@article{TenenboimSmirnovaWillmitzeretal.2014, author = {Tenenboim, Hezi and Smirnova, Julia and Willmitzer, Lothar and Steup, Martin and Brotman, Yariv}, title = {VMP1-deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesies}, series = {BMC plant biology}, volume = {14}, journal = {BMC plant biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2229}, doi = {10.1186/1471-2229-14-121}, pages = {13}, year = {2014}, abstract = {Background: The versatile Vacuole Membrane Protein 1 (VMP1) has been previously investigated in six species. It has been shown to be essential in macroautophagy, where it takes part in autophagy initiation. In addition, VMP1 has been implicated in organellar biogenesis; endo-, exo- and phagocytosis, and protein secretion; apoptosis; and cell adhesion. These roles underly its proven involvement in pancreatitis, diabetes and cancer in humans. Results: In this study we analyzed a VMP1 homologue from the green alga Chlamydomonas reinhardtii. CrVMP1 knockdown lines showed severe phenotypes, mainly affecting cell division as well as the morphology of cells and organelles. We also provide several pieces of evidence for its involvement in macroautophagy.}, language = {en} } @article{EccardLiesenjohann2014, author = {Eccard, Jana and Liesenjohann, Thilo}, title = {The importance of predation risk and missed opportunity costs for context-dependent foraging patterns}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0094107}, pages = {5}, year = {2014}, abstract = {Correct assessment of risks and costs of foraging is vital for the fitness of foragers. Foragers should avoid predation risk and balance missed opportunities. In risk-heterogeneous landscapes animals prefer safer locations over riskier, constituting a landscape of fear. Risk-uniform landscapes do not offer this choice, all locations are equally risky. Here we investigate the effects of predation risk in patches, travelling risk between patches, and missed social opportunities on foraging decisions in risk-uniform and risk-heterogeous landscapes. We investigated patch leaving decisions of 20 common voles (M. arvalis) in three experimental landscapes: safe risk-uniform, risky risk-uniform and risk-heterogeneous. We varied both the predation risk level and the predation risk distribution between two patches experimentally and in steps, assuming that our manipulation consequently yield different distributions and levels of risk while foraging, risk while travelling, and costs of missed, social opportunities (MSOCs). We measured mean GUDs (giving-up density of food left in the patch) for both patches as a measure of foraging gain, and delta GUD, the differences among patches, as a measure of the spatial distribution of foraging effort over a period of six hours. Distribution of foraging effort was most even in the safe risk-uniform landscapes and least even in the risk-heterogeneous landscape, with risky risk-uniform landscapes in between. Foraging gain was higher in the safe than in the two riskier landscapes (both uniform and heterogeneous). Results supported predictions for the effects of risk in foraging patches and while travelling between patches, however predictions for the effects of missed social opportunities were not met in this short term experiment. Thus, both travelling and foraging risk contribute to distinct patterns observable high risk, risk-uniform landscapes.}, language = {en} } @article{HuynenSuzukiOguraetal.2014, author = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)}, series = {BMC evolutionary biology}, volume = {14}, journal = {BMC evolutionary biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/1471-2148-14-75}, pages = {8}, year = {2014}, abstract = {Background: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.}, language = {en} } @article{GrimmAugusiakFocksetal.2014, author = {Grimm, Volker and Augusiak, Jacqueline and Focks, Andreas and Frank, Beatrice M. and Gabsi, Faten and Johnston, Alice S. A. and Liu, Chun and Martin, Benjamin T. and Meli, Mattia and Radchuk, Viktoriia and Thorbek, Pernille and Railsback, Steven Floyd}, title = {Towards better modelling and decision support: Documenting model development, testing, and analysis using TRACE}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2014.01.018}, pages = {129 -- 139}, year = {2014}, abstract = {The potential of ecological models for supporting environmental decision making is increasingly acknowledged. However, it often remains unclear whether a model is realistic and reliable enough. Good practice for developing and testing ecological models has not yet been established. Therefore, TRACE, a general framework for documenting a model's rationale, design, and testing was recently suggested. Originally TRACE was aimed at documenting good modelling practice. However, the word 'documentation' does not convey TRACE's urgency. Therefore, we re-define TRACE as a tool for planning, performing, and documenting good modelling practice. TRACE documents should provide convincing evidence that a model was thoughtfully designed, correctly implemented, thoroughly tested, well understood, and appropriately used for its intended purpose. TRACE documents link the science underlying a model to its application, thereby also linking modellers and model users, for example stakeholders, decision makers, and developers of policies. We report on first experiences in producing TRACE documents. We found that the original idea underlying TRACE was valid, but to make its use more coherent and efficient, an update of its structure and more specific guidance for its use are needed. The updated TRACE format follows the recently developed framework of model 'evaludation': the entire process of establishing model quality and credibility throughout all stages of model development, analysis, and application. TRACE thus becomes a tool for planning, documenting, and assessing model evaludation, which includes understanding the rationale behind a model and its envisaged use. We introduce the new structure and revised terminology of TRACE and provide examples. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{MeliPalmqvistForbesetal.2014, author = {Meli, Mattia and Palmqvist, Annemette and Forbes, Valery E. and Groeneveld, J{\"u}rgen and Grimm, Volker}, title = {Two pairs of eyes are better than one: Combining individual-based and matrix models for ecological risk assessment of chemicals}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.07.027}, pages = {40 -- 52}, year = {2014}, abstract = {Current chemical risk assessment procedures may result in imprecise estimates of risk due to sometimes arbitrary simplifying assumptions. As a way to incorporate ecological complexity and improve risk estimates, mechanistic effect models have been recommended. However, effect modeling has not yet been extensively used for regulatory purposes, one of the main reasons being uncertainty about which model type to use to answer specific regulatory questions. We took an individual-based model (IBM), which was developed for risk assessment of soil invertebrates and includes avoidance of highly contaminated areas, and contrasted it with a simpler, more standardized model, based on the generic metapopulation matrix model RAMAS. In the latter the individuals within a sub-population are not treated as separate entities anymore and the spatial resolution is lower. We explored consequences of model aggregation in terms of assessing population-level effects for different spatial distributions of a toxic chemical. For homogeneous contamination of the soil, we found good agreement between the two models, whereas for heterogeneous contamination, at different concentrations and percentages of contaminated area, RAMAS results were alternatively similar to IBM results with and without avoidance, and different food levels. This inconsistency is explained on the basis of behavioral responses that are included in the IBM but not in RAMAS. Overall, RAMAS was less sensitive than the IBM in detecting population-level effects of different spatial patterns of exposure. We conclude that choosing the right model type for risk assessment of chemicals depends on whether or not population-level effects of small-scale heterogeneity in exposure need to be detected. We recommend that if in doubt, both model types should be used and compared. Describing both models following the same standard format, the ODD protocol, makes them equally transparent and understandable. The simpler model helps to build up trust for the more complex model and can be used for more homogeneous exposure patterns. The more complex model helps detecting and understanding the limitations of the simpler model and is needed to ensure ecological realism for more complex exposure scenarios. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @article{GabsiHammersWirtzGrimmetal.2014, author = {Gabsi, Faten and Hammers-Wirtz, Monika and Grimm, Volker and Schaeffer, Andreas and Preuss, Thomas G.}, title = {Coupling different mechanistic effect models for capturing individual- and population-level effects of chemicals: Lessons from a case where standard risk assessment failed}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.06.018}, pages = {18 -- 29}, year = {2014}, abstract = {Current environmental risk assessment (ERA) of chemicals for aquatic invertebrates relies on standardized laboratory tests in which toxicity effects on individual survival, growth and reproduction are measured. Such tests determine the threshold concentration of a chemical below which no population-level effects are expected. How well this procedure captures effects on individuals and populations, however, remains an open question. Here we used mechanistic effect models, combining individual-level reproduction and survival models with an individual-based population model (IBM), to understand the individuals' responses and extrapolate them to the population level. We used a toxicant (Dispersogen A) for which adverse effects on laboratory populations were detected at the determined threshold concentration and thus challenged the conservatism of the current risk assessment method. Multiple toxicity effects on reproduction and survival were reported, in addition to effects on the F1 generation. We extrapolated commonly tested individual toxicity endpoints, reproduction and survival, to the population level using the IBM. Effects on reproduction were described via regression models. To select the most appropriate survival model, the IBM was run assuming either stochastic death (SD) or individual tolerance (IT). Simulations were run for different scenarios regarding the toxicant's effects: survival toxicity, reproductive toxicity, or survival and reproductive toxicity. As population-level endpoints, we used population size and structure and extinction risk. We found that survival represented as SD explained population dynamics better than IT. Integrating toxicity effects on both reproduction and survival yielded more accurate predictions of population effects than considering isolated effects. To fully capture population effects observed at high toxicant concentrations, toxicity effects transmitted to the F1 generation had to be integrated. Predicted extinction risk was highly sensitive to the assumptions about individual-level effects. Our results demonstrate that the endpoints used in current standard tests may not be sufficient for assessing the risk of adverse effects on populations. A combination of laboratory population experiments with mechanistic effect models is a powerful tool to better understand and predict effects on both individuals and populations. Mechanistic effect modelling thus holds great potential to improve the accuracy of ERA of chemicals in the future. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{ThammScheiner2014, author = {Thamm, Markus and Scheiner, Ricarda}, title = {PKG in honey bees: spatial expression, amfor gene expression, sucrose responsiveness, and division of labor}, series = {The journal of comparative neurology}, volume = {522}, journal = {The journal of comparative neurology}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0021-9967}, doi = {10.1002/cne.23500}, pages = {1786 -- 1799}, year = {2014}, abstract = {Division of labor is a hallmark of social insects. In honey bees, division of labor involves transition of female workers from one task to the next. The most distinct tasks are nursing (providing food for the brood) and foraging (collecting pollen and nectar). The brain mechanisms regulating this form of behavioral plasticity have largely remained elusive. Recently, it was suggested that division of labor is based on nutrition-associated signaling pathways. One highly conserved gene associated with food-related behavior across species is the foraging gene, which encodes a cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG). Our analysis of this gene reveals the presence of alternative splicing in the honey bee. One isoform is expressed in the brain. Expression of this isoform is most pronounced in the mushroom bodies, the subesophageal ganglion, and the corpora allata. Division of labor and sucrose responsiveness in honey bees correlate significantly with foraging gene expression in distinct brain regions. Activating PKG selectively increases sucrose responsiveness in nurse bees to the level of foragers, whereas the same treatment does not affect responsiveness to light. These findings demonstrate a direct link between PKG signaling in distinct brain areas and division of labor. Furthermore, they demonstrate that the difference in sensory responsiveness between nurse bees and foragers can be compensated for by activating PKG. Our findings on the function of PKG in regulating specific sensory responsiveness and social organization offer valuable indications for the function of the cGMP/PKG pathway in many other insects and vertebrates. J. Comp. Neurol. 522:1786-1799, 2014. (c) 2013 Wiley Periodicals, Inc.}, language = {en} } @article{SchatzOhlendorfBusseetal.2014, author = {Schatz, J. and Ohlendorf, B. and Busse, P. and Pelz, G. and Dolch, D. and Teubner, J. and Encarnacao, Jorge A. and Muehle, Ralf -Udo and Fischer, M. and Hoffmann, B. and Kwasnitschka, L. and Balkema-Buschmann, Anne and Mettenleiter, Thomas Christoph and Mueller, T. and Freuling, C. M.}, title = {Twenty years of active bat rabies surveillance in Germany}, series = {Epidemiology and infection}, volume = {142}, journal = {Epidemiology and infection}, number = {6}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0950-2688}, doi = {10.1017/S0950268813002185}, pages = {1155 -- 1166}, year = {2014}, abstract = {In Germany, active bat rabies surveillance was conducted between 1993 and 2012. A total of 4546 oropharyngeal swab samples from 18 bat species were screened for the presence of EBLV-1- , EBLV-2- and BBLV-specific RNA. Overall, 0 center dot 15\% of oropharyngeal swab samples tested EBLV-1 positive, with the majority originating from Eptesicus serotinus. Interestingly, out of seven RT-PCR-positive oropharyngeal swabs subjected to virus isolation, viable virus was isolated from a single serotine bat (E. serotinus). Additionally, about 1226 blood samples were tested serologically, and varying virus neutralizing antibody titres were found in at least eight different bat species. The detection of viral RNA and seroconversion in repeatedly sampled serotine bats indicates long-term circulation of the virus in a particular bat colony. The limitations of random-based active bat rabies surveillance over passive bat rabies surveillance and its possible application of targeted approaches for future research activities on bat lyssavirus dynamics and maintenance are discussed.}, language = {en} } @article{HagenMattayRaeuberetal.2014, author = {Hagen, Sven and Mattay, Dinah and Raeuber, Christina and Mueller, Kristian M. and Arndt, Katja Maren}, title = {Characterization and inhibition of AF10-mediated interaction}, series = {Journal of peptide science}, volume = {20}, journal = {Journal of peptide science}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1075-2617}, doi = {10.1002/psc.2626}, pages = {385 -- 397}, year = {2014}, abstract = {The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics. Copyright (c) 2014 European Peptide Society and John Wiley \& Sons, Ltd.}, language = {en} } @article{DolgenerFreudenbergerSchneeweissetal.2014, author = {Dolgener, Nicola and Freudenberger, L. and Schneeweiss, N. and Ibisch, P. L. and Tiedemann, Ralph}, title = {Projecting current and potential future distribution of the Fire-bellied toad Bombina bombina under climate change in north-eastern Germany}, series = {Regional environmental change}, volume = {14}, journal = {Regional environmental change}, number = {3}, publisher = {Springer}, address = {Heidelberg}, issn = {1436-3798}, doi = {10.1007/s10113-013-0468-9}, pages = {1063 -- 1072}, year = {2014}, abstract = {Environmental change is likely to have a strong impact on biodiversity, and many species may shift their distribution in response. In this study, we aimed at projecting the availability of suitable habitat for an endangered amphibian species, the Fire-bellied toad Bombina bombina, in Brandenburg (north-eastern Germany). We modelled a potential habitat distribution map based on (1) a database with 10,581 presence records for Bombina from the years 1990 to 2009, (2) current estimates for ecogeographical variables (EGVs) and (3) the future projection of these EGVs according to the statistical regional model, respectively, the soil and water integrated model, applying the maximum entropy approach (Maxent). By comparing current and potential future distributions, we evaluated the projected change in distribution of suitable habitats and identified the environmental variables most associated with habitat suitability that turned out to be climatic variables related to the hydrological cycle. Under the applied scenario, our results indicate increasing habitat suitability in many areas and an extended range of suitable habitats. However, even if the environmental conditions in Brandenburg may change as predicted, it is questionable whether the Fire-bellied toad will truly benefit, as dispersal abilities of amphibian species are limited and strongly influenced by anthropogenic disturbances, that is, intensive agriculture, habitat destruction and fragmentation. Furthermore, agronomic pressure is likely to increase on productive areas with fertile soils and high water retention capacities, indeed those areas suitable for B. bombina. All these changes may affect temporary pond hydrology as well as the reproductive success and breeding phenology of toads.}, language = {en} } @article{LischkeHiltJanseetal.2014, author = {Lischke, Betty and Hilt, Sabine and Janse, Jan H. and Kuiper, Jan J. and Mehner, Thomas and Mooij, Wolf M. and Gaedke, Ursula}, title = {Enhanced input of terrestrial particulate organic matter reduces the resilience of the clear-water state of shallow lakes: A model study}, series = {Ecosystems}, volume = {17}, journal = {Ecosystems}, number = {4}, publisher = {Springer}, address = {New York}, issn = {1432-9840}, doi = {10.1007/s10021-014-9747-7}, pages = {616 -- 626}, year = {2014}, abstract = {The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent.}, language = {en} } @article{KuekenshoenerWohlwendNiemoelleretal.2014, author = {Kuekenshoener, Tim and Wohlwend, Daniel and Niemoeller, Christoph and Dondapati, Padmarupa and Speck, Janina and Adeniran, Adebola V. and Nieth, Anita and Gerhardt, Stefan and Einsle, Oliver and Mueller, Kristian M. and Arndt, Katja Maren}, title = {Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system}, series = {Journal of structural biology}, volume = {186}, journal = {Journal of structural biology}, number = {3}, publisher = {Elsevier}, address = {San Diego}, issn = {1047-8477}, doi = {10.1016/j.jsb.2014.03.002}, pages = {335 -- 348}, year = {2014}, abstract = {The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of alpha-helix encoding sequences was designed and selected for interference with the coiled coil domain (CC) of a melanoma-associated basic-helix-loop-helix-leucine-zipper (bHLHLZ) protein, the microphthalmia associated transcription factor (MITF). One predominant sequence (iM10) was enriched during selection and showed remarkable protease resistance, high solubility and thermal stability while maintaining its specificity. Furthermore, it exhibited nanomolar range affinity towards the target peptide. A mutation screen indicated that target-binding helices of increased homodimer stability and improved expression rates were preferred in the selection process. The crystal structure of the iM10/MITF-CC heterodimer (2.1 angstrom) provided important structural insights and validated our design predictions. Importantly, iM10 did not only bind to the MITF coiled coil, but also to the markedly more stable HLHLZ domain of MITF. Characterizing the selected variants of the semi-rational library demonstrated the potential of the innovative bacterial selection approach. (C) 2014 Elsevier Inc. All rights reserved.}, language = {en} } @article{KlieNikoloskiSelbig2014, author = {Klie, Sebastian and Nikoloski, Zoran and Selbig, Joachim}, title = {Biological cluster evaluation for gene function prediction}, series = {Journal of computational biology}, volume = {21}, journal = {Journal of computational biology}, number = {6}, publisher = {Liebert}, address = {New Rochelle}, issn = {1066-5277}, doi = {10.1089/cmb.2009.0129}, pages = {428 -- 445}, year = {2014}, abstract = {Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set.}, language = {en} } @article{OmidbakhshfardWinckArvidssonetal.2014, author = {Omidbakhshfard, Mohammad Amin and Winck, Flavia Vischi and Arvidsson, Samuel Janne and Riano-Pachon, Diego M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana}, series = {Journal of integrative plant biology}, volume = {56}, journal = {Journal of integrative plant biology}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1672-9072}, doi = {10.1111/jipb.12151}, pages = {527 -- 538}, year = {2014}, abstract = {The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.}, language = {en} } @article{WimmelbacherBoernke2014, author = {Wimmelbacher, Matthias and B{\"o}rnke, Frederik}, title = {Redox activity of thioredoxin z and fructokinase-like protein 1 is dispensable for autotrophic growth of Arabidopsis thaliana}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru122}, pages = {2405 -- 2413}, year = {2014}, abstract = {Redox modulation of protein activity by thioredoxins (TRXs) plays a key role in cellular regulation. Thioredoxin z (TRX z) and its interaction partner fructokinase-like protein 1 (FLN1) represent subunits of the plastid-encoded RNA polymerase (PEP), suggesting a role of both proteins in redox regulation of chloroplast gene expression. Loss of TRX z or FLN1 expression generates a PEP-deficient phenotype and renders the plants incapable to grow autotrophically. This study shows that PEP function in trx z and fln1 plants can be restored by complementation with redox-inactive TRX z C106S and FLN1 C(105/106)A protein variants, respectively. The complemented plants showed wild-type levels of chloroplast gene expression and were restored in photosynthetic capacity, indicating that redox regulation of PEP through TRX z/FLN1 per se is not essential for autotrophic growth. Promoter-reporter gene studies indicate that TRX z and FLN1 are expressed during early phases of leaf development while expression ceases at maturation. Taken together, our data support a model in which TRX z and FLN1 are essential structural components of the PEP complex and their redox activity might only play a role in the fine tuning of PEP function.}, language = {en} } @article{MareljaDambowskyBolisetal.2014, author = {Marelja, Zvonimir and Dambowsky, Miriam and Bolis, Marco and Georgiou, Marina L. and Garattini, Enrico and Missirlis, Fanis and Leimk{\"u}hler, Silke}, title = {The four aldehyde oxidases of Drosophila melanogaster have different gene expression patterns and enzyme substrate specificities}, series = {The journal of experimental biology}, volume = {217}, journal = {The journal of experimental biology}, number = {12}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0022-0949}, doi = {10.1242/jeb.102129}, pages = {2201 -- 2211}, year = {2014}, abstract = {In the genome of Drosophila melanogaster, four genes coding for aldehyde oxidases (AOX1-4) were identified on chromosome 3. Phylogenetic analysis showed that the AOX gene cluster evolved via independent duplication events in the vertebrate and invertebrate lineages. The functional role and the substrate specificity of the distinct Drosophila AOX enzymes is unknown. Two loss-of-function mutant alleles in this gene region, low pyridoxal oxidase (Po-lpo) and aldehyde oxidase-1 (Aldox-1(n1)) are associated with a phenotype characterized by undetectable AOX enzymatic activity. However, the genes involved and the corresponding mutations have not yet been identified. In this study we characterized the activities, substrate specificities and expression profiles of the four AOX enzymes in D. melanogaster. We show that the Po-lpo-associated phenotype is the consequence of a structural alteration of the AOX1 gene. We identified an 11-bp deletion in the Po-lpo allele, resulting in a frame-shift event, which removes the molybdenum cofactor domain of the encoded enzyme. Furthermore, we show that AOX2 activity is detectable only during metamorphosis and characterize a Minos-AOX2 insertion in this developmental gene that disrupts its activity. We demonstrate that the Aldox-1(n1) phenotype maps to the AOX3 gene and AOX4 activity is not detectable in our assays.}, language = {en} } @article{DevosGraefField2014, author = {Devos, Damien P. and Gr{\"a}f, Ralph and Field, Mark C.}, title = {Evolution of the nucleus}, series = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, volume = {28}, journal = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, publisher = {Elsevier}, address = {London}, issn = {0955-0674}, doi = {10.1016/j.ceb.2014.01.004}, pages = {8 -- 15}, year = {2014}, abstract = {The nucleus represents a major evolutionary transition. As a consequence of separating translation from transcription many new functions arose, which likely contributed to the remarkable success of eukaryotic cells. Here we will consider what has recently emerged on the evolutionary histories of several key aspects of nuclear biology; the nuclear pore complex, the lamina, centrosomes and evidence for prokaryotic origins of relevant players.}, language = {en} } @article{KelmLenskiKelmetal.2014, author = {Kelm, Detlev H. and Lenski, Johannes and Kelm, Volker and Toelch, Ulf and Dziock, Frank}, title = {Seasonal bat activity in relation to distance to hedgerows in an agricultural landscape in central Europe and implications for wind energy development}, series = {Acta chiropterologica : international journal of bat biology}, volume = {16}, journal = {Acta chiropterologica : international journal of bat biology}, number = {1}, publisher = {Museum and Institute of Zoology, Polish Academy of Sciences}, address = {Warsaw}, issn = {1508-1109}, doi = {10.3161/150811014X683273}, pages = {65 -- 73}, year = {2014}, abstract = {Bat activity is often concentrated near linear and edge landscape structures such as hedgerows, but information about seasonal and species-specific bat activity near hedges is scarce despite their abundance in the cultural landscapes of central Europe. Exact knowledge on animals' habitat use, however, is key to effective landscape planning to avoid human-wildlife-conflicts, such as the construction of wind turbines in areas with high bat activity that may result in bat fatalities. We measured bat activity in relation to distance to hedgerows in an agricultural landscape in northeastern Germany. We recorded bat echolocation calls at ground level at 0, 50, 100 and 200 m distances from hedges at five sites during three nights in spring (April to June) and three nights in summer (July to October) at each site. For all bat species we found the overall activity to be similar between seasons, with the highest activity near the hedges, but with considerable variation in species-specific spatial activity patterns between spring and summer. While the genus Myotis and Pipistrellus pipistrellus were mostly active close to the hedges at a similar intensity over the entire study period (i.e. 84\% and 86\% of all bat passes, respectively), Nyctalus noctula and Pipistrellus nathusii showed generally less pronounced concentration of activity near the hedges, and increased activity away from the hedges in summer. Similarly, Pipistrellus pygmaeus showed decreased activity away from the hedges during both seasons, but with reduced activity near the hedges in summer. The observed behavioural changes in activity in relation to distance to hedgerows are likely due to migration or the bats foraging for different prey between seasons. Our findings are highly relevant for landscape planning and distance recommendations for the construction of wind turbines linked to their potential threat for bats.}, language = {en} } @article{MettlerMuehlhausHemmeetal.2014, author = {Mettler, Tabea and M{\"u}hlhaus, Timo and Hemme, Dorothea and Sch{\"o}ttler, Mark Aurel and Rupprecht, Jens and Idoine, Adam and Veyel, Daniel and Pal, Sunil Kumar and Yaneva-Roder, Liliya and Winck, Flavia Vischi and Sommer, Frederik and Vosloh, Daniel and Seiwert, Bettina and Erban, Alexander and Burgos, Asdrubal and Arvidsson, Samuel Janne and Schoenfelder, Stephanie and Arnold, Anne and Guenther, Manuela and Krause, Ursula and Lohse, Marc and Kopka, Joachim and Nikoloski, Zoran and M{\"u}ller-R{\"o}ber, Bernd and Willmitzer, Lothar and Bock, Ralph and Schroda, Michael and Stitt, Mark}, title = {Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {6}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.124537}, pages = {2310 -- 2350}, year = {2014}, abstract = {We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.}, language = {en} } @article{ValenteEtiennePhillimore2014, author = {Valente, Luis M. and Etienne, Rampal S. and Phillimore, Albert B.}, title = {The effects of island ontogeny on species diversity and phylogeny}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {281}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1784}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2013.3227}, pages = {9}, year = {2014}, abstract = {A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological time-scales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.}, language = {en} } @article{DeyAdamovskiFriebeetal.2014, author = {Dey, Pradip and Adamovski, Miriam and Friebe, Simon and Badalyan, Artavazd and Mutihac, Radu-Cristian and Paulus, Florian and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Haag, Rainer}, title = {Dendritic polyglycerol-poly(ethylene glycol)-based polymer networks for biosensing application}, series = {ACS applied materials \& interfaces}, volume = {6}, journal = {ACS applied materials \& interfaces}, number = {12}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/am502018x}, pages = {8937 -- 8941}, year = {2014}, abstract = {This work describes the formation of a new dendritic polyglycerol-poly(ethylene glycol)-based 3D polymer network as a matrix for immobilization of the redox enzyme periplasmatic aldehyde oxidoreductase to create an electrochemical biosensor. The novel network is built directly on the gold surface, where it simultaneously stabilizes the enzyme for up to 4 days. The prepared biosensors can be used for amperometric detection of benzaldehyde in the range of 0.8-400 mu M.}, language = {en} } @article{HahnReschkeLeimkuehleretal.2014, author = {Hahn, Aaron and Reschke, Stefan and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Ketoxime coupling of p-Acetylphenylalanine at neutral pH for site-directed spin labeling of human sulfite oxidase}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {118}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {25}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp503471j}, pages = {7077 -- 7084}, year = {2014}, abstract = {Site-directed spin labeling of the unnatural amino acid p-acetylphenylalanine (p-AcPhe) using oxime based coupling chemistry is successfully applied to investigate human sulfite oxidase (hSO), a protein containing an essential cysteine residue, which impedes the use of thiol based coupling chemistry. The protein was found to be sensitive toward typical reaction conditions of oxime coupling, namely, acidic reaction conditions and elevated temperatures. Thus, coupling at neutral pH and room temperature is mandatory. Three catalysts described in the literature to accelerate the reaction rate have been tested. Best spin labeling efficiencies were observed for p-methoxyaniline, while the other catalysts described in the literature to have even better performance for oxime coupling at neutral pH were substantially less active or led to precipitation of the protein. A clear correlation of spin labeling efficiency with the local environment of the residue is found, shedding some light on the importance of the sterically demanding reaction complex between p-AcPhe, the aniline catalyst, and the spin label for the reaction rate. The analysis of the line shape has shown that its interpretation in terms of local environment is more challenging as compared to the well-established spin labels based on cysteine chemistry. To this end the results presented here indicate that the larger steric demand of the spin labeled p-AcPhe can induce structural effects instead of reporting on them.}, language = {en} } @article{MahlowHejaziKuhnertetal.2014, author = {Mahlow, Sebastian and Hejazi, Mahdi and Kuhnert, Franziska and Garz, Andreas and Brust, Henrike and Baumann, Otto and Fettke, J{\"o}rg}, title = {Phosphorylation of transitory starch by -glucan, water dikinase during starch turnover affects the surface properties and morphology of starch granules}, series = {New phytologist : international journal of plant science}, volume = {203}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.12801}, pages = {495 -- 507}, year = {2014}, abstract = {Glucan, water dikinase (GWD) is a key enzyme of starch metabolism but the physico-chemical properties of starches isolated from GWD-deficient plants and their implications for starch metabolism have so far not been described. Transgenic Arabidopsis thaliana plants with reduced or no GWD activity were used to investigate the properties of starch granules. In addition, using various in vitro assays, the action of recombinant GWD, -amylase, isoamylase and starch synthase 1 on the surface of native starch granules was analysed. The internal structure of granules isolated from GWD mutant plants is unaffected, as thermal stability, allomorph, chain length distribution and density of starch granules were similar to wild-type. However, short glucan chain residues located at the granule surface dominate in starches of transgenic plants and impede GWD activity. A similarly reduced rate of phosphorylation by GWD was also observed in potato tuber starch fractions that differ in the proportion of accessible glucan chain residues at the granule surface. A model is proposed to explain the characteristic morphology of starch granules observed in GWD transgenic plants. The model postulates that the occupancy rate of single glucan chains at the granule surface limits accessibility to starch-related enzymes.}, language = {en} } @article{MummSchefflerHermanussen2014, author = {Mumm, Rebekka and Scheffler, Christiane and Hermanussen, Michael}, title = {Developing differential height, weight and body mass index references for girls that reflect the impact of the menarche}, series = {Acta paediatrica : nurturing the child}, volume = {103}, journal = {Acta paediatrica : nurturing the child}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0803-5253}, doi = {10.1111/apa.12625}, pages = {e312 -- e316}, year = {2014}, abstract = {Aim Growth is both a matter of amplitude and tempo. We aimed to develop references for body height, body weight and body mass index (BMI) with respect to tempo of maturity. Methods Data obtained from the German KiGGS study (2003-2006) on body height, body weight and presence or absence of the menarche were re-analysed in 3776 girls, aged 10-17years. We developed smoothed centiles for BMI-, body-height- and body-weight-for-age using the LMS method for premenarcheal and postmenarcheal girls. Results Body height, body weight and BMI differed significantly between premenarcheal and postmenarcheal girls. On average, postmenarcheal girls aged 11-17years were 5.3cm taller and 9.7kg heavier, and their BMI was 2.9kg/m2 higher than in premenarcheal girls of the same calendar age. Conclusion Adolescent BMI rises with calendar age and biological age. New reference charts for adolescent girls aged 10-18years were generated to be inserted into the currently used references to avoid misclassifying underweight and overweight pubertal girls.}, language = {en} } @article{RottstockJoshiKummeretal.2014, author = {Rottstock, Tanja and Joshi, Jasmin Radha and Kummer, Volker and Fischer, Markus}, title = {Higher plant diversity promotes higher diversity of fungal pathogens, while it decreases pathogen infection per plant}, series = {Ecology : a publication of the Ecological Society of America}, volume = {95}, journal = {Ecology : a publication of the Ecological Society of America}, number = {7}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {1907 -- 1917}, year = {2014}, abstract = {Fungal plant pathogens are common in natural communities where they affect plant physiology, plant survival, and biomass production. Conversely, pathogen transmission and infection may be regulated by plant community characteristics such as plant species diversity and functional composition that favor pathogen diversity through increases in host diversity while simultaneously reducing pathogen infection via increased variability in host density and spatial heterogeneity. Therefore, a comprehensive understanding of multi-host multi-pathogen interactions is of high significance in the context of biodiversity-ecosystem functioning. We investigated the relationship between plant diversity and aboveground obligate parasitic fungal pathogen ("pathogens" hereafter) diversity and infection in grasslands of a long-term, large-scale, biodiversity experiment with varying plant species (1-60 species) and plant functional group diversity (1-4 groups). To estimate pathogen infection of the plant communities, we visually assessed pathogen-group presence (i.e., rusts, powdery mildews, downy mildews, smuts, and leaf-spot diseases) and overall infection levels (combining incidence and severity of each pathogen group) in 82 experimental plots on all aboveground organs of all plant species per plot during four surveys in 2006. Pathogen diversity, assessed as the cumulative number of pathogen groups on all plant species per plot, increased log-linearly with plant species diversity. However, pathogen incidence and severity, and hence overall infection, decreased with increasing plant species diversity. In addition, co-infection of plant individuals by two or more pathogen groups was less likely with increasing plant community diversity. We conclude that plant community diversity promotes pathogen-community diversity while at the same time reducing pathogen infection levels of plant individuals.}, language = {en} } @article{CortesAvizandaJovaniAntonioDonazaretal.2014, author = {Cortes-Avizanda, Ainara and Jovani, Roger and Antonio Donazar, Jose and Grimm, Volker}, title = {Bird sky networks: How do avian scavengers use social information to find carrion?}, series = {Ecology : a publication of the Ecological Society of America}, volume = {95}, journal = {Ecology : a publication of the Ecological Society of America}, number = {7}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {1799 -- 1808}, year = {2014}, abstract = {The relative contribution of personal and social information to explain individual and collective behavior in different species and contexts is an open question in animal ecology. In particular, there is a major lack of studies combining theoretical and empirical approaches to test the relative relevance of different hypothesized individual behaviors to predict empirical collective patterns. We used an individual-based model to confront three hypotheses about the information transfer between social scavengers (Griffon Vultures, Gyps fulvus) when searching for carrion: (1) Vultures only use personal information during foraging ("nonsocial" hypothesis); (2) they create long chains of vultures by following both other vultures that are flying towards carcasses and vultures that are following other vultures that are flying towards carcasses ("chains of vultures" hypothesis); and (3) vultures are only attracted by other vultures that are sinking vertically to a carcass ("local enhancement" hypothesis). The chains of vultures hypothesis has been used in existing models, but never been confronted with field data. Testing is important, though, because these hypotheses could have different management implications. The model was parameterized to mimic the behavior and the densities of both Griffon Vultures and carcasses in a 10 000-km(2) study area in northeastern Spain. We compared the number of vultures attending simulated carcasses with those attending 25 continuously monitored experimental carcasses in the field. Social hypotheses outperformed the nonsocial hypothesis. The chains of vultures hypothesis overestimated the number of vultures feeding on carcasses; the local enhancement hypothesis fitted closely to the empirical data. Supported by our results, we discuss mechanistic and adaptive considerations that reveal that local enhancement may be the key social mechanism behind collective foraging in this and likely other avian scavengers and/or social birds. It also highlights the current need for more studies confronting alternative models of key behaviors with empirical patterns in order to understand how collective behavior emerges in animal societies.}, language = {en} } @article{ZulawskiSchulzeBraginetsetal.2014, author = {Zulawski, Monika and Schulze, Gunnar and Braginets, Rostyslav and Hartmann, Stefanie and Schulze, Waltraud X.}, title = {The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification}, series = {BMC genomics}, volume = {15}, journal = {BMC genomics}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-548}, pages = {14}, year = {2014}, abstract = {Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.}, language = {en} } @article{AlluSojaWuetal.2014, author = {Allu, Annapurna Devi and Soja, Aleksandra Maria and Wu, Anhui and Szymanski, Jedrzej and Balazadeh, Salma}, title = {Salt stress and senescence: identification of cross-talk regulatory components}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru173}, pages = {3993 -- 4008}, year = {2014}, abstract = {Leaf senescence is an active process with a pivotal impact on plant productivity. It results from extensive signalling cross-talk coordinating environmental factors with intrinsic age-related mechanisms. Although many studies have shown that leaf senescence is affected by a range of external parameters, knowledge about the regulatory systems that govern the interplay between developmental programmes and environmental stress is still vague. Salinity is one of the most important environmental stresses that promote leaf senescence and thus affect crop yield. Improving salt tolerance by avoiding or delaying senescence under stress will therefore play an important role in maintaining high agricultural productivity. Experimental evidence suggests that hydrogen peroxide (H2O2) functions as a common signalling molecule in both developmental and salt-induced leaf senescence. In this study, microarray-based gene expression profiling on Arabidopsis thaliana plants subjected to long-term salinity stress to induce leaf senescence was performed, together with co-expression network analysis for H2O2-responsive genes that are mutually up-regulated by salt induced-and developmental leaf senescence. Promoter analysis of tightly co-expressed genes led to the identification of seven cis-regulatory motifs, three of which were known previously, namely CACGTGT and AAGTCAA, which are associated with reactive oxygen species (ROS)-responsive genes, and CCGCGT, described as a stress-responsive regulatory motif, while the others, namely ACGCGGT, AGCMGNC, GMCACGT, and TCSTYGACG were not characterized previously. These motifs are proposed to be novel elements involved in the H2O2-mediated control of gene expression during salinity stress-triggered and developmental senescence, acting through upstream transcription factors that bind to these sites.}, language = {en} } @article{BalazadehSchildhauerAraujoetal.2014, author = {Balazadeh, Salma and Schildhauer, Joerg and Araujo, Wagner L. and Munne-Bosch, Sergi and Fernie, Alisdair R. and Proost, Sebastian and Humbeck, Klaus and M{\"u}ller-R{\"o}ber, Bernd}, title = {Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru119}, pages = {3975 -- 3992}, year = {2014}, abstract = {Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.}, language = {en} } @article{BrothersKoehlerAttermeyeretal.2014, author = {Brothers, Soren M. and Koehler, J. and Attermeyer, Katrin and Grossart, Hans-Peter and Mehner, T. and Meyer, N. and Scharnweber, Inga Kristin and Hilt, Sabine}, title = {A feedback loop links brownification and anoxia in a temperate, shallow lake}, series = {Limnology and oceanography}, volume = {59}, journal = {Limnology and oceanography}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.4319/lo.2014.59.4.1388}, pages = {1388 -- 1398}, year = {2014}, abstract = {This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.}, language = {en} } @article{BehrensFrankRaweletal.2014, author = {Behrens, Maik and Frank, Oliver and Rawel, Harshadrai Manilal and Ahuja, Gaurav and Potting, Christoph and Hofmann, Thomas and Meyerhof, Wolfgang and Korsching, Sigrun}, title = {ORA1, a Zebrafish Olfactory Receptor Ancestral to All Mammalian V1R Genes, Recognizes 4-Hydroxyphenylacetic Acid, a Putative Reproductive Pheromone}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {28}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.573162}, pages = {19778 -- 19788}, year = {2014}, abstract = {The teleost v1r-related ora genes are a small, highly conserved olfactory receptor gene family of only six genes, whose direct orthologues can be identified in lineages as far as that of cartilaginous fish. However, no ligands for fish olfactory receptor class A related genes (ORA) had been uncovered so far. Here we have deorphanized the ORA1 receptor using heterologous expression and calcium imaging. We report that zebrafish ORA1 recognizes with high specificity and sensitivity 4-hydroxyphenylacetic acid. The carboxyl group of this compound is required in a particular distance from the aromatic ring, whereas the hydroxyl group in the para-position is not essential, but strongly enhances the binding efficacy. Low concentrations of 4-hydroxyphenylacetic acid elicit increases in oviposition frequency in zebrafish mating pairs. This effect is abolished by naris closure. We hypothesize that 4-hydroxyphenylacetic acid might function as a pheromone for reproductive behavior in zebrafish. ORA1 is ancestral to mammalian V1Rs, and its putative function as pheromone receptor is reminiscent of the role of several mammalian V1Rs as pheromone receptors.}, language = {en} } @article{BrustLehmannFettke2014, author = {Brust, Henrike and Lehmann, Tanja and Fettke, J{\"o}rg}, title = {Analysis of the functional interaction of arabidopsis starch synthase and branching enzyme isoforms reveals that the cooperative action of SSI and BEs results in glucans with polymodal chain length distribution similar to amylopectin}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0102364}, pages = {14}, year = {2014}, abstract = {Starch synthase (SS) and branching enzyme (BE) establish the two glycosidic linkages existing in starch. Both enzymes exist as several isoforms. Enzymes derived from several species were studied extensively both in vivo and in vitro over the last years, however, analyses of a functional interaction of SS and BE isoforms are missing so far. Here, we present data from in vitro studies including both interaction of leaf derived and heterologously expressed SS and BE isoforms. We found that SSI activity in native PAGE without addition of glucans was dependent on at least one of the two BE isoforms active in Arabidopsis leaves. This interaction is most likely not based on a physical association of the enzymes, as demonstrated by immunodetection and native PAGE mobility analysis of SSI, BE2, and BE3. The glucans formed by the action of SSI/BEs were analysed using leaf protein extracts from wild type and be single mutants (Atbe2 and Atbe3 mutant lines) and by different combinations of recombinant proteins. Chain length distribution (CLD) patterns of the formed glucans were irrespective of SSI and BE isoforms origin and still independent of assay conditions. Furthermore, we show that all SS isoforms (SSI-SSIV) were able to interact with BEs and form branched glucans. However, only SSI/BEs generated a polymodal distribution of glucans which was similar to CLD pattern detected in amylopectin of Arabidopsis leaf starch. We discuss the impact of the SSI/BEs interplay for the CLD pattern of amylopectin.}, language = {en} } @article{DongYangLehnkuehleretal.2014, author = {Dong, Chao and Yang, Jing and Lehnkuehler, Silke and Kirk, Martin L.}, title = {Pyranopterin dithiolene distortions relevant to electron transfer in xanthine oxidase/dehydrogenase}, series = {Inorganic chemistry}, volume = {53}, journal = {Inorganic chemistry}, number = {14}, publisher = {American Chemical Society}, address = {Washington}, issn = {0020-1669}, doi = {10.1021/ic500873y}, pages = {7077 -- 7079}, year = {2014}, abstract = {The reducing substrates 4-thiolumazine and 2,4-dithiolumazine have been used to form Mo-IV-product complexes with xanthine oxidase (XO) and xanthine dehydrogenase. These Mo-IV-product complexes display an intense metal-to-ligand charge-transfer (MLCT) band in the near-infrared region of the spectrum. Optical pumping into this MLCT band yields resonance Raman spectra of the Mo site that are devoid of contributions from the highly absorbing FAD and 2Fe2S clusters in the protein. The resonance Raman spectra reveal in-plane bending modes of the bound product and low-frequency molybdenum dithiolene and pyranopterin dithiolene vibrational modes. This work provides keen insight into the role of the pyranopterin dithiolene in electron-transfer reactivity.}, language = {en} } @article{McNairNakagawaGrimm2014, author = {McNair, Alistair Senior and Nakagawa, Shinichi and Grimm, Volker}, title = {The evolutionary consequences of disrupted male mating signals: An agent-based modelling exploration of endocrine disrupting chemicals in the guppy}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0103100}, pages = {9}, year = {2014}, abstract = {Females may select a mate based on signalling traits that are believed to accurately correlate with heritable aspects of male quality. Anthropogenic actions, in particular chemicals released into the environment, are now disrupting the accuracy of mating signals to convey information about male quality. The long-term prediction for disrupted mating signals is most commonly loss of female preference. Yet, this prediction has rarely been tested using quantitative models. We use agent-based models to explore the effects of rapid disruption of mating signals. In our model, a gene determines survival. Males signal their level of genetic quality via a signal trait, which females use to select a mate. We allowed this system of sexual selection to become established, before introducing a disruption between the male signal trait and quality, which was similar in nature to that induced by exogenous chemicals. Finally, we assessed the capacity of the system to recover from this disruption. We found that within a relatively short time frame, disruption of mating signals led to a lasting loss of female preference. Decreases in mean viability at the population-level were also observed, because sexual-selection acting against newly arising deleterious mutations was relaxed. The ability of the population to recover from disrupted mating signals was strongly influenced by the mechanisms that promoted or maintained genetic diversity in traits under sexual selection. Our simple model demonstrates that environmental perturbations to the accuracy of male mating signals can result in a long-term loss of female preference for those signals within a few generations. What is more, the loss of this preference can have knock-on consequences for mean population fitness.}, language = {en} } @article{BiancoKetmaier2014, author = {Bianco, Pier Giorgio and Ketmaier, Valerio}, title = {A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae)}, series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, volume = {3841}, journal = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, number = {3}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1175-5326}, pages = {379 -- 402}, year = {2014}, abstract = {By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre-Messinian time, in the Lago Mare, entered the Mediterranean area during the Messinian Lago Mare phase of the Mediterranean Sea and survived only in the Tuscany-Latium district. This genus differs from Leucos in having large pearl organs on the central part of head and body scales in mature males and for the habitat preference, being a riverine-adapted species. It differs from Rutilus in pharyngeal teeth formula (5-5 in Sarmarutilus and 6-5 in Rutilus), size (small in Sarmarutilus and large in Rutilus) and for the preferential habitat (riverine vs. still water). Finally, lectotypes for Leucos basak, Leucos aula, and Sarmarutilus rubilio are designated.}, language = {en} } @article{LohmannTietjenBlaumetal.2014, author = {Lohmann, Dirk and Tietjen, Britta and Blaum, Niels and Joubert, David Francois and Jeltsch, Florian}, title = {Prescribed fire as a tool for managing shrub encroachment in semi-arid savanna rangelands}, series = {Journal of arid environments}, volume = {107}, journal = {Journal of arid environments}, publisher = {Elsevier}, address = {London}, issn = {0140-1963}, doi = {10.1016/j.jaridenv.2014.04.003}, pages = {49 -- 56}, year = {2014}, abstract = {Savanna rangelands worldwide are threatened by shrub encroachment, i.e. the increase of woody plant species at the cost of perennial grasses, causing a strong decline in the productivity of domestic livestock production. Although recent studies indicate that fire might be of great importance for semi-arid and arid savanna dynamics, it is largely not applied in the management of semi-arid rangelands especially with regard to woody plant control. We used the eco-hydrological savanna model EcoHyD to simulate the effects of different fire management strategies on semi-arid savanna vegetation and to assess their longterm suitability for semi-arid rangeland management. Simulation results show that prescribed fires, timed to kill tree seedlings prevented shrub encroachment for a broad range of livestock densities while the possible maximum long-term cattle densities on the simulated semi-arid rangeland in Namibia increased by more than 30\%. However, when grazing intensity was too high, fire management failed in preventing shrub encroachment. Our findings indicate that with regard to fire management a clear distinction between mesic and more arid savannas is necessary: While the frequency of fires is of relevance for mesic savannas, we recommend a fire management focussing on the timing of fire for semi-arid and arid savannas. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{StoofLeichsenringBernhardtPestryakovaetal.2014, author = {Stoof-Leichsenring, Kathleen Rosemarie and Bernhardt, Nadine and Pestryakova, Luidmila Agafyevna and Epp, Laura Saskia and Herzschuh, Ulrike and Tiedemann, Ralph}, title = {A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect}, series = {Journal of paleolimnolog}, volume = {52}, journal = {Journal of paleolimnolog}, number = {1-2}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-014-9779-1}, pages = {77 -- 93}, year = {2014}, abstract = {Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools for tracking differences between diatom lineages that are not visible in their morphologies. These markers revealed putatively high genetic diversity within the Staurosira/Staurosirella species complex, at a finer scale than is possible to resolve by microscopic determination. The rbcL markers may provide additional reliable information on the diversity of barely distinguishable minute benthic fragilarioids. Environmental sequencing may thus allow the tracking of spatial and temporal diversification in Siberian lakes, especially in the context of diatom responses to recent environmental changes, which remains a matter of controversy.}, language = {en} } @article{GraccevaHerdeGroothuisetal.2014, author = {Gracceva, Giulia and Herde, Antje and Groothuis, Ton G. G. and Koolhaas, Jaap M. and Palme, Rupert and Eccard, Jana}, title = {Turning shy on a winter's day: Effects of season on personality and stress response in Microtus arvalis}, series = {Ethology}, volume = {120}, journal = {Ethology}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0179-1613}, doi = {10.1111/eth.12246}, pages = {753 -- 767}, year = {2014}, abstract = {Animal personalities are by definition stable over time, but to what extent they may change during development and in adulthood to adjust to environmental change is unclear. Animals of temperate environments have evolved physiological and behavioural adaptations to cope with the cyclic seasonal changes. This may also result in changes in personality: suites of behavioural and physiological traits that vary consistently among individuals. Winter, typically the adverse season challenging survival, may require individuals to have shy/cautious personality, whereas during summer, energetically favourable to reproduction, individuals may benefit from a bold/risk-taking personality. To test the effects of seasonal changes in early life and in adulthood on behaviours (activity, exploration and anxiety), body mass and stress response, we manipulated the photoperiod and quality of food in two experiments to simulate the conditions of winter and summer. We used the common voles (Microtus arvalis) as they have been shown to display personality based on behavioural consistency over time and contexts. Summer-born voles allocated to winter conditions at weaning had lower body mass, a higher corticosterone increase after stress and a less active, more cautious behavioural phenotype in adulthood compared to voles born in and allocated to summer conditions. In contrast, adult females only showed plasticity in stress-induced corticosterone levels, which were higher in the animals that were transferred to the winter conditions than to those staying in summer conditions. These results suggest a sensitive period for season-related behavioural plasticity in which juveniles shift over the bold-shy axis.}, language = {en} } @article{GuoFuJuerchottetal.2014, author = {Guo, Ke-Tai and Fu, Peng and Juerchott, Kathrin and Motaln, Helena and Selbig, Joachim and Lah, Tamara T. and Tonn, J{\"o}rg-Christian and Schichor, Christian}, title = {The expression of Wnt-inhibitor DKK1 (Dickkopf 1) is determined by intercellular crosstalk and hypoxia in human malignant gliomas}, series = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, volume = {140}, journal = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, number = {8}, publisher = {Springer}, address = {New York}, issn = {0171-5216}, doi = {10.1007/s00432-014-1642-2}, pages = {1261 -- 1270}, year = {2014}, abstract = {Objective Wnt signalling pathways regulate proliferation, motility and survival in a variety of human cell types. Dickkopf 1 (DKK1) gene codes for a secreted Wnt inhibitory factor. It functions as tumour suppressor gene in breast cancer and as a pro-apoptotic factor in glioma cells. In this study, we aimed to demonstrate whether the different expression of DKK1 in human glioma-derived cells is dependent on microenvironmental factors like hypoxia and regulated by the intercellular crosstalk with bone-marrow-derived mesenchymal stem cells (bmMSCs). Methods Glioma cell line U87-MG, three cell lines from human glioblastoma grade IV (glioma-derived mesenchymal stem cells) and three bmMSCs were selected for the experiment. The expression of DKK1 in cell lines under normoxic/hypoxic environment or co-culture condition was measured using real-time PCR and enzyme-linked immunoadsorbent assay. The effect of DKK1 on cell migration and proliferation was evaluated by in vitro wound healing assays and sulphorhodamine assays, respectively. Results Glioma-derived cells U87-MG displayed lower DKK1 expression compared with bmMSCs. Hypoxia led to an overexpression of DKK1 in bmMSCs and U87-MG when compared to normoxic environment, whereas co-culture of U87-MG with bmMSCs induced the expression of DKK1 in both cell lines. Exogenous recombinant DKK1 inhibited cell migration on all cell lines, but did not have a significant effect on cell proliferation of bmMSCs and glioma cell lines. Conclusion In this study, we showed for the first time that the expression of DKK1 was hypoxia dependent in human malignant glioma cell lines. The induction of DKK1 by intracellular crosstalk or hypoxia stimuli sheds light on the intense adaption of glial tumour cells to environmental alterations.}, language = {en} } @article{CaronDeFrenneBrunetetal.2014, author = {Caron, Maria Mercedes and De Frenne, P. and Brunet, J. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Diekmann, M. and Graae, B. J. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, F. and Strimbeck, G. R. and Wulf, Monika and Verheyen, Kris}, title = {Latitudinal variation in seeds characteristics of Acer platanoides and A. pseudoplatanus}, series = {Plant ecology : an international journal}, volume = {215}, journal = {Plant ecology : an international journal}, number = {8}, publisher = {Springer}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-014-0343-x}, pages = {911 -- 925}, year = {2014}, abstract = {Climate change will likely affect population dynamics of numerous plant species by modifying several aspects of the life cycle. Because plant regeneration from seeds may be particularly vulnerable, here we assess the possible effects of climate change on seed characteristics and present an integrated analysis of seven seed traits (nutrient concentrations, samara mass, seed mass, wing length, seed viability, germination percentage, and seedling biomass) of Acer platanoides and A. pseudoplatanus seeds collected along a wide latitudinal gradient from Italy to Norway. Seed traits were analyzed in relation to the environmental conditions experienced by the mother trees along the latitudinal gradient. We found that seed traits of A. platanoides were more influenced by the climatic conditions than those of A. pseudoplatanus. Additionally, seed viability, germination percentage, and seedling biomass of A. platanoides were strongly related to the seed mass and nutrient concentration. While A. platanoides seeds were more influenced by the environmental conditions (generally negatively affected by rising temperatures), compared to A. pseudoplatanus, A. platanoides still showed higher germination percentage and seedling biomass than A. pseudoplatanus. Thus, further research on subsequent life-history stages of both species is needed. The variation in seed quality observed along the climatic gradient highlights the importance of studying the possible impact of climate change on seed production and species demography.}, language = {en} } @article{FilipBauerHillebrandetal.2014, author = {Filip, Joanna and Bauer, Barbara and Hillebrand, Helmut and Beniermann, Anna and Gaedke, Ursula and Moorthi, Stefanie D.}, title = {Multitrophic diversity effects depend on consumer specialization and species-specific growth and grazing rates}, series = {Oikos}, volume = {123}, journal = {Oikos}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.01219}, pages = {912 -- 922}, year = {2014}, abstract = {Ecosystem functioning is affected by horizontal (within trophic groups) and vertical (across trophic levels) biodiversity. Theory predicts that the effects of vertical biodiversity depend on consumer specialization. In a microcosm experiment, we investigated ciliate consumer diversity and specialization effects on algal prey biovolume, evenness and composition, and on ciliate biovolume production. The experimental data was complemented by a process-based model further analyzing the ecological mechanisms behind the observed diversity effects. Overall, increasing consumer diversity had no significant effect on prey biovolume or evenness. However, consumer specialization affected the prey community. Specialist consumers showed a stronger negative impact on prey biovolume and evenness than generalists. The model confirmed that this pattern was mainly driven by a single specialist with a high per capita grazing rate, consuming the two most productive prey species. When these were suppressed, the prey assemblage became dominated by a less productive species, consequently decreasing prey biovolume and evenness. Consumer diversity increased consumer biovolume, which was stronger for generalists than for specialists and highest in mixed combinations, indicating that consumer functional diversity, i.e. more diverse feeding strategies, increased resource use efficiency. Overall, our results indicate that consumer diversity effects on prey and consumers strongly depend on species-specific growth and grazing rates, which may be at least equally important as consumer specialization in driving consumer diversity effects across trophic levels.}, language = {en} } @article{PagelAndersonCrameretal.2014, author = {Pagel, J{\"o}rn and Anderson, Barbara J. and Cramer, Wolfgang and Fox, Richard and Jeltsch, Florian and Roy, David B. and Thomas, Chris D. and Schurr, Frank Martin}, title = {Quantifying range-wide variation in population trends from local abundance surveys and widespread opportunistic occurrence records}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {5}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, doi = {10.1111/2041-210X.12221}, pages = {751 -- 760}, year = {2014}, abstract = {2. We present a hierarchical model that integrates observations from multiple sources to estimate spatio-temporal abundance trends. The model links annual population densities on a spatial grid to both long-term count data and to opportunistic occurrence records from a citizen science programme. Specific observation models for both data types explicitly account for differences in data structure and quality. 3. We test this novel method in a virtual study with simulated data and apply it to the estimation of abundance dynamics across the range of a butterfly species (Pyronia tithonus) in Great Britain between 1985 and 2004. The application to simulated and real data demonstrates how the hierarchical model structure accommodates various sources of uncertainty which occur at different stages of the link between observational data and the modelled abundance, thereby it accounts for these uncertainties in the inference of abundance variations. 4. We show that by using hierarchical observation models that integrate different types of commonly available data sources, we can improve the estimates of variation in species abundances across space and time. This will improve our ability to detect regional trends and can also enhance the empirical basis for understanding range dynamics.}, language = {en} } @article{KabelitzKappelHennebergeretal.2014, author = {Kabelitz, Tina and Kappel, Christian and Henneberger, Kirstin and Benke, Eileen and Noeh, Christiane and B{\"a}urle, Isabel}, title = {eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in thee arabidopsis lineage}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {8}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.128512}, pages = {3261 -- 3271}, year = {2014}, abstract = {Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 39 end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 39 untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3' end of genes.}, language = {en} } @article{PavlovaNabeNielsenDietzetal.2014, author = {Pavlova, Viola and Nabe-Nielsen, Jacob and Dietz, Rune and Svenning, Jens-Christian and Vorkamp, Katrin and Riget, Frank Farso and Sonne, Christian and Letcher, Robert J. and Grimm, Volker}, title = {Field metabolic rate and PCB adipose tissue deposition efficiency in East Greenland polar bears derived from contaminant monitoring data}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0104037}, pages = {10}, year = {2014}, abstract = {Climate change will increasingly affect the natural habitat and diet of polar bears (Ursus maritimus). Understanding the energetic needs of polar bears is therefore important. We developed a theoretical method for estimating polar bear food consumption based on using the highly recalcitrant polychlorinated biphenyl (PCB) congener, 2,2',4,4',55-hexaCB (CB153) in bear adipose tissue as an indicator of food intake. By comparing the CB153 tissue concentrations in wild polar bears with estimates from a purposely designed individual-based model, we identified the possible combinations of field metabolic rates (FMR) and CB153 deposition efficiencies in East Greenland polar bears. Our simulations indicate that if 30\% of the CB153 consumed by polar bear individuals were deposited into their adipose tissue, the corresponding FMR would be only two times the basal metabolic rate. In contrast, if the modelled CB153 deposition efficiency were 10\%, adult polar bears would require six times more energy than that needed to cover basal metabolism. This is considerably higher than what has been assumed for polar bears in previous studies though it is similar to FMRs found in other marine mammals. An implication of this result is that even relatively small reductions in future feeding opportunities could impact the survival of East Greenland polar bears.}, language = {en} } @article{GossnerPasalicLangeetal.2014, author = {Gossner, Martin M. and Pasalic, Esther and Lange, Markus and Lange, Patricia and Boch, Steffen and Hessenm{\"o}ller, Dominik and M{\"u}ller, J{\"o}rg and Socher, Stephanie A. and Fischer, Markus and Schulze, Ernst-Detlef and Weisser, Wolfgang W.}, title = {Differential responses of herbivores and herbivory to management in temperate Eeuropean beech}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0104876}, pages = {16}, year = {2014}, abstract = {Forest management not only affects biodiversity but also might alter ecosystem processes mediated by the organisms, i.e. herbivory the removal of plant biomass by plant-eating insects and other arthropod groups. Aiming at revealing general relationships between forest management and herbivory we investigated aboveground arthropod herbivory in 105 plots dominated by European beech in three different regions in Germany in the sun-exposed canopy of mature beech trees and on beech saplings in the understorey. We separately assessed damage by different guilds of herbivores, i.e. chewing, sucking and scraping herbivores, gall-forming insects and mites, and leaf-mining insects. We asked whether herbivory differs among different forest management regimes (unmanaged, uneven-aged managed, even-aged managed) and among age-classes within even-aged forests. We further tested for consistency of relationships between regions, strata and herbivore guilds. On average, almost 80\% of beech leaves showed herbivory damage, and about 6\% of leaf area was consumed. Chewing damage was most common, whereas leaf sucking and scraping damage were very rare. Damage was generally greater in the canopy than in the understorey, in particular for chewing and scraping damage, and the occurrence of mines. There was little difference in herbivory among differently managed forests and the effects of management on damage differed among regions, strata and damage types. Covariates such as wood volume, tree density and plant diversity weakly influenced herbivory, and effects differed between herbivory types. We conclude that despite of the relatively low number of species attacking beech; arthropod herbivory on beech is generally high. We further conclude that responses of herbivory to forest management are multifaceted and environmental factors such as forest structure variables affecting in particular microclimatic conditions are more likely to explain the variability in herbivory among beech forest plots.}, language = {en} } @article{DechtriratGajovicEichelmannWojciketal.2014, author = {Dechtrirat, Decha and Gajovic-Eichelmann, Nenad and Wojcik, Felix and Hartmann, Laura and Bier, Frank Fabian and Scheller, Frieder W.}, title = {Electrochemical displacement sensor based on ferrocene boronic acid tracer and immobilized glycan for saccharide binding proteins and E. coli}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {58}, journal = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2014.02.028}, pages = {1 -- 8}, year = {2014}, abstract = {Pathogens such as viruses and bacteria use their envelope proteins and their adhesin lectins to recognize the glycan residues presented on the cell surface of the target tissues. This principle of recognition is used in a new electrochemical displacement sensor for the protein concanavalin A (ConA). A gold electrode was first modified with a self-assembled monolayer of a thiolated mannose/OEG conjugate and a ferrocene boroxol derivative was pre-assembled as reporter molecule onto the mannose surface. The novel tracer molecule based on a 2-hydroxymethyl phenyl boronic acid derivative binds even at neutral pH to the saccharides which could expand the application towards biological samples (i.e., urine and feces). Upon the binding of ConA, the tracer was displaced and washed away from the sensor surface leading to a decrease in the electrochemical signal. Using square wave voltammetry (SWV), the concentration of ConA in the sample solution could be determined in the dynamic concentration range established from 38 nmol L-1 to 5.76 mu mol L-1 with a reproducible detection limit of 1 mu g mL(-1) (38 nmol L-1) based on the signal-to-noise ratio (S/N=3) with fast response of 15 min. The new reporter molecule showed a reduced non-specific displacement by BSA and ribonuclease A. The sensor was also successfully transferred to the first proof of principle for the detection of Escherichia coli exhibiting a detection limit of approximately 6 x 102 cells/mL Specificity of the displacement by target protein ConA and E. coli was demonstrated since the control proteins (i.e., BSA and RNaseA) and the control E. coli strain, which lack of type 1 fimbriae, were ineffective. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{SicardThammMaronaetal.2014, author = {Sicard, Adrien and Thamm, Anna and Marona, Cindy and Lee, Young Wha and Wahl, Vanessa and Stinchcombe, John R. and Wright, Stephen I. and Kappel, Christian and Lenhard, Michael}, title = {Repeated evolutionary changes of leaf morphology caused by mutations to a homeobox gene}, series = {Current biology}, volume = {24}, journal = {Current biology}, number = {16}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2014.06.061}, pages = {1880 -- 1886}, year = {2014}, abstract = {Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology [1-3]. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation [4-6]. In animals, changes to "hot spot" genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions [4-8]. By contrast, only few such genes have been identified from plants [8-11], limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus [12] underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin [12], suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection.}, language = {en} } @article{DietrichLombardoAbdelilahSeyfried2014, author = {Dietrich, Ann-Christin and Lombardo, Veronica A. and Abdelilah-Seyfried, Salim}, title = {Blood flow and Bmp signaling control endocardial chamber morphogenesis}, series = {Developmental cell}, volume = {30}, journal = {Developmental cell}, number = {4}, publisher = {Cell Press}, address = {Cambridge}, issn = {1534-5807}, doi = {10.1016/j.devcel.2014.06.020}, pages = {367 -- 377}, year = {2014}, abstract = {During heart development, the onset of heartbeat and blood flow coincides with a ballooning of the cardiac chambers. Here, we have used the zebrafish as a vertebrate model to characterize chamber ballooning morphogenesis of the endocardium, a specialized population of endothelial cells that line the interior of the heart. By combining functional manipulations, fate mapping studies, and high-resolution imaging, we show that endocardial growth occurs without an influx of external cells. Instead, endocardial cell proliferation is regulated, both by blood flow and by Bmp signaling, in a manner independent of vascular endothelial growth factor (VEGF) signaling. Similar to myocardial cells, endocardial cells obtain distinct chamber-specific and inner- versus outer-curvature-specific surface area sizes. We find that the hemodynamic-sensitive transcription factor Klf2a is involved in regulating endocardial cell morphology. These findings establish the endocardium as the flow-sensitive tissue in the heart with a key role in adapting chamber growth in response to the mechanical stimulus of blood flow.}, language = {en} } @article{SpijkermanStojkovicBeardall2014, author = {Spijkerman, Elly and Stojkovic, Slobodanka and Beardall, John}, title = {CO2 acquisition in Chlamydomonas acidophila is influenced mainly by CO2, not phosphorus, availability}, series = {Photosynthesis research}, volume = {121}, journal = {Photosynthesis research}, number = {2-3}, publisher = {Springer}, address = {Dordrecht}, issn = {0166-8595}, doi = {10.1007/s11120-014-0016-6}, pages = {213 -- 221}, year = {2014}, abstract = {The extremophilic green microalga Chlamydomonas acidophila grows in very acidic waters (pH 2.3-3.4), where CO2 is the sole inorganic carbon source. Previous work has revealed that the species can accumulate inorganic carbon (Ci) and exhibits high affinity CO2 utilization under low-CO2 (air-equilibrium) conditions, similar to organisms with an active CO2 concentrating mechanism (CCM), whereas both processes are down-regulated under high CO2 (4.5 \% CO2) conditions. Responses of this species to phosphorus (Pi)-limited conditions suggested a contrasting regulation of the CCM characteristics. Therefore, we measured external carbonic anhydrase (CA(ext)) activities and protein expression (CAH1), the internal pH, Ci accumulation, and CO2-utilization in cells adapted to high or low CO2 under Pi-replete and Pi-limited conditions. Results reveal that C. acidophila expressed CA(ext) activity and expressed a protein cross-reacting with CAH1 (the CA(ext) from Chlamydomonas reinhardtii). Although the function of this CA remains unclear, CA(ext) activity and high affinity CO2 utilization were the highest under low CO2 conditions. C. acidophila accumulated Ci and expressed the CAH1 protein under all conditions tested, and C. reinhardtii also contained substantial amounts of CAH1 protein under Pi-limitation. In conclusion, Ci utilization is optimized in C. acidophila under ecologically relevant conditions, which may enable optimal survival in its extreme Ci- and Pi-limited habitat. The exact physiological and biochemical acclimation remains to be further studied.}, language = {en} } @article{NiCaoJeltschetal.2014, author = {Ni, Jian and Cao, Xianyong and Jeltsch, Florian and Herzschuh, Ulrike}, title = {Biome distribution over the last 22,000 yr in China}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {409}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2014.04.023}, pages = {33 -- 47}, year = {2014}, abstract = {Patterns of past vegetation changes over time and space can help facilitate better understanding of the interactions among climate, ecosystem, and human impact. Biome changes in China over the last 22,000 yr (calibrated radiocarbon date, a BP) were numerically reconstructed by using a standard approach of pollen-plant functional type-biome assignment (biomization). The biomization procedure involves pollen data from 2434 surface sites and 228 fossil sites with a high quality of pollen count and C-14 dating, 51 natural and three anthropogenic plant functional types (PFTs), as well as 19 natural and one anthropogenic biome. Surface pollen-based reconstruction of modern natural biome patterns is in good agreement (74.4\%) with actual vegetation distribution in China. However, modem large-scale anthropogenic biome reconstruction has not been successful based on the current setup of three anthropogenic PFTs (plantation, secondary, and disturbed PFT) because of the limitation of non-species level pollen identification and the difficulty in the clear assignment of disturbed PFTs. The non-anthropogenic biome distributions of 44 time slices at 500-year intervals show large-scale discrepant and changed vegetation patterns from the last glacial maximum (LGM) to the Holocene throughout China. From 22 ka BP to 19 ka BP, temperate grassland, xerophytic shrubland, and desert dominated northern China, whereas cold or cool forests flourished in central China. Warm-temperate evergreen forests were restricted to far southern China, and tropical forests were absent During 18.5 ka BP to 12 ka BP, cold, cool, and dry biomes extended to some parts of northern, westem, and eastern China. Warm-temperate evergreen and mixed forests gradually expanded to occupy the whole of southern China. A slight northward shift of forest biomes occurred from 15 ka BP to 12 lea BP. During 11.5 ka BP to 9 ka BP, temperate grassland and shrubland gradually stretched to northern and western China. Cold and cool forests widely expanded into northern and central China, as well as in the northern margin of South China along with temperate deciduous forest. Since the early mid-Holocene (approximately 8.5 ka BP to 5.5 ka BP), all forest biomes shifted northward at the expense of herbaceous and shrubby biomes. Simultaneously, cold and cool forest biomes occupied the marginal areas of the Tibetan Plateau and the high mountains in western China. During the middle to late Holocene, from 5 ka to the present, temperate grassland and xerophytic shrubland expanded to the south and east, whereas temperate deciduous forests slightly shifted southward. After 3 lea BP, forest biomes were absent in western China and on the Tibetan plateau surface. Dramatic biome shifts from the LGM to the Holocene were observed in the forest-grassland ecotone and transitional zones between temperate and subtropical climates, between subtropical and tropical regions, and in the mountainous margins of the eastern Tibetan Plateau. Evidence showed more human disturbances during the late Holocene. More pollen records and historical documents are therefore further needed to understand fully the human disturbance-induced large-scale forest changes. In addition, more classifications of anthropogenic biome or land cover, more distinct assignment of pollen taxa to anthropogenic PFTs, and more effective numerical and/or mechanistic techniques in building large-scale human disturbances are required. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} }