgaria (SCHEFFLER, 2011). The bat species Myotis myotis and M. daubentonii are infested with different ectoparasites in the Balkan region during the autumn swarming period than specimens of the same bat species in Central Europe. There is a strong need of further research for most host and ectoparasite species in the entire Balkan region. Y1 - 2013 ER - TY - JOUR A1 - Lisso, Janina A1 - Schröder, Florian A1 - Müssig, Carsten T1 - EXO modifies sucrose and trehalose responses and connects the extracellular carbon status to growth JF - Frontiers in plant science N2 - Plants have the capacity to adapt growth to changing environmental conditions. This implies the modulation of metabolism according to the availability of carbon (C). Particular interest in the response to the C availability is based on the increasing atmospheric levels of CO2. Several regulatory pathways that link the C status to growth have emerged. The extracellular EXO protein is essential for cell expansion and promotes shoot and root growth. Homologous proteins were identified in evolutionarily distant green plants. We show here that the EXO protein connects growth with C responses. The exo mutant displayed altered responses to exogenous sucrose supplemented to the growth medium. Impaired growth of the mutant in synthetic medium was associated with the accumulation of starch and anthocyanins, altered expression of sugar-responsive genes, and increased abscisic acid levels. Thus, EXO modulates several responses related to the C availability. Growth retardation on medium supplemented with 2-deoxy-glucose, mannose, and palatinose was similar to the wildtype. Trehalose feeding stimulated root growth and shoot biomass production of exoplants where as it inhibited growth of the wildtype. The phenotypic features of the exo mutant suggest that apoplastic processes coordinate growth and C responses. KW - EXO KW - growth KW - sugar response KW - trehalose KW - apoplast Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00219 SN - 1664-462X VL - 4 IS - 25 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Meissner, Sven A1 - Fastner, Jutta A1 - Dittmann-Thünemann, Elke T1 - Microcystin production revisited conjugate formation makes a major contribution JF - Environmental microbiology N2 - The impact of environmental stimuli on the production of the widespread cyanobacterial hepatotoxin microcystin (MC) is under debate. Whereas transcriptional studies of the biosynthetic genes suggest a clear influence of light conditions on toxin production the data for the metabolite itself are inconsistent and highly strain-specific. Here, we have reassessed the MC content by using two immunological detection techniques that allow a parallel quantification of MC in the methanolic extracts and the residual pellet fraction that contains high molecular weight proteins. Our results show a significant proportion of MC in the protein bound fraction in strains of Microcystis and Planktothrix and of the related toxin nodularin (NOD) in Nodularia. Moreover, we could show a very strong increase of MC after high light illumination in the protein fraction contributing to a significant overall increase in MC production under these conditions that is not seen in extracts analysed by LC-MS and ELISA. The fact that a considerable portion of MC is neglected with current analysis techniques was also confirmed for selected field samples. Immunofluorescence studies suggest strain-specific differences in the amount of MC conjugate formation. Y1 - 2013 U6 - https://doi.org/10.1111/1462-2920.12072 SN - 1462-2912 VL - 15 IS - 6 SP - 1810 EP - 1820 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Gulbins, Erich A1 - Palmada, Monica A1 - Reichel, Martin A1 - Lueth, Anja A1 - Boehmer, Christoph A1 - Amato, Davide A1 - Mueller, Christian P. A1 - Tischbirek, Carsten H. A1 - Groemer, Teja W. A1 - Tabatabai, Ghazaleh A1 - Becker, Katrin Anne A1 - Tripal, Philipp A1 - Staedtler, Sven A1 - Ackermann, Teresa F. A1 - van Brederode, Johannes A1 - Alzheimer, Christian A1 - Weller, Michael A1 - Lang, Undine E. A1 - Kleuser, Burkhard A1 - Grassme, Heike A1 - Kornhuber, Johannes T1 - Acid sphingomyelinase-ceramide system mediates effects of antidepressant drugs JF - Nature medicine N2 - Major depression is a highly prevalent severe mood disorder that is treated with antidepressants. The molecular targets of antidepressants require definition. We investigated the role of the acid sphingomyelinase (Asm)-ceramide system as a target for antidepressants. Therapeutic concentrations of the antidepressants amitriptyline and fluoxetine reduced Asm activity and ceramide concentrations in the hippocampus, increased neuronal proliferation, maturation and survival and improved behavior in mouse models of stress-induced depression. Genetic Asm deficiency abrogated these effects. Mice overexpressing Asm, heterozygous for acid ceramidase, treated with blockers of ceramide metabolism or directly injected with C16 ceramide in the hippocampus had higher ceramide concentrations and lower rates of neuronal proliferation, maturation and survival compared with controls and showed depression-like behavior even in the absence of stress. The decrease of ceramide abundance achieved by antidepressant-mediated inhibition of Asm normalized these effects. Lowering ceramide abundance may thus be a central goal for the future development of antidepressants. Y1 - 2013 U6 - https://doi.org/10.1038/nm.3214 SN - 1078-8956 VL - 19 IS - 7 SP - 934 EP - + PB - Nature Publ. Group CY - New York ER - TY - JOUR A1 - Bukovinszky, Tibor A1 - Helmsing, Nico R. A1 - Grau, R. A. A1 - Bakker, Elisabeth S. A1 - Bezemer, T. Martijn A1 - Vos, Matthijs A1 - Uittenhout, H. A1 - Verschoor, A. M. T1 - A device to study the behavioral responses of zooplankton to food quality and quantity JF - Journal of insect behavior N2 - In order to explore the behavioral mechanisms underlying aggregation of foragers on local resource patches, it is necessary to manipulate the location, quality and quantity of food patches. This requires careful control over the conditions in the foraging arena, which may be a challenging task in the case of aquatic resource-consumer systems, like that of freshwater zooplankton feeding on suspended algal cells. We present an experimental tool designed to aid behavioral ecologists in exploring the consequences of resource characteristics for zooplankton aggregation behavior and movement decisions under conditions where the boundaries and characteristics (quantity and quality) of food patches can be standardized. The aggregation behavior of Daphnia magna and D. galeata x hyalina was tested in relation to i) the presence or absence of food or ii) food quality, where algae of high or low nutrient (phosphorus) content were offered in distinct patches. Individuals of both Daphnia species chose tubes containing food patches and D. galeata x hyalina also showed a preference towards food patches of high nutrient content. We discuss how the described equipment complements other behavioral approaches providing a useful tool to understand animal foraging decisions in environments with heterogeneous resource distributions. KW - Foraging behavior KW - behavioral choice KW - food preference KW - Daphnia KW - flow-through vessel Y1 - 2013 U6 - https://doi.org/10.1007/s10905-012-9366-0 SN - 0892-7553 VL - 26 IS - 4 SP - 453 EP - 465 PB - Springer CY - New York ER - TY - JOUR A1 - Bentele, Kajetan A1 - Saffert, Paul A1 - Rauscher, Robert A1 - Ignatova, Zoya A1 - Bluethgen, Nils T1 - Efficient translation initiation dictates codon usage at gene start JF - Molecular systems biology N2 - The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5-10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate. KW - codon usage KW - mRNA structure KW - translation Y1 - 2013 U6 - https://doi.org/10.1038/msb.2013.32 SN - 1744-4292 VL - 9 IS - 6 PB - Nature Publ. Group CY - New York ER - TY - JOUR A1 - Sivanesan, Arumugam A1 - Ly, Khoa H. A1 - Adamkiewicz, Witold A1 - Stiba, Konstanze A1 - Leimkühler, Silke A1 - Weidinger, Inez M. T1 - Tunable electric field enhancement and redox chemistry on TiO2 Island films via covalent attachment to Ag or Au nanostructures JF - The journal of physical chemistry : C, Nanomaterials and interfaces N2 - Ag-TiO2 and Au-TiO2 hybrid electrodes were designed by covalent attachment of TiO2 nanoparticles to Ag or Au electrodes via an organic linker. The optical and electronic properties of these systems were investigated using the cytochrome b(5) (Cyt b(5)) domain of sulfite oxidase, exclusively attached to the TiO2 surface, as a Raman marker and model redox enzyme. Very strong SERR signals of Cyt b(5) were obtained for Ag-supported systems due to plasmonic field enhancement of Ag. Time-resolved surface-enhanced resonance Raman spectroscopic measurements yielded a remarkably fast electron transfer kinetic (k = 60 s(-1)) of Cyt b(5) to Ag. A much lower Raman intensity was observed for Au-supported systems with undefined and slow redox behavior. We explain this phenomenon on the basis of the different potential of zero charge of the two metals that largely influence the electronic properties of the TiO2 island film. Y1 - 2013 U6 - https://doi.org/10.1021/jp4032578 SN - 1932-7447 VL - 117 IS - 22 SP - 11866 EP - 11872 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Schaldach, Rüdiger A1 - Wimmer, Florian A1 - Koch, Jennifer A1 - Volland, Jan A1 - Geissler, Katja A1 - Köchy, Martin T1 - Model-based analysis of the environmental impacts of grazing management on Eastern Mediterranean ecosystems in Jordan JF - Journal of environmental management N2 - Eastern Mediterranean ecosystems are prone to desertification when under grazing pressure. Therefore, management of grazing intensity plays a crucial role to avoid or to diminish land degradation and to sustain both livelihoods and ecosystem functioning. The dynamic land-use model LandSHIFT was applied to a case study on the country level for Jordan. The impacts of different stocking densities on the environment were assessed through a set of simulation experiments for various combinations of climate input and assumptions about the development of livestock numbers. Indicators used for the analysis include a set of landscape metrics to account for habitat fragmentation and the "Human Appropriation of Net Primary Production" (HANPP), i.e., the difference between the amount of net primary production (NPP) that would be available in a natural ecosystem and the amount of NPP that remains under human management. Additionally, the potential of the economic valuation of ecosystem services, including landscape and grazing services, as an analysis concept was explored. We found that lower management intensities had a positive effect on HANPP but at the same time resulted in a strong increase of grazing area. This effect was even more pronounced under climate change due to a predominantly negative effect on the biomass productivity of grazing land. Also Landscape metrics tend to indicate decreasing habitat fragmentation as a consequence of lower grazing pressure. The valuation of ecosystem services revealed that low grazing intensity can lead to a comparatively higher economic value on the country level average. The results from our study underline the importance of considering grazing management as an important factor to manage dry-land ecosystems in a sustainable manner. KW - Sustainable management of Mediterranean grazing land KW - Land-use modeling KW - Climate change KW - Landscape metrics KW - Ecosystem service value KW - Human Appropriation of Net Primary Production (HANPP) Y1 - 2013 U6 - https://doi.org/10.1016/j.jenvman.2012.11.024 SN - 0301-4797 SN - 1095-8630 VL - 127 IS - 9 SP - S84 EP - S95 PB - Elsevier CY - London ER - TY - JOUR A1 - Boch, Steffen A1 - Prati, Daniel A1 - Müller, Jörg A1 - Socher, Stephanie A1 - Baumbach, Henryk A1 - Buscot, Francois A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Hessenmöller, Dominik A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, K. Eduard A1 - Pfeiffer, Simone A1 - Pommer, Ulf A1 - Schöning, Ingo A1 - Schulze, Ernst-Detlef A1 - Seilwinder, Claudia A1 - Weisser, Wolfgang W. A1 - Wells, Konstans A1 - Fischer, Markus T1 - High plant species richness indicates management-related disturbances rather than the conservation status of forests JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - There is a wealth of smaller-scale studies on the effects of forest management on plant diversity. However, studies comparing plant species diversity in forests with different management types and intensity, extending over different regions and forest stages, and including detailed information on site conditions are missing. We studied vascular plants on 1500 20 m x 20 m forest plots in three regions of Germany (Schwabische Alb, Hainich-Dun, Schorfheide-Chorin). In all regions, our study plots comprised different management types (unmanaged, selection cutting, deciduous and coniferous age-class forests, which resulted from clear cutting or shelterwood logging), various stand ages, site conditions, and levels of management-related disturbances. We analyzed how overall richness and richness of different plant functional groups (trees, shrubs, herbs, herbaceous species typically growing in forests and herbaceous light-demanding species) responded to the different management types. On average, plant species richness was 13% higher in age-class than in unmanaged forests, and did not differ between deciduous age-class and selection forests. In age-class forests of the Schwabische Alb and Hainich-Dun, coniferous stands had higher species richness than deciduous stands. Among age-class forests, older stands with large quantities of standing biomass were slightly poorer in shrub and light-demanding herb species than younger stands. Among deciduous forests, the richness of herbaceous forest species was generally lower in unmanaged than in managed forests, and it was even 20% lower in unmanaged than in selection forests in Hainich-Dun. Overall, these findings show that disturbances by management generally increase plant species richness. This suggests that total plant species richness is not suited as an indicator for the conservation status of forests, but rather indicates disturbances. KW - Biodiversity Exploratories KW - Coniferous plantations KW - Disturbance KW - Ellenberg indicator values KW - Forest management KW - Selection vs. age-class forests KW - Silviculture KW - Standing biomass KW - Typical forest species KW - Unmanaged vs. managed forests Y1 - 2013 U6 - https://doi.org/10.1016/j.baae.2013.06.001 SN - 1439-1791 VL - 14 IS - 6 SP - 496 EP - 505 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Plath, Martin A1 - Pfenninger, Markus A1 - Lerp, Hannes A1 - Riesch, Rüdiger A1 - Eschenbrenner, Christoph A1 - Slattery, Patrick A. A1 - Bierbach, David A1 - Herrmann, Nina A1 - Schulte, Matthias A1 - Arias-Rodriguez, Lenin A1 - Rimber Indy, Jeane A1 - Passow, Courtney A1 - Tobler, Michael T1 - Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments JF - Evolution N2 - We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RIs) was negatively correlated with the strength of natural selection (RIm), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage. KW - Ecological speciation KW - isolation-by-adaptation KW - local adaptation KW - Poecilia mexicana KW - reinforcement KW - sexual isolation Y1 - 2013 U6 - https://doi.org/10.1111/evo.12133 SN - 0014-3820 VL - 67 IS - 9 SP - 2647 EP - 2661 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Plue, Jan A1 - De Frenne, Pieter A1 - Acharya, Kamal P. A1 - Brunet, Jorg A1 - Chabrerie, Olivier A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Graae, Bente J. A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Kolb, Annette A1 - Lemke, Isgard A1 - Liira, Jaan A1 - Naaf, Tobias A1 - Shevtsova, Anna A1 - Verheyen, Kris A1 - Wulf, Monika A1 - Cousins, Sara A. O. T1 - Climatic control of forest herb seed banks along a latitudinal gradient JF - Global ecology and biogeography : a journal of macroecology N2 - Aim Seed banks are central to the regeneration strategy of many plant species. Any factor altering seed bank density thus affects plant regeneration and population dynamics. Although seed banks are dynamic entities controlled by multiple environmental drivers, climatic factors are the most comprehensive, but still poorly understood. This study investigates how climatic variation structures seed production and resulting seed bank patterns. Location Temperate forests along a 1900km latitudinal gradient in north-western (NW) Europe. Methods Seed production and seed bank density were quantified in 153 plots along the gradient for four forest herbs with different seed longevity: Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica. We tested the importance of climatic and local environmental factors in shaping seed production and seed bank density. Results Seed production was determined by population size, and not by climatic factors. G.urbanum and M.effusum seed bank density declined with decreasing temperature (growing degree days) and/or increasing temperature range (maximum-minimum temperature). P.nemoralis and S.sylvatica seed bank density were limited by population size and not by climatic variables. Seed bank density was also influenced by other, local environmental factors such as soil pH or light availability. Different seed bank patterns emerged due to differential seed longevities. Species with long-lived seeds maintained constant seed bank densities by counteracting the reduced chance of regular years with high seed production at colder northern latitudes. Main conclusions Seed bank patterns show clear interspecific variation in response to climate across the distribution range. Not all seed banking species may be as well equipped to buffer climate change via their seed bank, notably in short-term persistent species. Since the buffering capacity of seed banks is key to species persistence, these results provide crucial information to advance climatic change predictions on range shifts, community and biodiversity responses. KW - Climate change KW - interspecific variation KW - plant-climate interaction KW - seed longevity KW - seed production KW - temperate deciduous forest KW - temperature Y1 - 2013 U6 - https://doi.org/10.1111/geb.12068 SN - 1466-822X SN - 1466-8238 VL - 22 IS - 10 SP - 1106 EP - 1117 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wasof, Safaa A1 - Lenoir, Jonathan A1 - Gallet-Moron, Emilie A1 - Jamoneau, Aurelien A1 - Brunet, Jörg A1 - Cousins, Sara A. O. A1 - De Frenne, Pieter A1 - Diekmann, Martin A1 - Hermy, Martin A1 - Kolb, Annette A1 - Liira, Jaan A1 - Verheyen, Kris A1 - Wulf, Monika A1 - Decocq, Guillaume T1 - Ecological niche shifts of understorey plants along a latitudinal gradient of temperate forests in north-western Europe JF - Global ecology and biogeography : a journal of macroecology N2 - Aim In response to environmental changes and to avoid extinction, species may either track suitable environmental conditions or adapt to the modified environment. However, whether and how species adapt to environmental changes remains unclear. By focusing on the realized niche (i.e. the actual space that a species inhabits and the resources it can access as a result of limiting biotic factors present in its habitat), we here examine shifts in the realized-niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) of 26 common and widespread forest understorey plants across their distributional ranges. Location Temperate forests along a ca. 1800-km-long latitudinal gradient from northern France to central Sweden and Estonia. Methods We derived species' realized-niche width from a -diversity metric, which increases if the focal species co-occurs with more species. Based on the concept that species' scores in a detrended correspondence analysis (DCA) represent the locations of their realized-niche positions, we developed a novel approach to run species-specific DCAs allowing the focal species to shift its realized-niche position along the studied latitudinal gradient while the realized-niche positions of other species were held constant. Results None of the 26 species maintained both their realized-niche width and position along the latitudinal gradient. Few species (9 of 26: 35%) shifted their realized-niche width, but all shifted their realized-niche position. With increasing latitude, most species (22 of 26: 85%) shifted their realized-niche position for soil nutrients and pH towards nutrient-poorer and more acidic soils. Main conclusions Forest understorey plants shifted their realized niche along the latitudinal gradient, suggesting local adaptation and/or plasticity. This macroecological pattern casts doubt on the idea that the realized niche is stable in space and time, which is a key assumption of species distribution models used to predict the future of biodiversity, hence raising concern about predicted extinction rates. KW - Beta diversity KW - climate change KW - detrended correspondence analyses KW - Ellenberg indicator values KW - forest understorey plant species KW - niche optimum KW - niche width KW - plant community KW - realized niche Y1 - 2013 U6 - https://doi.org/10.1111/geb.12073 SN - 1466-822X VL - 22 IS - 10 SP - 1130 EP - 1140 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Fabian, Heinz A1 - Gast, Klaus A1 - Laue, Michael A1 - Jetzschmann, Katharina J. A1 - Naumann, Dieter A1 - Ziegler, Andreas A1 - Uchanska-Ziegler, Barbara T1 - IR spectroscopic analyses of amyloid fibril formation of beta(2)-microglobulin using a simplified procedure for its in vitro generation at neutral pH JF - Biophysical chemistry : an international journal devoted to the physical chemistry of biological phenomena N2 - beta(2)-microglobulin (beta(2)m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant beta(2)m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the beta-strands in the fully formed amyloid structure of beta(2)m. This study highlights the power of an approach to investigate the formation of beta(2)m fibrils by a combination of biophysical techniques including IR spectroscopy. KW - Amyloid fibril KW - beta(2)-microglobulin KW - Amyloidogenesis KW - IR spectroscopy Y1 - 2013 U6 - https://doi.org/10.1016/j.bpc.2013.05.001 SN - 0301-4622 VL - 179 IS - 5 SP - 35 EP - 46 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Prati, Daniel A1 - Gossner, Martin M. A1 - Alt, Fabian A1 - Boch, Steffen A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Lange, Markus A1 - Müller, Jörg A1 - Oelmann, Yvonne A1 - Pasalic, Esther A1 - Renner, Swen C. A1 - Socher, Stephanie A. A1 - Türke, Manfred A1 - Weisser, Wolfgang W. A1 - Fischer, Markus A1 - Hölzel, Norbert T1 - Does organic grassland farming benefit plant and arthropod diversity at the expense of yield and soil fertility? JF - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere N2 - Organic management is one of the most popular strategies to reduce negative environmental impacts of intensive agriculture. However, little is known about benefits for biodiversity and potential worsening of yield under organic grasslands management across different grassland types, i.e. meadow, pasture and mown pasture. Therefore, we studied the diversity of vascular plants and foliage-living arthropods (Coleoptera, Araneae, Heteroptera, Auchenorrhyncha), yield, fodder quality, soil phosphorus concentrations and land-use intensity of organic and conventional grasslands across three study regions in Germany. Furthermore, all variables were related to the time since conversion to organic management in order to assess temporal developments reaching up to 18 years. Arthropod diversity was significantly higher under organic than conventional management, although this was not the case for Araneae, Heteroptera and Auchenorrhyncha when analyzed separately. On the contrary, arthropod abundance, vascular plant diversity and also yield and fodder quality did not considerably differ between organic and conventional grasslands. Analyses did not reveal differences in the effect of organic management among grassland types. None of the recorded abiotic and biotic parameters showed a significant trend with time since transition to organic management, except soil organic phosphorus concentrations which decreased with time. This implies that permanent grasslands respond slower and probably weaker to organic management than crop fields do. However, as land-use intensity and inorganic soil phosphorus concentrations were significantly lower in organic grasslands, overcoming seed and dispersal limitation by re-introducing plant species might be needed to exploit the full ecological potential of organic grassland management. We conclude that although organic management did not automatically increase the diversity of all studied taxa, it is a reasonable and useful way to support agro-biodiversity. KW - Agri-environmental schemes KW - Fertilization KW - Fodder quality KW - Land-use intensity KW - Nitrogen KW - Biomass nutrient concentrations KW - Organic farming KW - Phosphorus KW - Species richness KW - Nutrient availability Y1 - 2013 U6 - https://doi.org/10.1016/j.agee.2013.05.019 SN - 0167-8809 VL - 177 IS - 3 SP - 1 EP - 9 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - Coupling biocatalysis with molecular imprinting in a biomimetic sensor JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition KW - biomimetic sensors KW - electropolymers KW - enzymes KW - hierarchical structures KW - molecularly imprinted polymers Y1 - 2013 U6 - https://doi.org/10.1002/anie.201305368 SN - 1433-7851 SN - 1521-3773 VL - 52 IS - 44 SP - 11521 EP - 11525 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Reschke, Stefan A1 - Sigfridsson, Kajsa G. V. A1 - Kaufmann, Paul A1 - Leidel, Nils A1 - Horn, Sebastian A1 - Gast, Klaus A1 - Schulzke, Carola A1 - Haumann, Michael A1 - Leimkühler, Silke T1 - Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in escherichia coli JF - The journal of biological chemistry N2 - The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme. Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M113.497453 SN - 0021-9258 SN - 1083-351X VL - 288 IS - 41 SP - 29736 EP - 29745 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Henze, Andrea A1 - Raila, Jens A1 - Scholze, Alexandra A1 - Zidek, Walter A1 - Tepel, Martin A1 - Schweigert, Florian J. T1 - Does N-Acetylcysteine modulate post-translational modifications of transthyretin in hemodialysis patients? JF - Antioxidants & redox signaling N2 - It is assumed that effects of the thiol antioxidant N-acetylcysteine (NAC) are mediated by interaction with protein-associated cysteine residues, however, information on protein level in vivo are missing. Therefore, we analyzed NAC-induced modifications of the protein transthyretin (TTR) in plasma of hemodialysis patients in a randomized, placebo-controlled study. TTR was selected due to its low molecular weight and the free cysteine residue in the polypeptide chain, which is known to be extensively modified by formation of mixed disulfides. The intravenous application of NAC during a hemodialysis session resulted in a substantial increase of native TTR from median 15% (range 8.8%-30%) to median 40% (37-50) and reduction of S-cysteinylated TTR [51% (44-60) vs. 6.6% (2.4-10)]. Additionally the pronounced formation of a TTR-NAC adduct was detected. However, all these modifications seemed to be reversible. Additionally, in vitro incubation of plasma with NAC confirmed the in vivo results and indicated that changes in post-translational modification pattern of TTR were a function of NAC concentration. Based on these observations and the essential metabolic and biochemical role of protein-associated cysteine residues we hypothesize that the interaction of NAC with proteins may explain altered protein functions due to modification of cysteine residues. Antioxid. Redox Signal. 19, 1166-1172. Y1 - 2013 U6 - https://doi.org/10.1089/ars.2012.5125 SN - 1523-0864 VL - 19 IS - 11 SP - 1166 EP - 1172 PB - Liebert CY - New Rochelle ER - TY - JOUR A1 - Schwarzer, Christian A1 - Heinken, Thilo A1 - Luthardt, Vera A1 - Joshi, Jasmin Radha T1 - Latitudinal shifts in species interactions interfere with resistance of southern but not of northern bog-plant communities to experimental climate change JF - The journal of ecology N2 - The persistence of species under changed climatic conditions depends on adaptations and plastic responses to these conditions and on interactions with their local plant community resulting in direct and indirect effects of changed climatic conditions. Populations at species' range margins may be especially crucial in containing a gene pool comprising adaptations to extreme climatic conditions. Many species of northern European bog ecosystems reach their southern lowland range limit in central Europe. In a common-garden experiment, we experimentally assessed the impact of projected climatic changes on five bog-plant species (including peat moss Sphagnum magellanicum) sampled along a latitudinal gradient of 1400km from Scandinavia to the marginal lowland populations in Germany. Populations were cultivated in monocultures and in experimental communities composed of all five species from their local community, and exposed to five combinations of three climate treatments (warming, fluctuating water-tables, fertilization) in a southern common garden. Whereas most monocultures showed a decreasing biomass production from southern to northern origins under southern environmental conditions, in the experimental mixed-species communities, an increasing biomass production towards northern communities was observed together with a shift in interspecific interactions along the latitudinal gradient. While negative dominance effects prevailed in southern communities, higher net biodiversity effects were observed in northern subarctic communities. The combined effects of climate treatments increased biomass production in monocultures of most origins. In communities, however, overall the treatments did not result in significantly changed biomass production. Among individual treatments, water-table fluctuations caused a significant decrease in biomass production, but only in southern communities, indicating higher vulnerability to changed climatic conditions. Here, negative effects of climate treatments on graminoids were not compensated by the slightly increased growth of peat moss that benefited from interspecific interactions only in northern communities.Synthesis. We conclude that shifting interactions within multispecies communities caused pronounced responses to changed climatic conditions in wetland communities of temperate southern marginal, but not of northern subarctic origin. Therefore, future models investigating the impacts of climate change on plant communities should consider geographical variation in species interactions an important factor influencing community responses to changed climatic conditions. KW - additive partitioning of biodiversity effects KW - biodiversity KW - ecosystem services KW - ecosystem stability KW - intraspecific divergence KW - multifactorial environmental change KW - nitrogen deposition KW - northern peatlands KW - Sphagnum magellanicum KW - wetland ecosystems Y1 - 2013 U6 - https://doi.org/10.1111/1365-2745.12158 SN - 0022-0477 SN - 1365-2745 VL - 101 IS - 6 SP - 1484 EP - 1497 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Brothers, Soren M. A1 - Hilt, Sabine A1 - Meyer, Stephanie A1 - Köhler, Jan T1 - Plant community structure determines primary productivity in shallow, eutrophic lakes JF - Freshwater biology N2 - Regime shifts are commonly associated with the loss of submerged macrophytes in shallow lakes; yet, the effects of this on whole-lake primary productivity remain poorly understood. This study compares the annual gross primary production (GPP) of two shallow, eutrophic lakes with different plant community structures but similar nutrient concentrations. Daily GPP rates were substantially higher in the lake containing submerged macrophytes (58623gCm(-2)year(-1)) than in the lake featuring only phytoplankton and periphyton (40823gCm(-2)year(-1); P<0.0001). Comparing lake-centre diel oxygen curves to compartmental estimates of GPP confirmed that single-site oxygen curves may provide unreliable estimates of whole-lake GPP. The discrepancy between approaches was greatest in the macrophyte-dominated lake during the summer, with a high proportion of GPP occurring in the littoral zone. Our empirical results were used to construct a simple conceptual model relating GPP to nutrient availability for these alternative ecological regimes. This model predicted that lakes featuring submerged macrophytes may commonly support higher rates of GPP than phytoplankton-dominated lakes, but only within a moderate range of nutrient availability (total phosphorus ranging from 30 to 100gL(-1)) and with mean lake depths shallower than 3 or 4m. We conclude that shallow lakes with a submerged macrophyte-epiphyton complex may frequently support a higher annual primary production than comparable lakes that contain only phytoplankton and periphyton. We thus suggest that a regime shift involving the loss of submerged macrophytes may decrease the primary productivity of many lakes, with potential consequences for the entire food webs of these ecosystems. KW - macrophytes KW - oxygen curves KW - periphyton KW - regime shift KW - trophic status Y1 - 2013 U6 - https://doi.org/10.1111/fwb.12207 SN - 0046-5070 VL - 58 IS - 11 SP - 2264 EP - 2276 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Sagolla, Kristina A1 - Löhmannsröben, Hans-Gerd A1 - Hille, Carsten T1 - Time-resolved fluorescence microscopy for quantitative Ca2+ imaging in living cells JF - Analytical & bioanalytical chemistry N2 - Calcium (Ca2+) is a ubiquitous intracellular second messenger and involved in a plethora of cellular processes. Thus, quantification of the intracellular Ca2+ concentration ([Ca2+](i)) and of its dynamics is required for a comprehensive understanding of physiological processes and potential dysfunctions. A powerful approach for studying [Ca2+](i) is the use of fluorescent Ca2+ indicators. In addition to the fluorescence intensity as a common recording parameter, the fluorescence lifetime imaging microscopy (FLIM) technique provides access to the fluorescence decay time of the indicator dye. The nanosecond lifetime is mostly independent of variations in dye concentration, allowing more reliable quantification of ion concentrations in biological preparations. In this study, the feasibility of the fluorescent Ca2+ indicator Oregon Green Bapta-1 (OGB-1) for two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was evaluated. In aqueous solution, OGB-1 displayed a Ca2+-dependent biexponential fluorescence decay behaviour, indicating the presence of a Ca2+-free and Ca2+-bound dye form. After sufficient dye loading into living cells, an in situ calibration procedure has also unravelled the Ca2+-free and Ca2+-bound dye forms from a global biexponential fluorescence decay analysis, although the dye's Ca2+ sensitivity is reduced. Nevertheless, quantitative [Ca2+](i) recordings and its stimulus-induced changes in salivary gland cells could be performed successfully. These results suggest that OGB-1 is suitable for 2P-FLIM measurements, which can gain access to cellular physiology. KW - Fluorescence lifetime KW - TCSPC KW - Two-photon excitation KW - 2P cross section KW - Epithelial ion transport KW - OGB-1 Y1 - 2013 U6 - https://doi.org/10.1007/s00216-013-7290-6 SN - 1618-2642 VL - 405 IS - 26 SP - 8525 EP - 8537 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Baumann, Tobias A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V JF - BMC biotechnology N2 - 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. KW - Cohesive ends KW - DNA cleavage KW - Genetic vectors KW - Modified primers KW - Molecular methods KW - Polymerase chain reaction KW - Recombinant Escherichia coli KW - Restriction enzymes Y1 - 2013 U6 - https://doi.org/10.1186/1472-6750-13-81 SN - 1472-6750 VL - 13 IS - 10 PB - BioMed Central CY - London ER - TY - JOUR A1 - Drygala, Frank A1 - Zoller, Hinrich T1 - Spatial use and interaction of the invasive raccoon dog and the native red fox in Central Europe - competition or coexistence? JF - European journal of wildlife research N2 - The main objective was to discover extent of interference and/or exploitative competition between the native red fox (Vulpes vulpes) and the introduced, invasive raccoon dog (Nyctereues proconoides) in the intensively used, agricultural landscape of northeast Germany (Mecklenburg-Western Pomerania) using very high frequency (VHF) radio telemetry. We recorded location data for 12 foxes and 16 raccoon dogs between July 2004 and December 2006. Species had similar average home range sizes estimated in each season (K95). Home ranges of adjacent raccoon dogs and foxes overlapped from 0.5 to 74.5 % with a mean of 26.4 %. We found a significantly different home range overlap index between the species showing that raccoon dog ranges shifted between seasons to a greater extent than red fox ranges. The raccoon dog differed significantly from the red fox in its use of habitat types, preferring dense vegetation cover and avoiding open areas. The red fox displayed less preference for or avoidance of specific habitat types. Moreover, an almost neutral inter-specific interaction index ranging from -0.12 to 0.12 indicates that raccoon dogs and red foxes ignored each other. It is concluded that widespread and available resources and differences in spatial use patterns prevent competition between red foxes and raccoon dogs in the agricultural landscape of northeast Germany. KW - Vulpes vulpes KW - Nyctereutes procyonoides KW - Space use KW - Habitat use KW - Invasive species Y1 - 2013 U6 - https://doi.org/10.1007/s10344-013-0722-y SN - 1612-4642 SN - 1439-0574 VL - 59 IS - 5 SP - 683 EP - 691 PB - Springer CY - New York ER - TY - JOUR A1 - Tanentzap, Andrew J. A1 - Lee, William G. A1 - Schulz, Katharina A. C. T1 - Niches drive peaked and positive relationships between diversity and disturbance in natural ecosystems JF - Ecosphere : the magazine of the International Ecology University N2 - A unified understanding of the relationship between disturbance and biodiversity is needed to predict biotic responses to global change. Recent advances have identified the need to deconstruct traditional models of disturbance into intensity and frequency to reconcile empirical studies that appear to generate contradictory associations between species diversity and disturbance. We integrate results from theoretical simulation modelling, field-based surveys of 5176 vegetation plots from 48 transects across 6 sites, and experimental pot-based manipulations of flooding to identify how disturbance drives species diversity within ephemeral wetlands in South Island, New Zealand. We find empirical, hump-shaped and positive relationships between species diversity and both disturbance intensity and frequency, mirroring patterns from a simulation model in which species differed in their demographic responses to disturbance. More generally, our simulations show that the relationships between diversity and disturbance shift from positive to hump-shaped to negative as species that are favored at low disturbance because of their resistance strategies, defined by low mortality and recruitment, decline within communities relative to resilient species. Resilient species with higher mortality and recruitment rates are instead favored as disturbance intensity and frequency intensify. Our theoretical findings suggest that sites must also have a third group of unique species with intermediate resilience and resistance. Analyses of community composition along our disturbance gradients support this prediction, emphasizing that shifts in community-level resistance and resilience drive empirical associations between diversity and disturbance. Overall, terrestrial plants may be unable to resist intense and frequent flooding, even with specialized traits. Only fast-growing species with high regeneration from seed may respond once flooding subsides and dominate community composition in these situations, especially on nutrient-rich soils. However, different strategies can co-occur at intermediate disturbance, ultimately increasing species richness. As disturbances become more pervasive globally, our results suggest that differences in the niches of species, rather than demographic stochasticity, drive biodiversity patterns. These niche-based processes may especially prevail, without accompanying losses in species richness, where sites are initially dominated by resistant taxa or life history strategies that balance resistance and resilience. KW - beta-diversity KW - coexistence KW - community structure KW - functional traits KW - intermediate disturbance hypothesis KW - neutral theory KW - trade-offs Y1 - 2013 U6 - https://doi.org/10.1890/ES13-00102.1 SN - 2150-8925 VL - 4 IS - 11 PB - Wiley CY - Washington ER - TY - JOUR A1 - Reschke, Stefan A1 - Niks, Dimitri A1 - Wilson, Heather A1 - Sigfridsson, Kajsa G. V. A1 - Haumann, Michael A1 - Rajagopalan, K. V. A1 - Hine, Russ A1 - Leimkühler, Silke T1 - Effect of exchange of the cysteine molybdenum ligand with selenocysteine on the structure and function of the active site in human sulfite oxidase JF - Biochemistry N2 - Sulfite oxidase (SO) is an essential molybdoenzyme for humans, catalyzing the final step in the degradation of sulfur-containing amino acids and lipids, which is the oxidation of sulfite to sulfate. The catalytic site of SO consists of a molybdenum ion bound to the dithiolene sulfurs of one molybdopterin (MPT) molecule, carrying two oxygen ligands, and is further coordinated by the thiol sulfur of a conserved cysteine residue. We have exchanged four non-active site cysteines in the molybdenum cofactor (Moco) binding domain of human SO (SOMD) with serine using site-directed mutagenesis. This facilitated the specific replacement of the active site Cys207 with selenocysteine during protein expression in Escherichia coli. The sulfite oxidizing activity (k(cat)/K-M) of SeSOMD4Ser was increased at least 1.5-fold, and the pH optimum was shifted to a more acidic value compared to those of SOMD4Ser and SOMD4Cys(wt) X-ray absorption spectroscopy revealed a Mow Se bond length of 2.51 A, likely caused by the specific binding of Sec207 to the molybdenum, and otherwise rather similar square-pyramidal S/Se(Cys)(O2MoS2)-S-VI(MPT) site structures in the three constructs. The low-pH form of the Mo(V) electron paramagnetic resonance (EPR) signal of SeSOM4Ser was altered compared to those of SOMD4Ser and SOMD4cy,(,), with g, in particular shifted to a lower magnetic field, due to the Se ligation at the molybdenum. In contrast, the Mo(V) EPR signal of the high-pH form was unchanged. The substantially stronger effect of substituting selenocysteine for cysteine at low pH as compared to high pH is most likely due to the decreased covalency of the Mo Se bond. Y1 - 2013 U6 - https://doi.org/10.1021/bi4008512 SN - 0006-2960 VL - 52 IS - 46 SP - 8295 EP - 8303 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hartmann, Tobias A1 - Leimkühler, Silke T1 - The oxygen-tolerant and NAD+-dependent formate dehydrogenase from Rhodobacter capsulatus is able to catalyze the reduction of CO2 to formate JF - The FEBS journal N2 - The formate dehydrogenase from Rhodobactercapsulatus (RcFDH) is an oxygen-tolerant protein with an ()(2) subunit composition that is localized in the cytoplasm. It belongs to the group of metal and NAD(+)-dependent FDHs with the coordination of a molybdenum cofactor, four [Fe4S4] clusters and one [Fe2S2] cluster associated with the -subunit, one [Fe4S4] cluster and one FMN bound to the -subunit, and one [Fe2S2] cluster bound to the -subunit. RcFDH was heterologously expressed in Escherichiacoli and characterized. Cofactor analysis showed that the bis-molybdopterin guanine dinucleotide cofactor is bound to the FdsA subunit containing a cysteine ligand at the active site. A turnover rate of 2189min(-1) with formate as substrate was determined. The back reaction for the reduction of CO2 was catalyzed with a k(cat) of 89min(-1). The preference for formate oxidation shows an energy barrier for CO2 reduction of the enzyme. Furthermore, the FMN-containing and [Fe4S4]-containing -subunit together with the [Fe2S2]-containing -subunit forms a diaphorase unit with activities for both NAD(+) reduction and NADH oxidation. In addition to the structural genes fdsG, fdsB, and fdsA, the fds operon in R.capsulatus contains the fdsC and fdsD genes. Expression studies showed that RcFDH is only active when both FdsC and FdsD are present. Both proteins are proposed to be involved in bis-molybdopterin guanine dinucleotide modification and insertion into RcFDH. KW - FeS cluster KW - FMN KW - formate dehydrogenase KW - molybdenum cofactor (Moco)-binding chaperone KW - molybdoenzyme Y1 - 2013 U6 - https://doi.org/10.1111/febs.12528 SN - 1742-464X SN - 1742-4658 VL - 280 IS - 23 SP - 6083 EP - 6096 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Xu, Xuan A1 - Wollenberger, Ursula A1 - Qian, Jing A1 - Lettau, Katrin A1 - Jung, Christiane A1 - Liu, Songqin T1 - Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite JF - Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society N2 - Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved. KW - Nitric oxide synthase KW - Tetrahydrobiopterin KW - N-omega-hydroxy-L-arginine KW - Indium tin oxide nanoparticles KW - Biocatalysis Y1 - 2013 U6 - https://doi.org/10.1016/j.bioelechem.2013.04.005 SN - 1567-5394 SN - 1521-186X VL - 94 IS - 47 SP - 7 EP - 12 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Jedrusik-Bode, Monika A1 - Studencka, Maja A1 - Smolka, Christian A1 - Baumann, Tobias A1 - Schmidt, Henning A1 - Kampf, Jan A1 - Paap, Franziska A1 - Martin, Sophie A1 - Tazi, Jamal A1 - Müller, Kristian M. A1 - Krüger, Marcus A1 - Braun, Thomas A1 - Bober, Eva T1 - The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals JF - Journal of cell science N2 - SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress. KW - C. elegans KW - G3BP KW - SIRT6 KW - Sirtuins KW - Stress KW - Stress granules Y1 - 2013 U6 - https://doi.org/10.1242/jcs.130708 SN - 0021-9533 SN - 1477-9137 VL - 126 IS - 22 SP - 5166 EP - + PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Lim, Sze Chern A1 - Friemel, Martin A1 - Marum, Justine E. A1 - Tucker, Elena J. A1 - Bruno, Damien L. A1 - Riley, Lisa G. A1 - Christodoulou, John A1 - Kirk, Edwin P. A1 - Boneh, Avihu A1 - DeGennaro, Christine M. A1 - Springer, Michael A1 - Mootha, Vamsi K. A1 - Rouault, Tracey A. A1 - Leimkühler, Silke A1 - Thorburn, David R. A1 - Compton, Alison G. T1 - Mutations in LYRM4, encoding ironsulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes JF - Human molecular genetics N2 - Ironsulfur clusters (ISCs) are important prosthetic groups that define the functions of many proteins. Proteins with ISCs (called ironsulfur or FeS proteins) are present in mitochondria, the cytosol, the endoplasmic reticulum and the nucleus. They participate in various biological pathways including oxidative phosphorylation (OXPHOS), the citric acid cycle, iron homeostasis, heme biosynthesis and DNA repair. Here, we report a homozygous mutation in LYRM4 in two patients with combined OXPHOS deficiency. LYRM4 encodes the ISD11 protein, which forms a complex with, and stabilizes, the sulfur donor NFS1. The homozygous mutation (c.203GT, p.R68L) was identified via massively parallel sequencing of 1000 mitochondrial genes (MitoExome sequencing) in a patient with deficiency of complexes I, II and III in muscle and liver. These three complexes contain ISCs. Sanger sequencing identified the same mutation in his similarly affected cousin, who had a more severe phenotype and died while a neonate. Complex IV was also deficient in her skeletal muscle. Several other FeS proteins were also affected in both patients, including the aconitases and ferrochelatase. Mutant ISD11 only partially complemented for an ISD11 deletion in yeast. Our in vitro studies showed that the l-cysteine desulfurase activity of NFS1 was barely present when co-expressed with mutant ISD11. Our findings are consistent with a defect in the early step of ISC assembly affecting a broad variety of FeS proteins. The differences in biochemical and clinical features between the two patients may relate to limited availability of cysteine in the newborn period and suggest a potential approach to therapy. Y1 - 2013 U6 - https://doi.org/10.1093/hmg/ddt295 SN - 0964-6906 SN - 1460-2083 VL - 22 IS - 22 SP - 4460 EP - 4473 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - De Frenne, Pieter A1 - Rodriguez-Sanchez, Francisco A1 - Coomes, David Anthony A1 - Bäten, Lander A1 - Versträten, Gorik A1 - Vellend, Mark A1 - Bernhardt-Römermann, Markus A1 - Brown, Carissa D. A1 - Brunet, Jörg A1 - Cornelis, Johnny A1 - Decocq, Guillaume M. A1 - Dierschke, Hartmut A1 - Eriksson, Ove A1 - Gilliam, Frank S. A1 - Hedl, Radim A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Hommel, Patrick A1 - Jenkins, Michael A. A1 - Kelly, Daniel L. A1 - Kirby, Keith J. A1 - Mitchell, Fraser J. G. A1 - Naaf, Tobias A1 - Newman, Miles A1 - Peterken, George A1 - Petrik, Petr A1 - Schultz, Jan A1 - Sonnier, Gregory A1 - Van Calster, Hans A1 - Waller, Donald M. A1 - Walther, Gian-Reto A1 - White, Peter S. A1 - Woods, Kerry D. A1 - Wulf, Monika A1 - Graae, Bente Jessen A1 - Verheyen, Kris T1 - Microclimate moderates plant responses to macroclimate warming JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., "thermophilization" of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that "climatic lags" may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of 12-67 y, we document significant thermophilization of ground-layer plant communities. These changes reflect concurrent declines in species adapted to cooler conditions and increases in species adapted to warmer conditions. However, thermophilization, particularly the increase of warm-adapted species, is attenuated in forests whose canopies have become denser, probably reflecting cooler growing-season ground temperatures via increased shading. As standing stocks of trees have increased in many temperate forests in recent decades, local microclimatic effects may commonly be moderating the impacts of macroclimate warming on forest understories. Conversely, increases in harvesting woody biomass-e.g., for bioenergy-may open forest canopies and accelerate thermophilization of temperate forest biodiversity. KW - climate change KW - forest management KW - understory KW - climatic debt KW - range shifts Y1 - 2013 U6 - https://doi.org/10.1073/pnas.1311190110 SN - 0027-8424 VL - 110 IS - 46 SP - 18561 EP - 18565 PB - National Acad. of Sciences CY - Washington 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 - Gardiner, Lauren M. A1 - Kocyan, Alexander A1 - Motes, Martin A1 - Roberts, David L. A1 - Emerson, Brent C. T1 - Molecular phylogenetics of Vanda and related genera (Orchidaceae) JF - Botanical journal of the Linnean Society N2 - The genus Vanda and its affiliated taxa are a diverse group of horticulturally important species of orchids occurring mainly in South-East Asia, for which generic limits are poorly defined. Here, we present a molecular study using sequence data from three plastid DNA regions. It is shown that Vanda s.l. forms a clade containing approximately 73 species, including the previously accepted genera Ascocentrum, Euanthe, Christensonia, Neofinetia and Trudelia, and the species Aerides flabellata. Resolution of the phylogenetic relationships of species in Vanda s.l. is relatively poor, but existing morphological classifications for Vanda are incongruent with the results produced. Some novel species relationships are revealed, and a new morphological sectional classification is proposed based on support for these groupings and corresponding morphological characters shared by taxa and their geographical distributions. The putative occurrence of multiple pollination syndromes in this group of taxa, combined with complex biogeographical history of the South-East Asian region, is discussed in the context of these results.(c) 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 549-572. KW - Aeridinae KW - Ascocentrum KW - classification KW - Euanthe KW - matK KW - morphology KW - Neofinetia KW - psbA-trnH KW - trnL KW - trnL-F Y1 - 2013 U6 - https://doi.org/10.1111/boj.12102 SN - 0024-4074 SN - 1095-8339 VL - 173 IS - 4 SP - 549 EP - 572 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bosserdt, Maria A1 - Gajovic-Eichelman, Nenad A1 - Scheller, Frieder W. T1 - Modulation of direct electron transfer of cytochrome c by use of a molecularly imprinted thin film JF - Analytical & bioanalytical chemistry N2 - We describe the preparation of a molecularly imprinted polymer film (MIP) on top of a self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) on gold, where the template cytochrome c (cyt c) participates in direct electron transfer (DET) with the underlying electrode. To enable DET, a non-conductive polymer film is electrodeposited from an aqueous solution of scopoletin and cyt c on to the surface of a gold electrode previously modified with MUA. The electroactive surface concentration of cyt c was 0.5 pmol cm(-2). In the absence of the MUA layer, no cyt c DET was observed and the pseudo-peroxidatic activity of the scopoletin-entrapped protein, assessed via oxidation of Ampliflu red in the presence of hydrogen peroxide, was only 30 % of that for the MIP on MUA. This result indicates that electrostatic adsorption of cyt c by the MUA-SAM substantially increases the surface concentration of cyt c during the electrodeposition step, and is a prerequisite for the productive orientation required for DET. After template removal by treatment with sulfuric acid, rebinding of cyt c to the MUA-MIP-modified electrode occurred with an affinity constant of 100,000 mol(-1) L, a value three times higher than that determined by use of fluorescence titration for the interaction between scopoletin and cyt c in solution. The DET of cyt c in the presence of myoglobin, lysozyme, and bovine serum albumin (BSA) reveals that the MIP layer suppresses the effect of competing proteins. KW - Cytochrome c KW - Molecularly imprinted polymer film KW - Mercaptoundecanoic acid KW - Direct electron transfer KW - Scopoletin (7-hydroxy-6-methoxycoumarin) Y1 - 2013 U6 - https://doi.org/10.1007/s00216-013-7009-8 SN - 1618-2642 VL - 405 IS - 20 SP - 6437 EP - 6444 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Zarattini, Paola A1 - Mura, Graziella A1 - Ketmaier, Valerio T1 - Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans. KW - Anostraca KW - Resting eggs KW - Morphometrics KW - Cytochrome oxidase I KW - Population structure Y1 - 2013 U6 - https://doi.org/10.1007/s10750-013-1487-8 SN - 0018-8158 VL - 713 IS - 1 SP - 19 EP - 34 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Snijman, Deirdre A. A1 - Kocyan, Alexander T1 - The genus Pauridia (Hypoxidaceae) amplified to include Hypoxis sect. Ianthe, Saniella and Spiloxene, with revised nomenclature and typification JF - Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy N2 - Recent phylogenetic analyses show that the species of the southern African genera Pauridia, Saniella and Spiloxene and the Australian, Tasmanian and New Zealand Hypoxis sect. Ianthe form a highly supported, monophyletic clade. In keeping with earlier suggestions that these taxa doubtfully warrant separate status, and to avoid the recognition of Hypoxis and Spiloxene as paraphyletic, we expand the circumscription of Pauridia to include Saniella, Spiloxene and Hypoxis sect. Ianthe. As a result 33 new combinations at specific and infraspecific level are proposed and one epitype, two neotypes and 30 lectotypes are newly designated. Three basionyms, of which Linnaeus, Linnaeus filius and Lamarck are the authors, are also typified (Amaryllis capensis, Hypoxis aquatica, and Hypoxis pumila). KW - Hypoxidaceae KW - Hypoxis KW - new combination KW - Pauridia KW - Saniella KW - Spiloxene KW - taxonomy KW - typification Y1 - 2013 U6 - https://doi.org/10.11646/phytotaxa.116.1.2 SN - 1179-3155 VL - 116 IS - 1 SP - 19 EP - 33 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Cheng, Shifeng A1 - van den Bergh, Erik A1 - Zeng, Peng A1 - Zhong, Xiao A1 - Xu, Jiajia A1 - Liu, Xin A1 - Hofberger, Johannes A1 - de Bruijn, Suzanne A1 - Bhide, Amey S. A1 - Kuelahoglu, Canan A1 - Bian, Chao A1 - Chen, Jing A1 - Fan, Guangyi A1 - Kaufmann, Kerstin A1 - Hall, Jocelyn C. A1 - Becker, Annette A1 - Bräutigam, Andrea A1 - Weber, Andreas P. M. A1 - Shi, Chengcheng A1 - Zheng, Zhijun A1 - Li, Wujiao A1 - Lv, Mingju A1 - Tao, Yimin A1 - Wang, Junyi A1 - Zou, Hongfeng A1 - Quan, Zhiwu A1 - Hibberd, Julian M. A1 - Zhang, Gengyun A1 - Zhu, Xin-Guang A1 - Xu, Xun A1 - Schranz, M. Eric T1 - The Tarenaya hassleriana Genome Provides insight Into Reproductive Trait and Genome Evolution of Crucifers JF - The plant cell N2 - The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.113480 SN - 1040-4651 VL - 25 IS - 8 SP - 2813 EP - 2830 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Czech, Andreas A1 - Wende, Sandra A1 - Moerl, Mario A1 - Pan, Tao A1 - Ignatova, Zoya T1 - Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Stress-induced changes of gene expression are crucial for survival of eukaryotic cells. Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels. In this study, we demonstrate that exposure to oxidative stress results in a quick repression of translation by deactivation of the aminoacylends of all transfer-RNA (tRNA). An oxidative-stress activated nuclease, angiogenin, cleaves first within the conserved single-stranded 3'-CCA termini of all tRNAs, thereby blocking their use in translation. This CCA deactivation is reversible and quickly repairable by the CCA-adding enzyme [ATP(CTP): tRNA nucleotidyltransferase]. Through this mechanism the eukaryotic cell dynamically represses and reactivates translation at low metabolic costs. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pgen.1003767 SN - 1553-7404 VL - 9 IS - 8 PB - PLoS CY - San Fransisco ER -