TY - JOUR A1 - Massie, Thomas Michael A1 - Weithoff, Guntram A1 - Kucklaender, Nina A1 - Gaedke, Ursula A1 - Blasius, Bernd T1 - Enhanced Moran effect by spatial variation in environmental autocorrelation JF - Nature Communications N2 - Spatial correlations in environmental stochasticity can synchronize populations over wide areas, a phenomenon known as the Moran effect. The Moran effect has been confirmed in field, laboratory and theoretical investigations. Little is known, however, about the Moran effect in a common ecological case, when environmental variation is temporally autocorrelated and this autocorrelation varies spatially. Here we perform chemostat experiments to investigate the temporal response of independent phytoplankton populations to autocorrelated stochastic forcing. In contrast to naive expectation, two populations without direct coupling can be more strongly correlated than their environmental forcing (enhanced Moran effect), if the stochastic variations differ in their autocorrelation. Our experimental findings are in agreement with numerical simulations and analytical calculations. The enhanced Moran effect is robust to changes in population dynamics, noise spectra and different measures of correlation-suggesting that noise-induced synchrony may play a larger role for population dynamics than previously thought. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms6993 SN - 2041-1723 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Kaba, Hani E. J. A1 - Maier, Natalia A1 - Schliebe-Ohler, Nicole A1 - Mayer, Yvonne A1 - Mueller, Peter P. A1 - van den Heuvel, Joop A1 - Schuchhardt, Johannes A1 - Hanack, Katja A1 - Bilitewski, Ursula T1 - Identification of whole pathogenic cells by monoclonal antibodies generated against a specific peptide from an immunogenic cell wall protein JF - Journal of microbiological methods N2 - We selected the immunogenic cell wall beta-(1,3)-glucosyltransferase Bgl2p from Candida albicans as a target protein for the production of antibodies. We identified a unique peptide sequence in the protein and generated monoclonal anti- C. albicans Bgl2p antibodies, which bound in particular to whole C. albicans cells. KW - Candida KW - Diagnostics KW - Flow cytometry KW - Peptides KW - Bgl2p Y1 - 2015 U6 - https://doi.org/10.1016/j.mimet.2014.11.003 SN - 0167-7012 SN - 1872-8359 VL - 108 SP - 61 EP - 69 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Yarman, Aysu A1 - Dechtrirat, Decha A1 - Bosserdt, Maria A1 - Jetzschmann, Katharina J. A1 - Gajovic-Eichelmann, Nenad A1 - Scheller, Frieder W. T1 - Cytochrome c-derived hybrid systems based on moleculary imprinted polymers JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - Hybrid architectures which combine a MIP with an immobilized affinity ligand or a biocatalyst sum up the advantages of both components. In this paper, hybrid architectures combining a layer of a molecularly imprinted electropolymer with a mini-enzyme or a self-assembled monolayer will be presented. (i) Microperoxidase-11 (MP-11) catalyzed oxidation of the drug aminopyrine on a product-imprinted sublayer: The peroxide dependent conversion of the analyte aminopyrine takes place in the MP-11 containing layer on top of a product-imprinted electropolymer on the indicator electrode. The hierarchical architecture resulted in the elimination of interfering signals for ascorbic acid and uric acid. An advantage of the new hierarchical structure is the separation of MIP formation by electropolymerization and immobilization of the catalyst. In this way it was for the first time possible to integrate an enzyme with a MIP layer in a sensor configuration. This combination has the potential to be transferred to other enzymes, e.g. P450, opening the way to clinically important analytes. (ii) Epitope-imprinted poly-scopoletin layer for binding of the C-terminal peptide and cytochrome c (Cyt c): The MIP binds both the target peptide and the parent protein almost eight times stronger than the non-imprinted polymer with affinities in the lower micromolar range. Exchange of only one amino acid in the peptide decreases the binding by a factor of five. (iii) MUA-poly-scopoletin MIP for cytochrome c: Cyt c bound to the MIP covered gold electrode exhibits direct electron transfer with a redox potential and rate constant typical for the native protein. The MIP cover layer suppresses the displacement of the target protein by BSA or myoglobin. The combination of protein imprinted polymers with an efficient electron transfer is a new concept for characterizing electroactive proteins such as Cyt c. The competition with other proteins shows that the MIP binds its target Cyt c preferentially and that molecular shape and the charge of protein determine the binding of interfering proteins. KW - Molecularly imprinted polymers KW - Microperoxidase-11 KW - Cytochrome c KW - Catalytically active MIPs KW - Epitope imprinting KW - Monoclonal MIPs Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400592 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 3 SP - 573 EP - 586 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Sundelof, Andreas A1 - Grimm, Volker A1 - Ulmestrand, Mats A1 - Fiksen, Oyvind T1 - Modelling harvesting strategies for the lobster fishery in northern Europe: the importance of protecting egg-bearing females JF - Population ecology KW - European lobster KW - Female moratorium KW - Individual-based model KW - Management KW - Minimum landing size KW - Yield per recruit (YPR) Y1 - 2015 U6 - https://doi.org/10.1007/s10144-014-0460-3 SN - 1438-3896 SN - 1438-390X VL - 57 IS - 1 SP - 237 EP - 251 PB - Springer CY - Tokyo ER - TY - JOUR A1 - Guha, S. A1 - Warsinke, Axel A1 - Tientcheu, Charles Merlin A1 - Schmalz, K. A1 - Meliani, C. A1 - Wenger, Ch. T1 - Label free sensing of creatinine using a 6 GHz CMOS near-field dielectric immunosensor JF - The analyst : the analytical journal of the Royal Society of Chemistry N2 - In this work we present a CMOS high frequency direct immunosensor operating at 6 GHz (C-band) for label free determination of creatinine. The sensor is fabricated in standard 0.13 mu m SiGe:C BiCMOS process. The report also demonstrates the ability to immobilize creatinine molecules on a Si3N4 passivation layer of the standard BiCMOS/CMOS process, therefore, evading any further need of cumbersome post processing of the fabricated sensor chip. The sensor is based on capacitive detection of the amount of non-creatinine bound antibodies binding to an immobilized creatinine layer on the passivated sensor. The chip bound antibody amount in turn corresponds indirectly to the creatinine concentration used in the incubation phase. The determination of creatinine in the concentration range of 0.88-880 mu M is successfully demonstrated in this work. A sensitivity of 35 MHz/10 fold increase in creatinine concentration (during incubation) at the centre frequency of 6 GHz is gained by the immunosensor. The results are compared with a standard optical measurement technique and the dynamic range and sensitivity is of the order of the established optical indication technique. The C-band immunosensor chip comprising an area of 0.3 mm(2) reduces the sensing area considerably, therefore, requiring a sample volume as low as 2 mu l. The small analyte sample volume and label free approach also reduce the experimental costs in addition to the low fabrication costs offered by the batch fabrication technique of CMOS/BiCMOS process. Y1 - 2015 U6 - https://doi.org/10.1039/c4an02194k SN - 0003-2654 SN - 1364-5528 VL - 140 IS - 9 SP - 3019 EP - 3027 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Müller, Jörg A1 - Boch, Steffen A1 - Blaser, Steffen A1 - Fischer, Markus A1 - Prati, Daniel T1 - Effects of forest management on bryophyte communities on deadwood JF - Nova Hedwigia : Zeitschrift für Kryptogamenkunde N2 - Epixylic bryophytes are important components of forest vegetation but are currently endangered by increment of wood harvest and intensive forest management. In this paper we present a study about the relationship between forest management, deadwood abundance, deadwood attributes and species richness of epixylic bryophytes on 30 plots comprising three forest types (managed coniferous, managed deciduous and unmanaged deciduous forests) in three regions in Germany. Additionally we analyzed the relations between deadwood attributes (wood species, decay, deadwood type, size) and bryophytes on deadwood items (n = 799) and calculated species interaction networks of wood species and bryophytes. Overall, species richness of epixylic bryophytes was positively related to deadwood abundance and diversity. The mean deadwood abundance was lowest in unmanaged forests (9.7 m(3) ha(-1)) compared with 15.0 m(3) ha(-1) in managed deciduous and 25.1 m(3) ha(-1) in managed coniferous forests. Accordingly, epixylic bryophyte species richness per plot increased from 7 species per 400 m(2) in unmanaged, 10 in managed deciduous and 16 in managed coniferous forests. The interaction network provided evidence of importance of tree-species diversity for bryophyte diversity and the relevance of particular wood species for rare bryophytes. Generally, the results demonstrate a considerable lack of deadwood in all forest types, even in unmanaged forests. Species richness of epixylic bryophytes was strongly limited by available substrates within the observed deadwood abundance ranging up to only 60 m(3) ha(-1). Altogether, this suggests a high demand to increase both abundance and diversity of deadwood in forests. KW - Coarse woody debris KW - cryptogams KW - deadwood KW - species interaction network KW - wood harvest Y1 - 2015 U6 - https://doi.org/10.1127/nova_hedwigia/2015/0242 SN - 0029-5035 VL - 100 IS - 3-4 SP - 423 EP - 438 PB - Cramer CY - Stuttgart ER - TY - JOUR A1 - Heinze, Johannes A1 - Bergmann, Joana A1 - Rillig, Matthias C. A1 - Joshi, Jasmin Radha T1 - Negative biotic soil-effects enhance biodiversity by restricting potentially dominant plant species in grasslands JF - Perspectives in plant ecology, evolution and systematics N2 - Interactions between soil microorganisms and plants can play a vital role for plant fitness and therefore also for plant community composition and biodiversity. However, little is known about how biotic plant soil interactions influence the local dominance and abundance of plant species and whether specific taxonomic or functional groups of plants are differentially affected by such biotic soil-effects. In two greenhouse experiments, we tested the biotic soil-effects of 33 grassland species differing in individual size and local abundance. We hypothesized that large plants that are not locally dominant (despite their size-related competitive advantage enabling them to potentially outshade competitors) are most strongly limited by negative biotic soil-effects. We sampled soils at the opposite ends of a gradient in land-use intensity in temperate grasslands to account for putative modulating effects of land-use intensity on biotic soil-effects. As hypothesized, large, but non-dominant species (especially grasses) experienced more negative biotic soil-effects compared with small and abundant plant species. Land-use intensity had contrasting effects on grasses and herbs resulting in more negative biotic soil-effects for grasses in less intensively managed grasslands. We conclude that biotic soil-effects contribute to the control of potentially dominant plants and hence enable species coexistence and biodiversity especially in species-rich less intensively managed grasslands. KW - Coexistence mechanisms KW - Plant soil feedbacks KW - Individual size KW - Local plant-abundance KW - Grassland diversity KW - Land-use intensity Y1 - 2015 U6 - https://doi.org/10.1016/j.ppees.2015.03.002 SN - 1433-8319 VL - 17 IS - 3 SP - 227 EP - 235 PB - Elsevier CY - Jena ER - TY - JOUR A1 - McKenna, Shane M. A1 - Leimkühler, Silke A1 - Herter, Susanne A1 - Turner, Nicholas J. A1 - Carnell, Andrew J. T1 - Enzyme cascade reactions: synthesis of furandicarboxylic acid (FDCA) and carboxylic acids using oxidases in tandem JF - Green chemistry : an international journal and green chemistry resource N2 - A one-pot tandem enzyme reaction using galactose oxidase M3-5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions. Y1 - 2015 U6 - https://doi.org/10.1039/c5gc00707k SN - 1463-9262 SN - 1463-9270 VL - 17 IS - 6 SP - 3271 EP - 3275 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Sprenger, Heike A1 - Rudack, Katharina A1 - Schudoma, Christian A1 - Neumann, Arne A1 - Seddig, Sylvia A1 - Peters, Rolf A1 - Zuther, Ellen A1 - Kopka, Joachim A1 - Hincha, Dirk K. A1 - Walther, Dirk A1 - Koehl, Karin T1 - Assessment of drought tolerance and its potential yield penalty in potato JF - Functional plant biology : an international journal of plant function N2 - Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied the genetic variance, predictability of field performance and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit of water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial dataset, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified the deviation of relative starch yield from the experimental median (DRYM) as the most efficient index. DRYM corresponded qualitatively to the partial least square model-based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding. KW - performance prediction KW - Solanum tuberosum KW - tolerance index KW - target environment Y1 - 2015 U6 - https://doi.org/10.1071/FP15013 SN - 1445-4408 SN - 1445-4416 VL - 42 IS - 7 SP - 655 EP - 667 PB - CSIRO CY - Clayton ER - TY - INPR A1 - Chattopadhyay, Madhab K. A1 - Chakraborty, Ranadhir A1 - Grossart, Hans-Peter A1 - Reddy, Gundlapally S. A1 - Jagannadham, Medicharla V. T1 - Antibiotic resistance of bacteria T2 - BioMed research international Y1 - 2015 U6 - https://doi.org/10.1155/2015/501658 SN - 2314-6133 SN - 2314-6141 PB - Hindawi Publishing Corp. CY - New York ER - TY - CHAP A1 - Spijkerman, Elly A1 - de Castro, Francisco A1 - Gaedke, Ursula T1 - Independent colimitation for Co2 and inorganic phosphorus T2 - European journal of phycology Y1 - 2015 SN - 0967-0262 SN - 1469-4433 VL - 50 SP - 98 EP - 99 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - CHAP A1 - Lachmann, Sabrina C. A1 - Spijkerman, Elly A1 - Maberly, Stephen C. T1 - Ecology matters: linking inorganic carbon acquisition to ecological preference in four species of microalgae (Chlorophyceae) T2 - European journal of phycology Y1 - 2015 SN - 0967-0262 SN - 1469-4433 VL - 50 SP - 98 EP - 98 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - CHAP A1 - Wegbrod, Jana T1 - Influence of interspecific competition on photosynthetic rates of algal communities T2 - European journal of phycology Y1 - 2015 SN - 0967-0262 SN - 1469-4433 VL - 50 SP - 71 EP - 72 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, P. A1 - Chabrerie, Olivier A1 - Cousins, S. A. O. A1 - De Backer, L. A1 - Decocq, G. A1 - Diekmann, M. A1 - Heinken, Thilo A1 - Kolb, A. A1 - Naaf, T. A1 - Plue, J. A1 - Selvi, F. A1 - Strimbeck, G. R. A1 - Wulf, M. A1 - Verheyen, Kris T1 - Impacts of warming and changes in precipitation frequency on the regeneration of two Acer species JF - Flora : morphology, distribution, functional ecology of plants KW - Seed provenance KW - Germination KW - Climate change KW - Interactive effects Y1 - 2015 U6 - https://doi.org/10.1016/j.flora.2015.05.005 SN - 0367-2530 SN - 1618-0585 VL - 214 SP - 24 EP - 33 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Lombardo, Veronica A. A1 - Otten, Cecile A1 - Abdelilah-Seyfried, Salim T1 - Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis JF - Journal of visualized experiments N2 - The zebrafish embryonic heart is composed of only a few hundred cells, representing only a small fraction of the entire embryo. Therefore, to prevent the cardiac transcriptome from being masked by the global embryonic transcriptome, it is necessary to collect sufficient numbers of hearts for further analyses. Furthermore, as zebrafish cardiac development proceeds rapidly, heart collection and RNA extraction methods need to be quick in order to ensure homogeneity of the samples. Here, we present a rapid manual dissection protocol for collecting functional/beating hearts from zebrafish embryos. This is an essential prerequisite for subsequent cardiac-specific RNA extraction to determine cardiac-specific gene expression levels by transcriptome analyses, such as quantitative real-time polymerase chain reaction (RT-qPCR). The method is based on differential adhesive properties of the zebrafish embryonic heart compared with other tissues; this allows for the rapid physical separation of cardiac from extracardiac tissue by a combination of fluidic shear force disruption, stepwise filtration and manual collection of transgenic fluorescently labeled hearts. KW - Developmental Biology KW - Issue 95 KW - zebrafish KW - embryo KW - heart KW - dissection KW - RNA KW - RT-qPCR Y1 - 2015 U6 - https://doi.org/10.3791/52087 SN - 1940-087X IS - 95 PB - JoVE CY - Cambridge ER - TY - JOUR A1 - Diekmann, Martin A1 - Müller, Josef A1 - Heinken, Thilo A1 - Dupre, Cecilia T1 - Survey and statistical analysis of plant reintroductions in Germany JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Aim - Plant reintroductions and other forms of targeted species translocations will in the future gain growing importance for nature conservation. In fragmented habitats, species reintroductions offer one of the most efficient tools for preserving or restoring plant diversity. In our study, we have compiled available data about plant reintroduction projects in Germany to answer the following questions: (1) What are the characteristics, habitat preferences and ecological strategies of species considered in plant reintroduction trials, and are these representative of the entire class of threatened species in Germany? (2) Is the judgment of the success or failure of plant reintroductions biased by the choice of species used in the experiments? (3) Do reintroduction efforts focus on those species for which Germany has a particularly high responsibility for conservation? Methods - Information about reintroduction projects in Germany were obtained from published and internet sources as well as unpublished reports. In our search we focused on single-species trials in the framework of scientific or conservation projects. For all threatened species included in our database, we compiled information on their systematics, life form, ecological strategies and habitat preferences. A list of all species being threatened nationally or regionally, comprising both reintroduced and not reintroduced species, served as a reference for statistical analysis. Results - The list of vascular plants used in conservation-oriented reintroductions consisted of 196 taxa. Species of families with large and conspicuous, mostly insect-pollinated flowers (for example, Orchidaceae) were over-represented among the reintroduced species compared to those threatened species not included in reintroduction trials. Species considered were also more often than expected found in semi-natural open habitats such as heathlands and grasslands. Notably, many projects focused on calcareous grasslands, characterized by dry, high-pH and infertile soils. In contrast, species of more near-natural vegetation (alpine and rocky formations, forests) were under-represented. About 25% of the species that were reintroduced are not threatened on the national scale. Out of 150 species for which Germany has a particularly high responsibility for conservation, only 14 (9.3%) were reintroduced. For only about 1/3 of all reintroduction attempts, success or failure were documented; whereas the success rate appears to be relatively low in nutrient-poor environments, trials with nutrient-demanding and competitive species were more successful. Conclusions - We conclude that conservation-oriented reintroduction attempts should focus more on species for which the country or a region has a particular high responsibility. Reintroductions, to a larger extent than at present, also need to consider the different chances of success in different habitat types and environments. KW - conservation responsibility KW - Ellenberg indicator values KW - Grime strategy KW - habitat type KW - life form KW - red list Y1 - 2015 SN - 0722-494X IS - 35 SP - 249 EP - 265 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Budzik, Karolina A. A1 - Zuwala, Krystyna A1 - Kupfer, Alexander A1 - Gower, David J. A1 - Wilkinson, Mark T1 - Diverse anatomy of the tongue and taste organs in five species of caecilian (Amphibia: Gymnophiona) JF - Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography N2 - Limited previous studies on caecilian taste organs have demonstrated the presence of very few taste buds in the oral epithelium, while providing somewhat contradictory reports of their distribution within the oropharynx and across taxa. Here we report on the gross morphology of the tongue and explore the distribution, number and morphology of taste organs of five caecilian species representing five families, focusing upon variation within the group and investigating whether larvae and adults have the same type of taste organs. We find that taste buds are widespread in the oropharynx of caecilians and that they occur both in adults and larvae of a species with a biphasic life history. Thus Gymnophiona differ substantially from Batriachia, which have distinct larval and adult taste organs. KW - Amphibian KW - Number of taste organs KW - Sensory zone KW - Taste buds Y1 - 2015 U6 - https://doi.org/10.1016/j.jcz.2015.04.007 SN - 0044-5231 VL - 257 SP - 103 EP - 109 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Corno, Gianluca A1 - Salka, Ivette A1 - Pohlmann, Kirsten A1 - Hall, Alex R. A1 - Grossart, Hans-Peter T1 - Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms JF - Aquatic microbial ecology : international journal N2 - Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems. KW - Aggregation KW - Flagellate grazing KW - Ecological interactions KW - Microbial carbon transfer KW - Polymer degradation KW - System ecology Y1 - 2015 U6 - https://doi.org/10.3354/ame01765 SN - 0948-3055 SN - 1616-1564 VL - 76 IS - 1 SP - 27 EP - + PB - Institute of Mathematical Statistics CY - Oldendorf Luhe ER - TY - JOUR A1 - Bhaskar, Thanga Bhuvanesh Vijaya A1 - Ma, Nan A1 - Lendlein, Andreas A1 - Roch, Toralf T1 - The interaction of human macrophage subsets with silicone as a biomaterial JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Silicones are widely used as biomaterials for medical devices such as extracorporeal equipments. However, there is often conflicting evidence about their supposed cell-and histocompatibility. Macrophages could mediate silicone-induced adverse responses such as foreign body reaction and fibrous encapsulation. The polarization behaviour of macrophages could determine the clinical outcome after implantation of biomaterials. Induction of classically activated macrophages (CAM) may induce and support uncontrolled inflammatory responses and undesired material degradation. In contrast, polarization into alternatively activated macrophages (AAM) is assumed to support healing processes and implant integration. This study compared the interaction of non-polarized macrophages (M0), CAM, and AAM with commercially available tissue culture polystyrene (TCP) and a medical grade silicone-based biomaterial, regarding the secretion of inflammatory mediators such as cytokines and chemokines. Firstly, by using the Limulus amoebocyte lysate (LAL) test the silicone films were shown to be free of soluble endotoxins, which is the prerequisite to investigate their interaction with primary immune cells. Primary human monocyte-derived macrophages (M0) were polarized into CAM and AAM by addition of suitable differentiation factors. These macrophage subsets were incubated on the materials for 24 hours and their viability and cytokine secretion was assessed. In comparison to TCP, cell adhesion was lower on silicone after 24 hours for all three macrophage subsets. However, compared to TCP, silicone induced higher levels of certain inflammatory and chemotactic cytokines in M0, CAM, and AAM macrophage subsets. Conclusively, it was shown that silicone has the ability to induce a pro-inflammatory state to different magnitudes dependent on the macrophage subsets. This priming of the macrophage phenotype by silicone could explain the incidence of severe foreign body complications observed in vivo. KW - Biomaterials KW - silicone KW - macrophage subsets KW - cytokines/chemokines Y1 - 2015 U6 - https://doi.org/10.3233/CH-151991 SN - 1386-0291 SN - 1875-8622 VL - 61 IS - 2 SP - 119 EP - 133 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Tasior, Mariusz A1 - Bald, Ilko A1 - Deperasinska, Irena A1 - Cywinski, Piotr J. A1 - Gryko, Daniel T. T1 - An internal charge transfer-dependent solvent effect in V-shaped azacyanines JF - Organic & biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry Y1 - 2015 U6 - https://doi.org/10.1039/c5ob01633a SN - 1477-0520 SN - 1477-0539 VL - 13 IS - 48 SP - 11714 EP - 11720 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Pathe-Neuschaefer-Rube, Andrea A1 - Neuschaefer-Rube, Frank A1 - Genz, Lara A1 - Püschel, Gerhard Paul T1 - Botulinum Neurotoxin Dose-Dependently Inhibits Release of Neurosecretory Vesicle-Targeted Luciferase from Neuronal Cells JF - Alternatives to animal experimentation : ALTEX ; a journal for new paths in biomedical science N2 - Botulinum toxin is a bacterial toxin that inhibits neurotransmitter release from neurons and thereby causes a flaccid paralysis. It is used as drug to treat a number of serious ailments and, more frequently, for aesthetic medical interventions. Botulinum toxin for pharmacological applications is isolated from bacterial cultures. Due to partial denaturation of the protein, the specific activity of these preparations shows large variations. Because of its extreme potential toxicity, pharmacological preparations must be carefully tested for their activity. For the current gold standard, the mouse lethality assay, several hundred thousand mice are killed per year. Alternative methods have been developed that suffer from one or more of the following deficits: In vitro enzyme assays test only the activity of the catalytic subunit of the toxin. Enzymatic and cell based immunological assays are specific for just one of the different serotypes. The current study takes a completely different approach that overcomes these limitations: Neuronal cell lines were stably transfected with plasmids coding for luciferases of different species, which were N-terminally tagged with leader sequences that redirect the luciferase into neuro-secretory vesicles. From these vesicles, luciferases were released upon depolarization of the cells. The depolarization-dependent release was efficiently inhibited by botulinum toxin in a concentration range (1 to 100 pM) that is used in pharmacological preparations. The new assay might thus be an alternative to the mouse lethality assay and the immunological assays already in use. KW - Botulinum toxin KW - cell-based assay KW - mouse lethality assay Y1 - 2015 SN - 1868-596X SN - 1868-8551 VL - 32 IS - 4 SP - 297 EP - 306 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Teasdale, Matthew David A1 - van Doorn, N. L. A1 - Fiddyment, S. A1 - Webb, C. C. A1 - Hofreiter, Michael A1 - Collins, Matthew J. A1 - Bradley, Daniel G. T1 - Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing JF - Philosophical transactions of the Royal Society of London : B, Biological sciences N2 - Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock. KW - parchment KW - next generation sequencing KW - ancient DNA KW - ZooMS KW - sheep Y1 - 2015 U6 - https://doi.org/10.1098/rstb.2013.0379 SN - 0962-8436 SN - 1471-2970 VL - 370 IS - 1660 PB - Royal Society CY - London ER - TY - JOUR A1 - Ludwig, Arne A1 - Reissmann, Monika A1 - Benecke, Norbert A1 - Bellone, Rebecca A1 - Sandoval-Castellanos, Edson A1 - Cieslak, Michael A1 - González-Fortes, Gloria M. A1 - Morales-Muniz, Arturo A1 - Hofreiter, Michael A1 - Pruvost, Melanie T1 - Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses JF - Philosophical transactions of the Royal Society of London : B, Biological sciences N2 - Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times. KW - ancient DNA KW - coat colour KW - domestication KW - Equus KW - palaeogenetics KW - population Y1 - 2015 U6 - https://doi.org/10.1098/rstb.2013.0386 SN - 0962-8436 SN - 1471-2970 VL - 370 IS - 1660 PB - Royal Society CY - London ER - TY - INPR A1 - Hagelberg, Erika A1 - Hofreiter, Michael A1 - Keyser, Christine T1 - Ancient DNA: the first three decades T2 - Philosophical transactions of the Royal Society of London : B, Biological sciences KW - ancient DNA KW - human evolutionary genetics KW - palaeogenomics Y1 - 2015 U6 - https://doi.org/10.1098/rstb.2013.0371 SN - 0962-8436 SN - 1471-2970 VL - 370 IS - 1660 PB - Royal Society CY - London ER - TY - JOUR A1 - Nowak, Michael D. A1 - Russo, Giancarlo A1 - Schlapbach, Ralph A1 - Cuong Nguyen Huu, A1 - Lenhard, Michael A1 - Conti, Elena T1 - The draft genome of Primula veris yields insights into the molecular basis of heterostyly JF - Genome biology : biology for the post-genomic era N2 - Background: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole. Y1 - 2015 U6 - https://doi.org/10.1186/s13059-014-0567-z SN - 1465-6906 SN - 1474-760X VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Renz, Marc A1 - Otten, Cecile A1 - Faurobert, Eva A1 - Rudolph, Franziska A1 - Zhu, Yuan A1 - Boulday, Gwenola A1 - Duchene, Johan A1 - Mickoleit, Michaela A1 - Dietrich, Ann-Christin A1 - Ramspacher, Caroline A1 - Steed, Emily A1 - Manet-Dupe, Sandra A1 - Benz, Alexander A1 - Hassel, David A1 - Vermot, Julien A1 - Huisken, Jan A1 - Tournier-Lasserve, Elisabeth A1 - Felbor, Ute A1 - Sure, Ulrich A1 - Albiges-Rizo, Corinne A1 - Abdelilah-Seyfried, Salim T1 - Regulation of beta 1 Integrin-Klf2-Mediated angiogenesis by CCM proteins JF - Developmental cell N2 - Mechanotransduction pathways are activated in response to biophysical stimuli during the development or homeostasis of organs and tissues. In zebrafish, the blood-flow-sensitive transcription factor Klf2a promotes VEGF-dependent angiogenesis. However, the means by which the Klf2a mechanotransduction pathway is regulated to prevent continuous angiogenesis remain unknown. Here we report that the upregulation of klf2 mRNA causes enhanced egfl7 expression and angiogenesis signaling, which underlies cardiovascular defects associated with the loss of cerebral cavernous malformation (CCM) proteins in the zebrafish embryo. Using CCM-protein-depleted human umbilical vein endothelial cells, we show that the misexpression of KLF2 mRNA requires the extracellular matrix-binding receptor beta 1 integrin and occurs in the absence of blood flow. Downregulation of beta 1 integrin rescues ccm mutant cardiovascular malformations in zebrafish. Our work reveals a beta 1 integrin-Klf2-Egfl7-signaling pathway that is tightly regulated by CCM proteins. This regulation prevents angiogenic overgrowth and ensures the quiescence of endothelial cells. Y1 - 2015 U6 - https://doi.org/10.1016/j.devcel.2014.12.016 SN - 1534-5807 SN - 1878-1551 VL - 32 IS - 2 SP - 181 EP - 190 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Proost, Sebastian A1 - Van Bel, Michiel A1 - Vaneechoutte, Dries A1 - Van de Peer, Yves A1 - Inze, Dirk A1 - Müller-Röber, Bernd A1 - Vandepoele, Klaas T1 - PLAZA 3.0: an access point for plant comparative genomics JF - Nucleic acids research N2 - Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. Y1 - 2015 U6 - https://doi.org/10.1093/nar/gku986 SN - 0305-1048 SN - 1362-4962 VL - 43 IS - D1 SP - D974 EP - D981 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Imholt, Christian A1 - Reil, Daniela A1 - Eccard, Jana A1 - Jacob, Daniela A1 - Hempelmann, Nils A1 - Jacob, Jens T1 - Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus) JF - Pest management science N2 - BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry KW - climate change KW - population dynamics KW - bank vole KW - regression tree KW - outbreak Y1 - 2015 U6 - https://doi.org/10.1002/ps.3838 SN - 1526-498X SN - 1526-4998 VL - 71 IS - 2 SP - 166 EP - 172 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Kirchner, Sebastian A1 - Ignatova, Zoya T1 - Emerging roles of tRNA in adaptive translation, signalling dynamics and disease JF - Nature reviews N2 - tRNAs, nexus molecules between mRNAs and proteins, have a central role in translation. Recent discoveries have revealed unprecedented complexity of tRNA biosynthesis, modification patterns, regulation and function. In this Review, we present emerging concepts regarding how tRNA abundance is dynamically regulated and how tRNAs (and their nucleolytic fragments) are centrally involved in stress signalling and adaptive translation, operating across a wide range of timescales. Mutations in tRNAs or in genes affecting tRNA biogenesis are also linked to complex human diseases with surprising heterogeneity in tissue vulnerability, and we highlight cell-specific aspects that modulate the disease penetrance of tRNA-based pathologies. Y1 - 2015 U6 - https://doi.org/10.1038/nrg3861 SN - 1471-0056 SN - 1471-0064 VL - 16 IS - 2 SP - 98 EP - 112 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Benina, Maria A1 - Ribeiro, Dimas Mendes A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. T1 - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels. KW - Arabidopsis KW - gene regulation KW - oxidative stress KW - tissue-specific KW - translation Y1 - 2015 U6 - https://doi.org/10.1111/pce.12355 SN - 0140-7791 SN - 1365-3040 VL - 38 IS - 2 SP - 349 EP - 363 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Tittel, Joerg A1 - Allgaier, Martin A1 - Frindte, Katharina A1 - Wurzbacher, Christian A1 - Hilt, Sabine A1 - Kamjunke, Norbert A1 - Grossart, Hans-Peter T1 - Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition JF - Microbial ecology N2 - The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties. KW - Bacterial growth efficiency KW - Continuous cultures KW - Carbon decomposition KW - Leaf litter KW - Photolysis Y1 - 2015 U6 - https://doi.org/10.1007/s00248-014-0549-4 SN - 0095-3628 SN - 1432-184X VL - 69 IS - 2 SP - 361 EP - 371 PB - Springer CY - New York ER - TY - JOUR A1 - Warren, Ben H. A1 - Simberloff, Daniel A1 - Ricklefs, Robert E. A1 - Aguilee, Robin A1 - Condamine, Fabien L. A1 - Gravel, Dominique A1 - Morlon, Helene A1 - Mouquet, Nicolas A1 - Rosindell, James A1 - Casquet, Juliane A1 - Conti, Elena A1 - Cornuault, Josselin A1 - Maria Fernandez-Palacios, Jose A1 - Hengl, Tomislav A1 - Norder, Sietze J. A1 - Rijsdijk, Kenneth F. A1 - Sanmartin, Isabel A1 - Strasberg, Dominique A1 - Triantis, Kostas A. A1 - Valente, Luis M. A1 - Whittaker, Robert J. A1 - Gillespie, Rosemary G. A1 - Emerson, Brent C. A1 - Thebaud, Christophe T1 - Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson JF - Ecology letters N2 - The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, An equilibrium theory of insular zoogeography', was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re-assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution - understanding ecosystem functioning, speciation and diversification - frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future. KW - Community assembly KW - diversification KW - ecosystem functioning KW - genomics KW - island biogeography KW - islands as model systems KW - speciation Y1 - 2015 U6 - https://doi.org/10.1111/ele.12398 SN - 1461-023X SN - 1461-0248 VL - 18 IS - 2 SP - 200 EP - 217 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Stillman, Richard A. A1 - Railsback, Steven Floyd A1 - Giske, Jarl A1 - Berger, Uta A1 - Grimm, Volker T1 - Making Predictions in a Changing World: The Benefits of Individual-Based Ecology JF - Bioscience N2 - Ecologists urgently need a better ability to predict how environmental change affects biodiversity. We examine individual-based ecology (IBE), a research paradigm that promises better a predictive ability by using individual-based models (IBMs) to represent ecological dynamics as arising from how individuals interact with their environment and with each other. A key advantage of IBMs is that the basis for predictions-fitness maximization by individual organisms-is more general and reliable than the empirical relationships that other models depend on. Case studies illustrate the usefulness and predictive success of long-term IBE programs. The pioneering programs had three phases: conceptualization, implementation, and diversification. Continued validation of models runs throughout these phases. The breakthroughs that make IBE more productive include standards for describing and validating IBMs, improved and standardized theory for individual traits and behavior, software tools, and generalized instead of system-specific IBMs. We provide guidelines for pursuing IBE and a vision for future IBE research. KW - ecology KW - fitness-maximization KW - individual-based KW - modeling KW - prediction Y1 - 2015 U6 - https://doi.org/10.1093/biosci/biu192 SN - 0006-3568 SN - 1525-3244 VL - 65 IS - 2 SP - 140 EP - 150 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Reinhard, Sandy A1 - Renner, Sandra A1 - Kupfer, Alexander T1 - Sexual dimorphism and age of Mediterranean salamanders JF - Zoology N2 - We analysed sexual size dimorphism (SSD) for two Mediterranean species of the "true" salamander clade possessing distinct life histories (Salamandra algira and Mertensiella caucasica) and equilibrated the morphometric approach to individual age by using skeletochronology. For species that have a short breeding season and live at high altitudes, such as Mediterranean amphibians, the fecundity advantage hypothesis predicts female-biased SSD to maximise reproductive success. Our results showed no SSD in either species; however, morphometric data indicated a male-biased dimorphism in limb (arm and leg) dimensions in both species when compared to body size. Limb dimorphisms are likely related to the particular mating system, which involves an amplexus during spermatophore transfer. Arm length appeared sexually dimorphic during ontogeny both in viviparous Salamandra algira and oviparous Mertensiella caucasica. A review on SSD indicated monomorphy of body size as a common lineage-specific pattern among the "true" salamander clade, but also the common presence of other traits such as sexually dimorphic limb proportions. (C) 2014 Elsevier GmbH. All rights reserved. KW - Amphibia KW - Salamanders KW - Life history KW - Sexual dimorphism KW - Skeletochronology Y1 - 2015 U6 - https://doi.org/10.1016/j.zool.2014.08.002 SN - 0944-2006 VL - 118 IS - 1 SP - 19 EP - 26 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Germonpre, Mietje A1 - Sablin, Mikhail V. A1 - Laznickova-Galetova, Martina A1 - Despres, Viviane A1 - Stevens, Rhiannon E. A1 - Stiller, Mathias A1 - Hofreiter, Michael T1 - Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014) JF - Journal of archaeological science N2 - This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary. (C) 2014 Elsevier Ltd. All rights reserved. KW - Canid morphotype KW - Dog KW - Domestication KW - Palaeolithic KW - Pleistocene KW - Wolf Y1 - 2015 U6 - https://doi.org/10.1016/j.jas.2014.11.035 SN - 0305-4403 SN - 1095-9238 VL - 54 SP - 210 EP - 216 PB - Elsevier CY - London ER - TY - JOUR A1 - Horn, Sebastian A1 - Hempel, Stefan A1 - Ristow, Michael A1 - Rillig, Matthias C. A1 - Kowarik, Ingo A1 - Caruso, Tancredi T1 - Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland JF - Acta oecologica : international journal of ecology N2 - Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved. KW - Assembly pattern KW - Dispersal limitation KW - Festuca brevipila KW - Niche partitioning KW - Null model KW - Plant community ecology KW - Variance partitioning Y1 - 2015 U6 - https://doi.org/10.1016/j.actao.2015.01.004 SN - 1146-609X SN - 1873-6238 VL - 63 SP - 56 EP - 62 PB - Elsevier CY - Paris ER - TY - JOUR A1 - van Gerven, Luuk P. A. A1 - Brederveld, Robert J. A1 - de Klein, Jeroen J. M. A1 - DeAngelis, Don L. A1 - Downing, Andrea S. A1 - Faber, Michiel A1 - Gerla, Daan J. A1 - Janse, Jan H. A1 - Janssen, Annette B. G. A1 - Jeuken, Michel A1 - Kooi, Bob W. A1 - Kuiper, Jan J. A1 - Lischke, Betty A1 - Liu, Sien A1 - Petzoldt, Thomas A1 - Schep, Sebastiaan A. A1 - Teurlincx, Sven A1 - Thiange, Christophe A1 - Trolle, Dennis A1 - van Nes, Egbert H. A1 - Mooij, Wolf M. T1 - Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach JF - Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology N2 - Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers. KW - Database Approach To Modelling KW - DATM KW - PCLake KW - PCDitch KW - OSIRIS KW - ACSL KW - R KW - GRIND KW - DUFLOW KW - DELWAQ KW - Modelling Framework KW - Model Implementation KW - Model Analysis KW - Differential Equations KW - Community-based Modelling Y1 - 2015 U6 - https://doi.org/10.1127/fal/2015/0631 SN - 1863-9135 VL - 186 IS - 1-2 SP - 5 EP - 20 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Robert, Helene S. A1 - Grunewald, Wim A1 - Sauer, Michael A1 - Cannoot, Bernard A1 - Soriano, Mercedes A1 - Swarup, Ranjan A1 - Weijers, Dolf A1 - Bennett, Malcolm A1 - Boutilier, Kim A1 - Friml, Jiri T1 - Plant embryogenesis requires AUX/LAX-mediated auxin influx JF - Development : Company of Biologists N2 - The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop between MONOPTEROS-(ARF5)dependent auxin signalling and auxin transport. This MONOPTEROS dependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling. KW - Arabidopsis thaliana embryogenesis KW - Auxin transport KW - AUX1 KW - LIKE-AUX1 (LAX) KW - MONOPTEROS (ARF5) KW - PIN KW - Brassica napus KW - Microspore Y1 - 2015 U6 - https://doi.org/10.1242/dev.115832 SN - 0950-1991 SN - 1477-9129 VL - 142 IS - 4 SP - 702 EP - 711 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Petrov, Veselin A1 - Hille, Jacques A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - ROS-mediated abiotic stress-induced programmed cell death in plants JF - Frontiers in plant science N2 - During the course of their ontogenesis plants are continuously exposed to a large variety of abiotic stress factors which can damage tissues and jeopardize the survival of the organism unless properly countered. While animals can simply escape and thus evade stressors, plants as sessile organisms have developed complex strategies to withstand them. When the intensity of a detrimental factor is high, one of the defense programs employed by plants is the induction of programmed cell death (PCD). This is an active, genetically controlled process which is initiated to isolate and remove damaged tissues thereby ensuring the survival of the organism. The mechanism of PCD induction usually includes an increase in the levels of reactive oxygen species (ROS) which are utilized as mediators of the stress signal. Abiotic stress-induced PCD is not only a process of fundamental biological importance, but also of considerable interest to agricultural practice as it has the potential to significantly influence crop yield. Therefore, numerous scientific enterprises have focused on elucidating the mechanisms leading to and controlling PCD in response to adverse conditions in plants. This knowledge may help develop novel strategies to obtain more resilient crop varieties with improved tolerance and enhanced productivity. The aim of the present review is to summarize the recent advances in research on ROS-induced PCD related to abiotic stress and the role of the organelles in the process. KW - abiotic stress KW - programmed cell death KW - reactive oxygen species KW - signal transduction KW - stress adaptation Y1 - 2015 U6 - https://doi.org/10.3389/fpls.2015.00069 SN - 1664-462X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Geissler, Peter A1 - Poyarkov, Nikolay A. A1 - Grismer, Lee A1 - Nguyen, Truong Q. A1 - An, Hang T. A1 - Neang, Thy A1 - Kupfer, Alexander A1 - Ziegler, Thomas A1 - Böhme, Wolfgang A1 - Müller, Hendrik T1 - New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969 JF - Organisms, diversity & evolution : official journal of the Gesellschaft für Biologische Systematik N2 - Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided. KW - Biogeography KW - Caecilians KW - Indochina KW - Cambodia KW - Laos KW - Thailand KW - Vietnam KW - mtDNA KW - Barcoding KW - COI KW - cyt b KW - Phylogeny KW - Integrative taxonomy Y1 - 2015 U6 - https://doi.org/10.1007/s13127-014-0190-6 SN - 1439-6092 SN - 1618-1077 VL - 15 IS - 1 SP - 143 EP - 174 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Pietra, Stefano A1 - Lang, Patricia A1 - Grebe, Markus T1 - SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana JF - Physiologia plantarum N2 - Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning. Y1 - 2015 U6 - https://doi.org/10.1111/ppl.12257 SN - 0031-9317 SN - 1399-3054 VL - 153 IS - 3 SP - 440 EP - 453 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. A1 - Goodchild, Helen A1 - Speller, Camilla F. A1 - Barlow, Axel A1 - González-Fortes, Gloria M. A1 - Thomas, Jessica A. A1 - Ludwig, Arne A1 - Collins, Matthew J. T1 - The future of ancient DNA: Technical advances and conceptual shifts JF - Bioessays : ideas that push the boundaries N2 - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. KW - ancient DNA KW - hybridisation capture KW - multi-locus data KW - next generation sequencing (NGS) KW - palaeogenomics KW - population genomics Y1 - 2015 U6 - https://doi.org/10.1002/bies.201400160 SN - 0265-9247 SN - 1521-1878 VL - 37 IS - 3 SP - 284 EP - 293 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Schwarte, Sandra A1 - Wegner, Fanny A1 - Havenstein, Katja A1 - Groth, Detlef A1 - Steup, Martin A1 - Tiedemann, Ralph T1 - Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana JF - Plant molecular biology : an international journal of fundamental research and genetic engineering N2 - Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts. KW - Arabidopsis thaliana KW - Divergent evolution KW - Intraspecific genetic variation KW - Positive selection KW - Starch metabolizing enzymes KW - Transcript levels Y1 - 2015 U6 - https://doi.org/10.1007/s11103-015-0293-2 SN - 0167-4412 SN - 1573-5028 VL - 87 IS - 4-5 SP - 489 EP - 519 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Zurell, Damaris A1 - Eggers, Ute A1 - Kaatz, Michael A1 - Rotics, Shay A1 - Sapir, Nir A1 - Wikelski, Martin A1 - Nathan, Ran A1 - Jeltsch, Florian T1 - Individual-based modelling of resource competition to predict density-dependent population dynamics: a case study with white storks JF - Oikos N2 - Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual-based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine-scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density-dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions. Y1 - 2015 U6 - https://doi.org/10.1111/oik.01294 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 3 SP - 319 EP - 330 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Mendel, Ralf R. A1 - Leimkühler, Silke T1 - The biosynthesis of the molybdenum cofactors JF - Journal of biological inorganic chemistry N2 - The biosynthesis of the molybdenum cofactors (Moco) is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified to date. In all molybdoenzymes except nitrogenase, molybdenum is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into three general steps, with a fourth one present only in bacteria and archaea: (1) formation of the cyclic pyranopterin monophosphate, (2) formation of MPT, (3) insertion of molybdenum into molybdopterin to form Moco, and (4) additional modification of Moco in bacteria with the attachment of a nucleotide to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on the biosynthesis of Moco in bacteria, humans and plants. KW - Molybdenum KW - Molybdenum cofactor KW - cPMP KW - bis-MGD KW - Sulfuration KW - Sulfite oxidase Y1 - 2015 U6 - https://doi.org/10.1007/s00775-014-1173-y SN - 0949-8257 SN - 1432-1327 VL - 20 IS - 2 SP - 337 EP - 347 PB - Springer CY - New York ER - TY - JOUR A1 - Kössl, Manfred A1 - Hechavarria, Julio A1 - Voss, Cornelia A1 - Schaefer, Markus A1 - Vater, Marianne T1 - Bat auditory cortex - model for general mammalian auditory computation or special design solution for active time perception? JF - European journal of neuroscience N2 - Audition in bats serves passive orientation, alerting functions and communication as it does in other vertebrates. In addition, bats have evolved echolocation for orientation and prey detection and capture. This put a selective pressure on the auditory system in regard to echolocation-relevant temporal computation and frequency analysis. The present review attempts to evaluate in which respect the processing modules of bat auditory cortex (AC) are a model for typical mammalian AC function or are designed for echolocation-unique purposes. We conclude that, while cortical area arrangement and cortical frequency processing does not deviate greatly from that of other mammals, the echo delay time-sensitive dorsal cortex regions contain special designs for very powerful time perception. Different bat species have either a unique chronotopic cortex topography or a distributed salt-and-pepper representation of echo delay. The two designs seem to enable similar behavioural performance. KW - chronotopy KW - echolocation KW - fovea KW - salt-and-pepper KW - target range Y1 - 2015 U6 - https://doi.org/10.1111/ejn.12801 SN - 0953-816X SN - 1460-9568 VL - 41 IS - 5 SP - 518 EP - 532 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Zhang, Houbin A1 - Hanke-Gogokhia, Christin A1 - Jiang, Li A1 - Li, Xiaobo A1 - Wang, Pu A1 - Gerstner, Cecilia D. A1 - Frederick, Jeanne M. A1 - Yang, Zhenglin A1 - Baehr, Wolfgang T1 - Mistrafficking of prenylated proteins causes retinitis pigmentosa 2 JF - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology N2 - The retinitis pigmentosa 2 polypeptide (RP2) functions as a GTPase-activating protein (GAP) for ARL3 (Arf-like protein 3), a small GTPase. ARL3 is an effector of phosphodiesterase 6 Delta (PDE6D), a prenyl-binding protein and chaperone of prenylated protein in photoreceptors. Mutations in the human RP2 gene cause X-linked retinitis pigmentosa (XLRP) and cone-rod dystrophy (XL-CORD). To study mechanisms causing XLRP, we generated an RP2 knockout mouse. The RP2h(-/-) mice exhibited a slowly progressing rod-cone dystrophy simulating the human disease. RP2h(-/-) scotopic a-wave and photopic b-wave amplitudes declined at 1 mo of age and continued to decline over the next 6 mo. Prenylated PDE6 subunits and G-protein coupled receptor kinase 1 (GRK1) were unable to traffic effectively to the RP2h(-/-) outer segments. Mechanistically, absence of RP2 GAP activity increases ARL3-GTP levels, forcing PDE6D to assume a predominantly "closed" conformation that impedes binding of lipids. Lack of interaction disrupts trafficking of PDE6 and GRK1 to their destination, the photoreceptor outer segments. We propose that hyperactivity of ARL3-GTP in RP2 knockout mice and human patients with RP2 null alleles leads to XLRP resembling recessive rod-cone dystrophy. KW - rod-cone dystrophy KW - ARL3 KW - PDE6D KW - RP2 KW - XLRP Y1 - 2015 U6 - https://doi.org/10.1096/fj.14-257915 SN - 0892-6638 SN - 1530-6860 VL - 29 IS - 3 SP - 932 EP - 942 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Castellini, Alberto A1 - Paltrinieri, Daniele A1 - Manca, Vincenzo T1 - MP-GeneticSynth: inferring biological network regulations from time series JF - Bioinformatics N2 - MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis. Y1 - 2015 U6 - https://doi.org/10.1093/bioinformatics/btu694 SN - 1367-4803 SN - 1460-2059 VL - 31 IS - 5 SP - 785 EP - 787 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Dammhahn, Melanie A1 - Rakotondramanana, Claude Fabienne A1 - Goodman, Steven M. T1 - Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar: stable isotopes reveal fine-grained niche differentiation among cryptic species JF - Journal of tropical ecology N2 - Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0% in delta N-15, i.e. two trophic levels, and 4.2% in delta C-13 with a community mean of 11.3% in delta N-15 and - 21.0% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4%, delta C-13: 1.0%) with a community mean of 8.0% delta N-15 and - 21.7% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa. KW - Chiroptera KW - community structure KW - congeneric species KW - ecological niches KW - migration KW - Neoromicia KW - Pipistrellus KW - Scotophilus KW - stable carbon KW - stable nitrogen Y1 - 2015 U6 - https://doi.org/10.1017/S0266467414000741 SN - 0266-4674 SN - 1469-7831 VL - 31 SP - 153 EP - 164 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Alseekh, Saleh A1 - Tohge, Takayuki A1 - Wendenberg, Regina A1 - Scossa, Federico A1 - Omranian, Nooshin A1 - Li, Jie A1 - Kleessen, Sabrina A1 - Giavalisco, Patrick A1 - Pleban, Tzili A1 - Müller-Röber, Bernd A1 - Zamir, Dani A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. T1 - Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato JF - The plant cell N2 - A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism. Y1 - 2015 U6 - https://doi.org/10.1105/tpc.114.132266 SN - 1040-4651 SN - 1532-298X VL - 27 IS - 3 SP - 485 EP - 512 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Knapp, Michael A1 - Lalueza-Fox, Carles A1 - Hofreiter, Michael T1 - Re-inventing ancient human DNA JF - Investigative Genetics N2 - For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next-or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research. KW - Archaic humans KW - Human evolution KW - Human population genomics KW - Next/second-generation sequencing Y1 - 2015 U6 - https://doi.org/10.1186/s13323-015-0020-4 SN - 2041-2223 VL - 6 PB - BioMed Central CY - London ER - TY - JOUR A1 - Gorochowski, Thomas E. A1 - Ignatova, Zoya A1 - Bovenberg, Roel A. L. A1 - Roubos, Johannes A. T1 - Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate JF - Nucleic acids research N2 - Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. Y1 - 2015 U6 - https://doi.org/10.1093/nar/gkv199 SN - 0305-1048 SN - 1362-4962 VL - 43 IS - 6 SP - 3022 EP - 3032 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Pechouskova, Eva A1 - Dammhahn, Melanie A1 - Brameier, Markus A1 - Fichtel, Claudia A1 - Kappeler, Peter M. A1 - Huchard, Elise T1 - MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener JF - Immunogenetics N2 - The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe's mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB. KW - Primates KW - Cheirogaleidae KW - Microcebus berthae KW - 454 pyrosequencing Y1 - 2015 U6 - https://doi.org/10.1007/s00251-015-0827-4 SN - 0093-7711 SN - 1432-1211 VL - 67 IS - 4 SP - 229 EP - 245 PB - Springer CY - New York ER - TY - JOUR A1 - Köslin-Findeklee, Fabian A1 - Rizi, Vajiheh Safavi A1 - Becker, Martin A. A1 - Parra-Londono, Sebastian A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Kunze, Reinhard A1 - Horst, Walter J. T1 - Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.) JF - Plant science : an international journal of experimental plant biology N2 - High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved. KW - Brassica napus KW - Genotypic differences KW - Leaf senescence KW - Molecular marker KW - N efficiency KW - Stay-green Y1 - 2015 U6 - https://doi.org/10.1016/j.plantsci.2014.11.018 SN - 0168-9452 VL - 233 SP - 174 EP - 185 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Alter, S. Elizabeth A1 - Meyer, Matthias A1 - Post, Klaas A1 - Czechowski, Paul A1 - Gravlund, Peter A1 - Gaines, Cork A1 - Rosenbaum, Howard C. A1 - Kaschner, Kristin A1 - Turvey, Samuel T. A1 - van der Plicht, Johannes A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100 JF - Molecular ecology N2 - Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range. KW - ancient DNA KW - climate change KW - last glacial maximum KW - marine mammal Y1 - 2015 U6 - https://doi.org/10.1111/mec.13121 SN - 0962-1083 SN - 1365-294X VL - 24 IS - 7 SP - 1510 EP - 1522 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Paul, Christiane A1 - Mamonekene, Victor A1 - Vater, Marianne A1 - Feulner, Philine G. D. A1 - Engelmann, Jacob A1 - Tiedemann, Ralph A1 - Kirschbaum, Frank T1 - Comparative histology of the adult electric organ among four species of the genus Campylomormyrus (Teleostei: Mormyridae) JF - Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology N2 - The electric organ (EO) of weakly electric mormyrids consists of flat, disk-shaped electrocytes with distinct anterior and posterior faces. There are multiple species-characteristic patterns in the geometry of the electrocytes and their innervation. To further correlate electric organ discharge (EOD) with EO anatomy, we examined four species of the mormyrid genus Campylomormyrus possessing clearly distinct EODs. In C. compressirostris, C. numenius, and C. tshokwe, all of which display biphasic EODs, the posterior face of the electrocytes forms evaginations merging to a stalk system receiving the innervation. In C. tamandua that emits a triphasic EOD, the small stalks of the electrocyte penetrate the electrocyte anteriorly before merging on the anterior side to receive the innervation. Additional differences in electrocyte anatomy among the former three species with the same EO geometry could be associated with further characteristics of their EODs. Furthermore, in C. numenius, ontogenetic changes in EO anatomy correlate with profound changes in the EOD. In the juvenile the anterior face of the electrocyte is smooth, whereas in the adult it exhibits pronounced surface foldings. This anatomical difference, together with disparities in the degree of stalk furcation, probably contributes to the about 12 times longer EOD in the adult. KW - Mormyridae KW - Campylomormyrus KW - Electric organ discharge KW - Electrocyte geometry KW - Electric organ ontogeny Y1 - 2015 U6 - https://doi.org/10.1007/s00359-015-0995-6 SN - 0340-7594 SN - 1432-1351 VL - 201 IS - 4 SP - 357 EP - 374 PB - Springer CY - New York ER - TY - JOUR A1 - Weithoff, Guntram A1 - Rocha, Marcia R. A1 - Gaedke, Ursula T1 - Comparing seasonal dynamics of functional and taxonomic diversity reveals the driving forces underlying phytoplankton community structure JF - Freshwater biology N2 - In most biodiversity studies, taxonomic diversity is the measure for the multiplicity of species and is often considered to represent functional diversity. However, trends in taxonomic diversity and functional diversity may differ, for example, when many functionally similar but taxonomically different species co-occur in a community. The differences between these diversity measures are of particular interest in diversity research for understanding diversity patterns and their underlying mechanisms. We analysed a temporally highly resolved 20-year time series of lake phytoplankton to determine whether taxonomic diversity and functional diversity exhibit similar or contrasting seasonal patterns. We also calculated the functional mean of the community in n-dimensional trait space for each sampling day to gain further insights into the seasonal dynamics of the functional properties of the community. We found an overall weak positive relationship between taxonomic diversity and functional diversity with a distinct seasonal pattern. The two diversity measures showed synchronous behaviour from early spring to mid-summer and a more complex and diverging relationship from autumn to late winter. The functional mean of the community exhibited a recurrent annual pattern with the most prominent changes before and after the clear-water phase. From late autumn to winter, the functional mean of the community and functional diversity were relatively constant while taxonomic diversity declined, suggesting competitive exclusion during this period. A further decline in taxonomic diversity concomitant with increasing functional diversity in late winter to early spring is seen as a result of niche diversification together with competitive exclusion. Under these conditions, several different sets of traits are suitable to thrive, but within one set of functional traits only one, or very few, morphotypes can persist. Taxonomic diversity alone is a weak descriptor of trait diversity in phytoplankton. However, the combined analysis of taxonomic diversity and functional diversity, along with the functional mean of the community, allows for deeper insights into temporal patterns of community assembly and niche diversification. KW - algae KW - biodiversity KW - functional traits KW - seasonality KW - time series Y1 - 2015 U6 - https://doi.org/10.1111/fwb.12527 SN - 0046-5070 SN - 1365-2427 VL - 60 IS - 4 SP - 758 EP - 767 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Cochard, Roland A1 - Edwards, Peter J. A1 - Weber, Ewald T1 - Post-ranching tree-grass interactions in secondary Acacia zanzibarica woodlands in coastal Tanzania - an experimental study JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Questions: We studied a humid savanna rangeland., abandoned in 2000, where intensive cattle grazing had led to widespread encroachment by Acacia zanzibarica. We asked whether the acacia trees were able to regenerate in the absence of domesJic livestock, either beneath acacia canopies or in artificial clearings. Location: Tropical coastal Tanzania (former Mkwaja Ranch, now in Saadani National Park). Methods: We set out a total of 48 plots on four sites in November 2001, and assigned them to three treatments: trees felled (FN), trees felled and the stumps poisoned (FP) with Triclopyr, and no intervention (controls, NN). We analysed soils of plots for texture and nutrients. In two wet (July 2002 and 2003) and one dry (February 2003) seasons we assessed grass and tree leaf biomass and transpiration rates, and counted acacia seedlings and resprouts. The effects of treatments (controlled for site and other co-variables) on grass growth and acacia rectaiitment were determined statistically using general linear models (GLM). Results: Acacia leaves had a much higher stomatal conductance than grasses, with the consequence that total evapotranspiration in woodland was higher than in clearings. In the wet seasons, grass biomass and seedling densities were significantly higher in clearings than in control plots, which we attributed to more.favourable moisture conditions, In the dry season, by contrast, we found no differences, and all seedlings had died. On FN plots, 71% of stumps, and on FP plots, 11% resprouted (coppicing), but only a quarter of these shoots survived until July 2003. Root suckering occurred spontaneously at low densities. No root suckers or resprouts grew beyond the grass layer. Conclusions: Acacia woodlands do not regenerate in the absence of cattle grazing, and tree cutting in combination with appropriate fire management could potentially accelerate re-establishment of open grassland. However, regeneration might occur in the future due to the increasing wildlife populations within the new national park. KW - Bush encroachment KW - Clearing formation KW - Grass flush KW - Savanna rangeland dynamics KW - Sprouting KW - Tree recruitment Y1 - 2015 U6 - https://doi.org/10.1111/avsc.12134 SN - 1402-2001 SN - 1654-109X VL - 18 IS - 2 SP - 297 EP - 310 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Contin, Andrea A1 - Frasca, Stefano A1 - Vivekananthan, Jeevanthi A1 - Leimkühler, Silke A1 - Wollenberger, Ursula A1 - Plumere, Nicolas A1 - Schuhmann, Wolfgang T1 - A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation. KW - pH responsive hydrogel KW - External stimuli KW - Biofuel cell KW - Self-powered biosensor KW - Solvation Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400621 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 4 SP - 938 EP - 944 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hönicke, Christiane A1 - Bliss, Peter A1 - Moritz, Robin F. A. T1 - Effect of density on traffic and velocity on trunk trails of Formica pratensis JF - The science of nature N2 - The allocation of large numbers of workers facilitates the swift intake of locally available resources which is essential for ant colony survival. To organise the traffic between nest and food source, the black-meadow ant Formica pratensis establishes permanent trunk trails, which are maintained by the ants. To unravel the ant organisation and potential traffic rules on these trails, we analysed velocity and lane segregation under various densities by experimentally changing feeding regimes. Even under the highest ant densities achieved, we never observed any traffic jams. On the contrary, velocity increased after supplementary feeding despite an enhanced density. Furthermore, inbound ants returning to the nest had a higher velocity than those leaving the colony. Whilst at low and medium density the ants used the centre of the trail, they used the full width of the trail at high density. Outbound ants also showed some degree of lane segregation which contributes to traffic organisation. KW - Density KW - Trunk trail KW - Traffic KW - Lateralization KW - Formica pratensis Y1 - 2015 U6 - https://doi.org/10.1007/s00114-015-1267-6 SN - 0028-1042 SN - 1432-1904 VL - 102 IS - 3-4 PB - Springer CY - Heidelberg ER - TY - CHAP A1 - Donohue, Patrick A1 - Smith, Mychal Daijon A1 - Bröker, Nina Kristin A1 - Doering, Carolin A1 - Mattos, Carla A1 - Barbirz, Stefanie T1 - Multiple Solvent Crystal Structures of phage P22 tailspike protein: An analysis of binding site hot spots and surface hydration T2 - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology Y1 - 2015 SN - 0892-6638 SN - 1530-6860 VL - 29 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Röthlein, Christoph A1 - Miettinen, Markus S. A1 - Ignatova, Zoya T1 - A flexible approach to assess fluorescence decay functions in complex energy transfer systems JF - BMC biophysics N2 - Background: Time-correlated Forster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions. Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems. Conclusion: This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems. KW - Time resolved FRET KW - Monte-Carlo simulations KW - Complex heterogeneous systems KW - Protein aggregation Y1 - 2015 U6 - https://doi.org/10.1186/s13628-015-0020-z SN - 2046-1682 VL - 8 PB - BioMed Central CY - London ER - TY - JOUR A1 - Schrapers, Peer A1 - Hartmann, Tobias A1 - Kositzki, Ramona A1 - Dau, Holger A1 - Reschke, Stefan A1 - Schulzke, Carola A1 - Leimkühler, Silke A1 - Haumann, Michael T1 - 'Sulfido and Cysteine Ligation Changes at the Molybdenum Cofactor during Substrate Conversion by Formate Dehydrogenase (FDH) from Rhodobacter capsulatus JF - Inorganic chemistry N2 - Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO-) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Moligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH. Y1 - 2015 U6 - https://doi.org/10.1021/ic502880y SN - 0020-1669 SN - 1520-510X VL - 54 IS - 7 SP - 3260 EP - 3271 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Zeng, Ting A1 - Pankratov, Dmitry A1 - Falk, Magnus A1 - Leimkühler, Silke A1 - Shleev, Sergey A1 - Wollenberger, Ursula T1 - Miniature direct electron transfer based sulphite/oxygen enzymatic fuel cells JF - Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics N2 - A direct electron transfer (DET) based sulphite/oxygen biofuel cell is reported that utilises human sulphite oxidase (hSOx) and Myrothecium verrucaria bilirubin oxidase (MvBOx) and nanostructured gold electrodes. For bioanode construction, the nanostructured gold microelectrodes were further modified with 3,3'-dithiodipropionic acid di(N-hydroxysuccinimide ester) to which polyethylene imine was covalently attached. hSOx was adsorbed onto this chemically modified nanostructured electrode with high surface loading of electroactive enzyme and in presence of sulphite high anodic bioelectrocatalytic currents were generated with an onset potential of 0.05 V vs. NHE. The biocathode contained MyBOx directly adsorbed to the deposited gold nanoparticles for cathodic oxygen reduction starting at 0.71 V vs. NHE. Both enzyme electrodes were integrated to a DET-type biofuel cell. Power densities of 8 and 1 mu W cm(-2) were achieved at 0.15 V and 0.45 V of cell voltages, respectively, with the membrane based biodevices under aerobic conditions. (C) 2014 Elsevier B.V. All rights reserved. KW - Enzymatic fuel cell KW - Microscale electrode KW - Direct electron transfer KW - Sulphite oxidase KW - Bilirubin oxidase Y1 - 2015 U6 - https://doi.org/10.1016/j.bios.2014.10.080 SN - 0956-5663 SN - 1873-4235 VL - 66 SP - 39 EP - 42 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, Pieter A1 - Brunet, Jörg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Graae, Bente Jessen A1 - Heinken, Thilo A1 - Kolb, Annette A1 - Lenoir, Jonathan A1 - Naaf, Tobias A1 - Plue, Jan A1 - Selvi, Federico A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Divergent regeneration responses of two closely related tree species to direct abiotic and indirect biotic effects of climate change JF - Forest ecology and management N2 - Changing temperature and precipitation can strongly influence plant reproduction. However, also biotic interactions might indirectly affect the reproduction and recruitment success of plants in the context of climate change. Information about the interactive effects of changes in abiotic and biotic factors is essential, but still largely lacking, to better understand the potential effects of a changing climate on plant populations. Here we analyze the regeneration from seeds of Acer platanoides and Acer pseudoplatanus, two currently secondary forest tree species from seven regions along a 2200 km-wide latitudinal gradient in Europe. We assessed the germination, seedling survival and growth during two years in a common garden experiment where temperature, precipitation and competition with the understory vegetation were manipulated. A. platanoides was more sensitive to changes in biotic conditions while A. pseudoplatanus was affected by both abiotic and biotic changes. In general, competition reduced (in A. platanoides) and warming enhanced (in A. pseudoplatanus) germination and survival, respectively. Reduced competition strongly increased the growth of A. platanoides seedlings. Seedling responses were independent of the conditions experienced by the mother tree during seed production and maturation. Our results indicate that, due to the negative effects of competition on the regeneration of A. platanoides, it is likely that under stronger competition (projected under future climatic conditions) this species will be negatively affected in terms of germination, survival and seedling biomass. Climate-change experiments including both abiotic and biotic factors constitute a key step forward to better understand the response of tree species' regeneration to climate change. (C) 2015 Elsevier B.V. All rights reserved. KW - Acer KW - Regeneration KW - Latitudinal gradient KW - Temperature KW - Precipitation KW - Competition Y1 - 2015 U6 - https://doi.org/10.1016/j.foreco.2015.01.003 SN - 0378-1127 SN - 1872-7042 VL - 342 SP - 21 EP - 29 PB - Elsevier CY - Amsterdam ER - TY - GEN A1 - Xiang, Hai A1 - Hofreiter, Michael A1 - Zhao, Xingbo T1 - Reply to Peng et al.: Archaeological contexts should not be ignored for early chicken domestication T2 - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2015 U6 - https://doi.org/10.1073/pnas.1502207112 SN - 0027-8424 VL - 112 IS - 16 SP - E1972 EP - E1973 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Reinhard, Sandy A1 - Renner, Sandra A1 - Kupfer, Alexander T1 - Age and fecundity in Salamandra algira (Caudata: Salamandridae) JF - Salamandra : German journal of herpetology N2 - Amphibians are characterised by potentially indefinite growth. Their body size reflects a trade-off between growth and reproduction. Consequently, growth decreases or even ceases after maturation. Furthermore, the sexes often mature at different ages (sexual bimaturity). We examined fecundity patterns of the terrestrial salamander Salamandra algira (Salamandridae) and tested if age, body size and the fecundity of both sexes are connected and how these reproductive traits interact. We revealed positive correlations for female size, age and fecundity traits, i.e., egg number and volume. The male number of testes lobes was also positively correlated with age. Our study provides basic data on a rarely studied terrestrial salamandrid. Further collection-based research is needed to obtain additional data aiding the understanding of life history evolution of the Salamandridae. KW - Fecundity KW - salamanders KW - Urodela KW - Salamandra KW - skeletochronology Y1 - 2015 SN - 0036-3375 VL - 51 IS - 1 SP - 19 EP - 24 PB - Deutsche Gesellschaft für Herpetologie und Terrarienkunde CY - Darmstadt ER - TY - JOUR A1 - Hüttl, Christine A1 - Hettrich, Cornelia A1 - Riedel, Melanie A1 - Henklein, Petra A1 - Rawel, Harshadrai Manilal A1 - Bier, Frank Fabian T1 - Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition JF - Chemical biology & drug design N2 - A straightforward synthesis strategy to multimerize a peptide mimotopes for antibody B13-DE1 recognition is described based on lysine dendrons as multivalent scaffolds. Lysine dendrons that possess N-terminal alkyne residues at the periphery were quantitative functionalized with azido peptides using click chemistry. The solid-phase peptide synthesis (SPPS) allows preparing the peptide dendron in high purity and establishing the possibility of automation. The presented peptide dendron is a promising candidate as multivalent ligand and was used for antibody B13-DE1 recognition. The binding affinity increases with higher dendron generation without loss of specificity. The analysis of biospecific interaction between the synthesized peptide dendron and the antibody was done via surface plasmon resonance (SPR) technique. The presented results show a promising tool for investigations of antigen-antibody reactions. KW - click chemistry KW - lysine dendron KW - peptide mimotopes KW - solid-phase peptide synthesis KW - surface plasmon resonance Y1 - 2015 U6 - https://doi.org/10.1111/cbdd.12444 SN - 1747-0277 SN - 1747-0285 VL - 85 IS - 5 SP - 565 EP - 573 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Liesenjohann, Thilo A1 - Liesenjohann, Monique A1 - Trebaticka, Lenka A1 - Sundell, Janne A1 - Haapakoski, Marko A1 - Ylonen, Hannu A1 - Eccard, Jana T1 - State-dependent foraging: lactating voles adjust their foraging behavior according to the presence of a potential nest predator and season JF - Behavioral ecology and sociobiology N2 - Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors "shrew presence" and "season." We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother's foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision. KW - Myodes glareolus KW - Optimal foraging KW - Sorex araneus KW - Nest protection KW - Seasonality KW - Interference Y1 - 2015 U6 - https://doi.org/10.1007/s00265-015-1889-x SN - 0340-5443 SN - 1432-0762 VL - 69 IS - 5 SP - 747 EP - 754 PB - Springer CY - New York ER - TY - JOUR A1 - Hu, Chenlin A1 - Völler, Ginka A1 - Sussmuth, Roderich A1 - Dittmann-Thünemann, Elke A1 - Kehr, Jan-Christoph T1 - Functional assessment of mycosporine-like amino acids in Microcystis aeruginosa strain PCC 7806 JF - Environmental microbiology N2 - The biological role of the widespread mycosporine-like amino acids (MAAs) in cyanobacteria is under debate. Here, we have constructed and characterized two mutants impaired in MAA biosynthesis in the bloom-forming cyanobacterium Microcystis aeruginosaPCC 7806. We could identify shinorine as the sole MAA type of the strain, which is exclusively located in the extracellular matrix. Bioinformatic studies as wells as polymerase chain reaction screening revealed that the ability to produce MAAs is sporadically distributed within the genus. Growth experiments and reactive oxygen species quantification with wild-type and mutant strains did not support a role of shinorine in protection against UV or other stress conditions in M.aeruginosaPCC 7806. The shinorine content per dry weight of cells as well as transcription of the mys gene cluster was not significantly elevated in response to UV-A, UV-B or any other stress condition tested. Remarkably, both mutants exhibited pronounced morphological changes compared with the wild type. We observed an increased accumulation and an enhanced hydrophobicity of the extracellular matrix. Our study suggests that MAAs in Microcystis play a negligible role in protection against UV radiation but might be a strain-specific trait involved in extracellular matrix formation and cell-cell interaction. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12577 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 5 SP - 1548 EP - 1559 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Meissner, Sven A1 - Steinhauser, Dirk A1 - Dittmann-Thünemann, Elke T1 - Metabolomic analysis indicates a pivotal role of the hepatotoxin microcystin in high light adaptation of Microcystis JF - Environmental microbiology N2 - Microcystis is a freshwater cyanobacterium frequently forming nuisance blooms in the summer months. The genus belongs to the predominant producers of the potent hepatotoxin microcystin. The success of Microcystis and its remarkable resistance to high light conditions are not well understood. Here, we have compared the metabolic response of Microcystis aeruginosaPCC7806, its microcystin-deficient mcyB mutant (Mut) and the cyanobacterial model organism SynechocystisPCC6803 to high light exposure of 250molphotonsm(-2)s(-1) using GC/MS-based metabolomics. Microcystis wild type and Mut show pronounced differences in their metabolic reprogramming upon high light. Seventeen percent of the detected metabolites showed significant differences between the two genotypes after high light exposure. Whereas the microcystin-producing wild type shows a faster accumulation of glycolate upon high light illumination, loss of microcystin leads to an accumulation of general stress markers such as trehalose and sucrose. The study further uncovers differences in the high light adaptation of the bloom-forming cyanobacterium Microcystis and the model cyanobacterium Synechocystis. Most notably, Microcystis invests more into carbon reserves such as glycogen after high light exposure. Our data shed new light on the lifestyle of bloom-forming cyanobacteria, the role of the widespread toxin microcystin and the metabolic diversity of cyanobacteria. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12565 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 5 SP - 1497 EP - 1509 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Choi, Young-Joon A1 - Klosterman, Steven J. A1 - Kummer, Volker A1 - Voglmayr, Hermann A1 - Shin, Hyeon-Dong A1 - Thines, Marco T1 - Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach JF - Molecular phylogenetics and evolution N2 - Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. (C) 2015 Elsevier Inc. All rights reserved. KW - Cospeciation KW - Host shift KW - Multi-locus phylogeny KW - Oomycetes KW - Peronospora farinosa KW - Species tree Y1 - 2015 U6 - https://doi.org/10.1016/j.ympev.2015.03.003 SN - 1055-7903 SN - 1095-9513 VL - 86 SP - 24 EP - 34 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Nikoloski, Zoran A1 - Stitt, Mark A1 - Kragler, Friedrich T1 - Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth JF - The plant journal N2 - Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge. KW - plant growth KW - hyponasty KW - 3D imaging KW - light-field camera KW - Arabidopsis thaliana KW - pgm KW - technical advance Y1 - 2015 U6 - https://doi.org/10.1111/tpj.12833 SN - 0960-7412 SN - 1365-313X VL - 82 IS - 4 SP - 693 EP - 706 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Venail, Patrick A1 - Gross, Kevin A1 - Oakley, Todd H. A1 - Narwani, Anita A1 - Allan, Eric A1 - Flombaum, Pedro A1 - Isbell, Forest A1 - Joshi, Jasmin Radha A1 - Reich, Peter B. A1 - Tilman, David A1 - van Ruijven, Jasper A1 - Cardinale, Bradley J. T1 - Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies JF - Functional ecology : an official journal of the British Ecological Society N2 - Hundreds of experiments have now manipulated species richness (SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above-ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. In contrast to the non-significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions. KW - biodiversity KW - community biomass KW - data synthesis KW - ecosystem functioning KW - grasslands KW - phylogenetic diversity KW - relatedness KW - stability Y1 - 2015 U6 - https://doi.org/10.1111/1365-2435.12432 SN - 0269-8463 SN - 1365-2435 VL - 29 IS - 5 SP - 615 EP - 626 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Omranian, Nooshin A1 - Kleessen, Sabrina A1 - Tohge, Takayuki A1 - Klie, Sebastian A1 - Basler, Georg A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Differential metabolic and coexpression networks of plant metabolism JF - Trends in plant science N2 - Recent analyses have demonstrated that plant metabolic networks do not differ in their structural properties and that genes involved in basic metabolic processes show smaller coexpression than genes involved in specialized metabolism. By contrast, our analysis reveals differences in the structure of plant metabolic networks and patterns of coexpression for genes in (non)specialized metabolism. Here we caution that conclusions concerning the organization of plant metabolism based on network-driven analyses strongly depend on the computational approaches used. KW - plant specialized metabolism KW - metabolic networks KW - gene coexpression KW - differential network analysis Y1 - 2015 U6 - https://doi.org/10.1016/j.tplants.2015.02.002 SN - 1360-1385 VL - 20 IS - 5 SP - 266 EP - 268 PB - Elsevier CY - London ER - TY - JOUR A1 - Wannicke, Nicola A1 - Frindte, Katharina A1 - Gust, Giselher A1 - Liskow, Iris A1 - Wacker, Alexander A1 - Meyer, Andreas A1 - Grossart, Hans-Peter T1 - Measuring bacterial activity and community composition at high hydrostatic pressure using a novel experimental approach: a pilot study JF - FEMS microbiology ecology N2 - In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 +/- 1.4 and 3.9 +/- 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 +/- 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 +/- 1.5 and 2.9 +/- 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump. KW - hydrostatic pressure KW - pressure chamber KW - piezophilic bacteria KW - deep-sea bacterial community KW - bacterial production KW - stable isotopes KW - membrane fatty acids Y1 - 2015 U6 - https://doi.org/10.1093/femsec/fiv036 SN - 0168-6496 SN - 1574-6941 VL - 91 IS - 5 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schwarzenberger, Anke A1 - Wacker, Alexander T1 - Melatonin synthesis follows a daily cycle in Daphnia JF - Journal of plankton research N2 - In freshwater systems, Daphnia has been demonstrated to show adaptive responses following the light-dark cycle. The adjustment of these responses to the change of day and night is probably transmitted via the hormone melatonin. The rate-limiting enzyme in melatonin synthesis is the arylalkylamine N-transferase (AANAT). We identified three genes coding for insect-like AANATs in Daphnia, of which we measured the gene expression in an ecologically relevant light-dark cycle. We demonstrated that Daphnia's insect-like AANAT gene expression oscillated in a daily manner, and that the highest peak of expression after the onset of darkness was followed by a peak of melatonin production at midnight. Moreover, we could show an oscillation of endogenous melatonin synthesis in Daphnia. In most organisms, melatonin synthesis is due to rhythmic expression of genes of the circadian clock, since transcription of aanats is directly linked to a circadian transcription factor. We could demonstrate that putative clock genes and insect-like AANAT genes of Daphnia were equally expressed. Therefore, we propose that melatonin synthesis is coupled to the expression of Daphnia clock genes, and that insect-like AANATs of crustaceans have a similar function as AANATs of vertebrates: The initiation of melatonin synthesis. In future studies with Daphnia, it will be necessary to take the time of day into account since melatonin concentrations might influence stress responses. KW - arylalkylamine N-transferase KW - insect-like AANAT KW - qPCR KW - circadian clock KW - clock genes Y1 - 2015 U6 - https://doi.org/10.1093/plankt/fbv029 SN - 0142-7873 SN - 1464-3774 VL - 37 IS - 3 SP - 636 EP - 644 PB - Oxford Univ. Press CY - Oxford ER - TY - CHAP A1 - Hofreiter, Michael A1 - Barlow, Axel A1 - Paijmans, Johanna L. A. A1 - Westbury, Michael V. T1 - Genomic analyses from highly degraded DNA T2 - Genome Y1 - 2015 SN - 0831-2796 SN - 1480-3321 VL - 58 IS - 5 SP - 228 EP - 228 PB - NRC Research Press CY - Ottawa ER - TY - JOUR A1 - Groeneveld, Jürgen A1 - Johst, Karin A1 - Kawaguchi, So A1 - Meyer, Bettina A1 - Teschke, Mathias A1 - Grimm, Volker T1 - How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - The Southern Ocean ecosystem is characterized by extreme seasonal changes in environmental factors such as day length, sea ice extent and food availability. The key species Antarctic krill (Euphausia superba) has evolved metabolic and behavioural seasonal rhythms to cope with these seasonal changes. We investigate the switch between a physiological less active and active period for adult krill, a rhythm which seems to be controlled by internal biological clocks. These biological clocks can be synchronized by environmental triggers such as day length and food availability. They have evolved for particular environmental regimes to synchronize predictable seasonal environmental changes with important life cycle functions of the species. In a changing environment the time when krill is metabolically active and the time of peak food availability may not overlap if krill's seasonal activity is solely determined by photoperiod (day length). This is especially true for the Atlantic sector of the Southern Ocean where the spatio-temporal ice cover dynamics are changing substantially with rising average temperatures. We developed an individual-based model for krill to explore the impact of photoperiod and food availability on the growth and demographics of krill. We simulated dynamics of local krill populations (with no movement of krill assumed) along a south-north gradient for different triggers of metabolic activity and different levels of food availability below the ice. We also observed the fate of larval krill which cannot switch to low metabolism and therefore are likely to overwinter under ice. Krill could only occupy the southern end of the gradient, where algae bloom only lasts for a short time, when alternative food supply under the ice was high and metabolic activity was triggered by photoperiod. The northern distribution was limited by lack of overwintering habitat for krill larvae due to short duration of sea ice cover even for high food content under the ice. The variability of the krill's length-frequency distributions varied for different triggers of metabolic activity, but did not depend on the sea ice extent. Our findings suggest a southward shift of krill populations due to reduction in the spatial sea ice extent, which is consistent with field observations. Overall, our results highlight the importance of the explicit consideration of spatio-temporal sea ice dynamics especially for larval krill together with temporal synchronization through internal clocks, triggered by environmental factors (photoperiod and food) in adult krill for the population modelling of krill. (C) 2015 Elsevier B.V. All rights reserved. KW - Dynamic energy budget theory KW - Individual based model KW - Southern Ocean KW - Sea ice KW - Climate change KW - Marine ecology Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.009 SN - 0304-3800 SN - 1872-7026 VL - 303 SP - 78 EP - 86 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Weiß, Lina A1 - Jeltsch, Florian T1 - The response of simulated grassland communities to the cessation of grazing JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Changes in land-use are supposed to be among the severest prospective threats to plant diversity worldwide. In semi-natural temperate grasslands, the cessation of traditional land use like livestock grazing is considered to be one of the most important drivers of the diversity loss witnessed within the last decades. Despite of the enormous number of studies on successional pathways following grazing abandonment there is no general pattern of how grassland communities are affected in terms of diversity, trait composition and pace of succession. To gain a comprehensive picture is difficult given the heterogeneity of environments and the time and effort needed for long-term investigations. We here use a proven individual- and trait-based grassland community model to analyze short- and long-term consequences of grazing abandonment under different assumptions of resource availability, pre-abandonment grazing intensity and regional isolation of communities. Grazing abandonment led to a decrease of plant functional type (PFT) diversity in all but two scenarios in the long-term. In short-term we also found an increase or no change in Shannon diversity for several scenarios. With grazing abandonment we overall found an increase in maximum plant mass, clonal integration and longer lateral spread, a decrease in rosette plant types and in stress tolerant plants, as well as an increase in grazing tolerant and a decrease in grazing avoiding plant types. Observed changes were highly dependent on the regional configuration of communities, prevalent resource conditions and land use intensity before abandonment. While long-term changes took around 10-20 years in resource rich conditions, new equilibria established in resource poor conditions only after 30-40 years. Our results confirm the potential threats caused by recent land-use changes and the assumption that oligotrophic communities are more resistant than mesotrophic communities also for long-term abandonment. Moreover, results revealed that species-rich systems are not per se more resistant than species-poor grasslands. (C) 2015 Elsevier B.V. All rights reserved. KW - Diversity KW - Individual-based model KW - Land use intensity KW - Seed immigration KW - Abandonment KW - Resistance Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.002 SN - 0304-3800 SN - 1872-7026 VL - 303 SP - 1 EP - 11 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Peng, Lei A1 - Utesch, Tillmann A1 - Yarman, Aysu A1 - Jeoung, Jae-Hun A1 - Steinborn, Silke A1 - Dobbek, Holger A1 - Mroginski, Maria Andrea A1 - Tanne, Johannes A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein JF - Chemistry - a European journal N2 - Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant k(s) values between 0.93 and 2.86 s(-1) and apparent formal potentials E-app(0)' between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH. KW - electrochemistry KW - electron transfer KW - heme proteins KW - molecular modeling KW - monolayers Y1 - 2015 U6 - https://doi.org/10.1002/chem.201405932 SN - 0947-6539 SN - 1521-3765 VL - 21 IS - 20 SP - 7596 EP - 7602 PB - Wiley-VCH CY - Weinheim ER - TY - GEN A1 - Xiang, Hai A1 - Gao, Jianqiang A1 - Yu, Baoquan A1 - Hofreiter, Michael A1 - Zhao, Xingbo T1 - Reply to Peters et al.: Further discussions confirm early Holocene chicken domestication in northern China T2 - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2015 U6 - https://doi.org/10.1073/pnas.1503956112 SN - 0027-8424 VL - 112 IS - 19 SP - E2416 EP - E2416 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Hess, Anne-Katrin A1 - Saffert, Paul A1 - Liebeton, Klaus A1 - Ignatova, Zoya T1 - Optimization of Translation Profiles Enhances Protein Expression and Solubility JF - PLoS one N2 - mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0127039 SN - 1932-6203 VL - 10 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Kanzleiter, Timo A1 - Jaehnert, Markus A1 - Schulze, Gunnar A1 - Selbig, Joachim A1 - Hallahan, Nicole A1 - Schwenk, Robert Wolfgang A1 - Schürmann, Annette T1 - Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice JF - American journal of physiology : Endocrinology and metabolism N2 - The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice (n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs (P < 0.05, meth diff >5%, coverage > 10) in their putative promoter regions. Alignment with gene expression data (n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors (Plexin A2) as well as genes that participate in muscle hypertrophy (Igfbp4) and motor neuron innervation (Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training. KW - DNA methylation KW - regular exercise training KW - muscle development Y1 - 2015 U6 - https://doi.org/10.1152/ajpendo.00289.2014 SN - 0193-1849 SN - 1522-1555 VL - 308 IS - 10 SP - E912 EP - E920 PB - American Chemical Society CY - Bethesda ER - TY - JOUR A1 - Synodinos, Alexios D. A1 - Tietjen, Britta A1 - Jeltsch, Florian T1 - Facilitation in drylands: Modeling a neglected driver of savanna dynamics JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Our current understanding regarding the functioning of the savanna ecosystem describes savannas as either competition- or disturbance-dependent. Within this generalized view, the role and importance of facilitation have been mostly neglected. This study presents a mathematical model of savannas with coupled soil moisture-vegetation dynamics, which includes interspecific competition and environmental disturbance. We find that there exist environmental and climatic conditions where grass facilitation toward trees plays an important role in supporting tree cover and by extension preserving the savanna biome. We, therefore, argue that our theoretical results in combination with the first empirical studies on the subject should stimulate further research into the role of facilitation in the savanna ecosystem, particularly when analyzing the impact of past and projected climatic changes on it. (C) 2015 Elsevier B.V. All rights reserved. KW - Ecohydrological modeling KW - ODE model KW - Coexistence KW - Biome shifts KW - Fire KW - Grazing Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.015 SN - 0304-3800 SN - 1872-7026 VL - 304 SP - 11 EP - 21 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Yokoyama, Kenichi A1 - Leimkühler, Silke T1 - The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria JF - Biochimica et biophysica acta : Molecular cell research N2 - The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved. KW - Molybdenum-iron-iron-sulfur cluster KW - Molybdenum cofactor KW - tRNA KW - Sulfur transfer KW - L-Cysteine desulfurase Y1 - 2015 U6 - https://doi.org/10.1016/j.bbamcr.2014.09.021 SN - 0167-4889 SN - 0006-3002 VL - 1853 IS - 6 SP - 1335 EP - 1349 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Ishida, Seiji A1 - Nozaki, Daiki A1 - Grossart, Hans-Peter A1 - Kagami, Maiko T1 - Novel basal, fungal lineages from freshwater phytoplankton and lake samples JF - Environmental microbiology reports N2 - Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems. Y1 - 2015 U6 - https://doi.org/10.1111/1758-2229.12268 SN - 1758-2229 VL - 7 IS - 3 SP - 435 EP - 441 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Di Giacomo, Adrian S. A1 - Di Giacomo, Alejandro G. A1 - Kliger, Rafi A1 - Reboreda, Juan C. A1 - Tiedemann, Ralph A1 - Mahler, Bettina T1 - No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed Tyrant Alectrurus risora, an endangered grassland species JF - Bird conservation international N2 - The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Ibera wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (Phi(ST) = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations. Y1 - 2015 U6 - https://doi.org/10.1017/S0959270914000203 SN - 0959-2709 SN - 1474-0001 VL - 25 IS - 2 SP - 127 EP - 138 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Seifert, Linda I. A1 - Weithoff, Guntram A1 - Vos, Matthijs T1 - Extreme heat changes post-heat wave community reassembly JF - Ecology and evolution N2 - Climate forecasts project further increases in extremely high-temperature events. These present threats to biodiversity, as they promote population declines and local species extinctions. This implies that ecological communities will need to rely more strongly on recovery processes, such as recolonization from a meta-community context. It is poorly understood how differences in extreme event intensity change the outcome of subsequent community reassembly and if such extremes modify the biotic environment in ways that would prevent the successful re-establishment of lost species. We studied replicated aquatic communities consisting of algae and herbivorous rotifers in a design that involved a control and two different heat wave intensity treatments (29 degrees C and 39 degrees C). Animal species that suffered heat-induced extinction were subsequently re-introduced at the same time and density, in each of the two treatments. The 39 degrees C treatment led to community closure in all replicates, meaning that a previously successful herbivore species could not re-establish itself in the postheat wave community. In contrast, such closure never occurred after a 29 degrees C event. Heat wave intensity determined the number of herbivore extinctions and strongly affected algal relative abundances. Re-introduced herbivore species were thus confronted with significantly different food environments. This ecological legacy generated by heat wave intensity led to differences in the failure or success of herbivore species re-introductions. Reassembly was significantly more variable, and hence less predictable, after an extreme heat wave, and was more canalized after a moderate one. Our results pertain to relatively simple communities, but they suggest that ecological legacies introduced by extremely high-temperature events may change subsequent ecological recovery and even prevent the successful re-establishment of lost species. Knowing the processes promoting and preventing ecological recovery is crucial to the success of species re-introduction programs and to our ability to restore ecosystems damaged by environmental extremes. KW - Biodiversity KW - climate change KW - conservation KW - ecological restoration KW - extinction KW - extreme temperature events KW - global warming KW - maximum temperature KW - variability Y1 - 2015 U6 - https://doi.org/10.1002/ece3.1490 SN - 2045-7758 VL - 5 IS - 11 SP - 2140 EP - 2148 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Thiele, Jan C. A1 - Grimm, Volker T1 - Replicating and breaking models: good for you and good for ecology JF - Oikos N2 - There are two major limitations to the potential of computational models in ecology for producing general insights: their design is path-dependent, reflecting different underlying questions, assumptions, and data, and there is too little robustness analysis exploring where the model mechanisms explaining certain observations break down. We here argue that both limitations could be overcome if modellers in ecology would more often replicate existing models, try to break the models, and explore modifications. Replication comprises the re-implementation of an existing model and the replication of its results. Breaking models means to identify under what conditions the mechanisms represented in a model can no longer explain observed phenomena. The benefits of replication include less effort being spent to enter the iterative stage of model development and having more time for systematic robustness analysis. A culture of replication would lead to increased credibility, coherence and efficiency of computational modelling and thereby facilitate theory development. Y1 - 2015 U6 - https://doi.org/10.1111/oik.02170 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 6 SP - 691 EP - 696 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Manning, Pete A1 - Gossner, Martin M. A1 - Bossdorf, Oliver A1 - Allan, Eric A1 - Zhang, Yuan-Ye A1 - Prati, Daniel A1 - Blüthgen, Nico A1 - Boch, Steffen A1 - Böhm, Stefan A1 - Börschig, Carmen A1 - Hölzel, Norbert A1 - Jung, Kirsten A1 - Klaus, Valentin H. A1 - Klein, Alexandra Maria A1 - Kleinebecker, Till A1 - Krauss, Jochen A1 - Lange, Markus A1 - Müller, Jörg A1 - Pasalic, Esther A1 - Socher, Stephanie A. A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Weiner, Christiane A1 - Werner, Michael A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Renner, Swen C. A1 - Wells, Konstans A1 - Buscot, Francois A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, Karl Eduard A1 - Weisser, Wolfgang W. A1 - Fischer, Markus T1 - Grassland management intensification weakens the associations among the diversities of multiple plant and animal taxa JF - Ecology : a publication of the Ecological Society of America N2 - Land-use intensification is a key driver of biodiversity change. However, little is known about how it alters relationships between the diversities of different taxonomic groups, which are often correlated due to shared environmental drivers and trophic interactions. Using data from 150 grassland sites, we examined how land-use intensification (increased fertilization, higher livestock densities, and increased mowing frequency) altered correlations between the species richness of 15 plant, invertebrate, and vertebrate taxa. We found that 54% of pairwise correlations between taxonomic groups were significant and positive among all grasslands, while only one was negative. Higher land-use intensity substantially weakened these correlations(35% decrease in rand 43% fewer significant pairwise correlations at high intensity), a pattern which may emerge as a result of biodiversity declines and the breakdown of specialized relationships in these conditions. Nevertheless, some groups (Coleoptera, Heteroptera, Hymenoptera and Orthoptera) were consistently correlated with multidiversity, an aggregate measure of total biodiversity comprised of the standardized diversities of multiple taxa, at both high and lowland-use intensity. The form of intensification was also important; increased fertilization and mowing frequency typically weakened plant-plant and plant-primary consumer correlations, whereas grazing intensification did not. This may reflect decreased habitat heterogeneity under mowing and fertilization and increased habitat heterogeneity under grazing. While these results urge caution in using certain taxonomic groups to monitor impacts of agricultural management on biodiversity, they also suggest that the diversities of some groups are reasonably robust indicators of total biodiversity across a range of conditions. KW - Biodiversity indicators KW - correlation KW - fertilization KW - grassland management KW - grazing KW - land-use change KW - land-use intensity KW - mowing KW - multidiversity KW - multitrophic interactions Y1 - 2015 U6 - https://doi.org/10.1890/14-1307.1 SN - 0012-9658 SN - 1939-9170 VL - 96 IS - 6 SP - 1492 EP - 1501 PB - Wiley CY - Washington ER - TY - JOUR A1 - Yildirim-Semerci, Cigdem A1 - Benayahu, Dafna A1 - Adamovski, Miriam A1 - Wollenberger, Ursula T1 - An Electrochemical Assay for Monitoring Differentiation of the Osteoblastic Cell Line (MBA-15) on the Sensor Chip JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - An electrochemical assay for the indication of the activity of the cell bound differentiation marker alkaline phosphatase (ALP) is proposed using voltammetry on an in-vitro cell culture. The basis of the assay is cultivation of cells on gold microelectrodes in wells of a microplate, catalytic hydrolysis of p-aminophenyl phosphate by ALP and indication of p-aminophenol oxidation by square wave voltammetry (SWV) with the sensors onto which the cells attached. The morphology of the bone marrow stromal cell line (MBA-15) on the electrode surface was investigated and it exhibited in vitro osteogenic characteristics. Since ALP is expressed on the cell surface in early differentiation stage of osteoblastic cells, its activity was followed after different culture times over a period of 144 h by recording repetitive voltammograms at different time points upon addition of the substrate p-aminophenyl phosphate. The ALP activity was estimated from the signal increase related to formation rate of p-aminophenol and the number of cells. The highest value was measured at 120 h, when the cells reached confluence. The results of the electrochemical activity assay are consistent with the colorimetric acquired value from p-nitrophenol formation rate. KW - Alkaline phosphatase KW - Osteoblast KW - Voltammetry KW - Biomarker KW - p-Aminophenol Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400684 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 6 SP - 1350 EP - 1358 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Gräf, Ralph A1 - Batsios, Petros A1 - Meyer, Irene T1 - Evolution of centrosomes and the nuclear lamina: Amoebozoan assets JF - European journal of cell biology N2 - The current eukaryotic tree of life groups most eukaryotes into one of five supergroups, the Opisthokonta, Amoebozoa, Archaeplastida, Excavata and SAR (Stramenopile, Alveolata, Rhizaria). Molecular and comparative morphological analyses revealed that the last eukaryotic common ancestor (LECA) already contained a rather sophisticated equipment of organelles including a mitochondrion, an endomembrane system, a nucleus with a lamina, a microtubule-organizing center (MTOC), and a flagellar apparatus. Recent studies of MTOCs, basal bodies/centrioles, and nuclear envelope organization of organisms in different supergroups have clarified our picture of how the nucleus and MTOCs co-evolved from LECA to extant eukaryotes. In this review we summarize these findings with special emphasis on valuable contributions of research on a lamin-like protein, nuclear envelope proteins, and the MTOC in the amoebozoan model organism Dictyostelium discoideum. (C) 2015 Elsevier GmbH. All rights reserved. KW - LINC complex KW - Sun1 KW - Nuclear lamina KW - Lamin KW - Nuclear envelope KW - Centrosome KW - Basal body KW - Centriole KW - LEM-domain Y1 - 2015 U6 - https://doi.org/10.1016/j.ejcb.2015.04.004 SN - 0171-9335 SN - 1618-1298 VL - 94 IS - 6 SP - 249 EP - 256 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Camargo, Rodolfo Gonzalez A1 - dos Reis Riccardi, Daniela Mendes A1 - Teixeira Ribeiro, Henrique Quintas A1 - Carnevali Junior, Luiz Carlos A1 - de Matos-Neto, Emidio Marques A1 - Enjiu, Lucas A1 - Neves, Rodrigo Xavier A1 - Carola Correia Lima, Joanna Darck A1 - Figueredo, Raquel Galvao A1 - Martins de Alcantara, Paulo Sergio A1 - Maximiano, Linda A1 - Otoch, Jose A1 - Batista Jr., Miguel Luiz A1 - Püschel, Gerhard Paul A1 - Seelaender, Marilia T1 - NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients JF - Nutrients N2 - Cancer cachexia, of which the most notable symptom is severe and rapid weight loss, is present in the majority of patients with advanced cancer. Inflammatory mediators play an important role in the development of cachexia, envisaged as a chronic inflammatory syndrome. The white adipose tissue (WAT) is one of the first compartments affected in cancer cachexia and suffers a high rate of lipolysis. It secretes several cytokines capable of directly regulating intermediate metabolism. A common pathway in the regulation of the expression of pro-inflammatory cytokines in WAT is the activation of the nuclear transcription factor kappa-B (NF-B). We have examined the gene expression of the subunits NF-Bp65 and NF-Bp50, as well as NF-Bp65 and NF-Bp50 binding, the gene expression of pro-inflammatory mediators under NF-B control (IL-1, IL-6, INF-, TNF-, MCP-1), and its inhibitory protein, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IB-). The observational study involved 35 patients (control group, n = 12 and cancer group, n = 23, further divided into cachectic and non-cachectic). NF-Bp65 and its target genes expression (TNF-, IL-1, MCP-1 and IB-) were significantly higher in cachectic cancer patients. Moreover, NF-Bp65 gene expression correlated positively with the expression of its target genes. The results strongly suggest that the NF-B pathway plays a role in the promotion of WAT inflammation during cachexia. KW - cancer cachexia KW - inflammation KW - white adipose tissue KW - NF-B KW - IB Y1 - 2015 U6 - https://doi.org/10.3390/nu7064465 SN - 2072-6643 VL - 7 IS - 6 SP - 4465 EP - 4479 PB - MDPI CY - Basel ER - TY - CHAP A1 - Hanke-Gogokhia, Christin A1 - Frederick, Jeanne M. A1 - Zhang, Houbin A1 - Baehr, Wolfgang T1 - ARL3 regulates transport of prenylated and acylated proteins to photoreceptor outer segment in mouse retina T2 - Investigative ophthalmology & visual science Y1 - 2015 SN - 0146-0404 SN - 1552-5783 VL - 56 IS - 7 PB - Association for Research in Vision and Opthalmology CY - Rockville ER - TY - JOUR A1 - Adamla, Frauke A1 - Ignatova, Zoya T1 - Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans JF - Scientific reports N2 - Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process. Y1 - 2015 U6 - https://doi.org/10.1038/srep10692 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Tedder, Andrew A1 - Carleial, Samuel A1 - Golebiewska, Martyna A1 - Kappel, Christian A1 - Shimizu, Kentaro K. A1 - Stift, Marc T1 - Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae) JF - PLoS one N2 - Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0126618 SN - 1932-6203 VL - 10 IS - 6 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Allhoff, Korinna Theresa A1 - Ritterskamp, Daniel A1 - Rall, Björn C. A1 - Drossel, Barbara A1 - Guill, Christian T1 - Evolutionary food web model based on body masses gives realistic networks with permanent species turnover JF - Scientific reports N2 - The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50% of the network are not observed. Y1 - 2015 U6 - https://doi.org/10.1038/srep10955 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Pinhasi, Ron A1 - Fernandes, Daniel A1 - Sirak, Kendra A1 - Novak, Mario A1 - Connell, Sarah A1 - Alpaslan-Roodenberg, Songul A1 - Gerritsen, Fokke A1 - Moiseyev, Vyacheslav A1 - Gromov, Andrey A1 - Raczky, Pal A1 - Anders, Alexandra A1 - Pietrusewsky, Michael A1 - Rollefson, Gary A1 - Jovanovic, Marija A1 - Trinhhoang, Hiep A1 - Bar-Oz, Guy A1 - Oxenham, Marc A1 - Matsumura, Hirofumi A1 - Hofreiter, Michael T1 - Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone JF - PLoS one N2 - The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0129102 SN - 1932-6203 VL - 10 IS - 6 PB - PLoS CY - San Fransisco ER -