@article{MassieWeithoffKucklaenderetal.2015, author = {Massie, Thomas Michael and Weithoff, Guntram and Kucklaender, Nina and Gaedke, Ursula and Blasius, Bernd}, title = {Enhanced Moran effect by spatial variation in environmental autocorrelation}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms6993}, pages = {8}, year = {2015}, abstract = {Spatial correlations in environmental stochasticity can synchronize populations over wide areas, a phenomenon known as the Moran effect. The Moran effect has been confirmed in field, laboratory and theoretical investigations. Little is known, however, about the Moran effect in a common ecological case, when environmental variation is temporally autocorrelated and this autocorrelation varies spatially. Here we perform chemostat experiments to investigate the temporal response of independent phytoplankton populations to autocorrelated stochastic forcing. In contrast to naive expectation, two populations without direct coupling can be more strongly correlated than their environmental forcing (enhanced Moran effect), if the stochastic variations differ in their autocorrelation. Our experimental findings are in agreement with numerical simulations and analytical calculations. The enhanced Moran effect is robust to changes in population dynamics, noise spectra and different measures of correlation-suggesting that noise-induced synchrony may play a larger role for population dynamics than previously thought.}, language = {en} } @article{KabaMaierSchliebeOhleretal.2015, author = {Kaba, Hani E. J. and Maier, Natalia and Schliebe-Ohler, Nicole and Mayer, Yvonne and Mueller, Peter P. and van den Heuvel, Joop and Schuchhardt, Johannes and Hanack, Katja and Bilitewski, Ursula}, title = {Identification of whole pathogenic cells by monoclonal antibodies generated against a specific peptide from an immunogenic cell wall protein}, series = {Journal of microbiological methods}, volume = {108}, journal = {Journal of microbiological methods}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-7012}, doi = {10.1016/j.mimet.2014.11.003}, pages = {61 -- 69}, year = {2015}, abstract = {We selected the immunogenic cell wall beta-(1,3)-glucosyltransferase Bgl2p from Candida albicans as a target protein for the production of antibodies. We identified a unique peptide sequence in the protein and generated monoclonal anti- C. albicans Bgl2p antibodies, which bound in particular to whole C. albicans cells.}, language = {en} } @misc{YarmanDechtriratBosserdtetal.2015, author = {Yarman, Aysu and Dechtrirat, Decha and Bosserdt, Maria and Jetzschmann, Katharina J. and Gajovic-Eichelmann, Nenad and Scheller, Frieder W.}, title = {Cytochrome c-derived hybrid systems based on moleculary imprinted polymers}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {27}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {3}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400592}, pages = {573 -- 586}, year = {2015}, abstract = {Hybrid architectures which combine a MIP with an immobilized affinity ligand or a biocatalyst sum up the advantages of both components. In this paper, hybrid architectures combining a layer of a molecularly imprinted electropolymer with a mini-enzyme or a self-assembled monolayer will be presented. (i) Microperoxidase-11 (MP-11) catalyzed oxidation of the drug aminopyrine on a product-imprinted sublayer: The peroxide dependent conversion of the analyte aminopyrine takes place in the MP-11 containing layer on top of a product-imprinted electropolymer on the indicator electrode. The hierarchical architecture resulted in the elimination of interfering signals for ascorbic acid and uric acid. An advantage of the new hierarchical structure is the separation of MIP formation by electropolymerization and immobilization of the catalyst. In this way it was for the first time possible to integrate an enzyme with a MIP layer in a sensor configuration. This combination has the potential to be transferred to other enzymes, e.g. P450, opening the way to clinically important analytes. (ii) Epitope-imprinted poly-scopoletin layer for binding of the C-terminal peptide and cytochrome c (Cyt c): The MIP binds both the target peptide and the parent protein almost eight times stronger than the non-imprinted polymer with affinities in the lower micromolar range. Exchange of only one amino acid in the peptide decreases the binding by a factor of five. (iii) MUA-poly-scopoletin MIP for cytochrome c: Cyt c bound to the MIP covered gold electrode exhibits direct electron transfer with a redox potential and rate constant typical for the native protein. The MIP cover layer suppresses the displacement of the target protein by BSA or myoglobin. The combination of protein imprinted polymers with an efficient electron transfer is a new concept for characterizing electroactive proteins such as Cyt c. The competition with other proteins shows that the MIP binds its target Cyt c preferentially and that molecular shape and the charge of protein determine the binding of interfering proteins.}, language = {en} } @article{SundelofGrimmUlmestrandetal.2015, author = {Sundelof, Andreas and Grimm, Volker and Ulmestrand, Mats and Fiksen, Oyvind}, title = {Modelling harvesting strategies for the lobster fishery in northern Europe: the importance of protecting egg-bearing females}, series = {Population ecology}, volume = {57}, journal = {Population ecology}, number = {1}, publisher = {Springer}, address = {Tokyo}, issn = {1438-3896}, doi = {10.1007/s10144-014-0460-3}, pages = {237 -- 251}, year = {2015}, language = {en} } @article{GuhaWarsinkeTientcheuetal.2015, author = {Guha, S. and Warsinke, Axel and Tientcheu, Charles Merlin and Schmalz, K. and Meliani, C. and Wenger, Ch.}, title = {Label free sensing of creatinine using a 6 GHz CMOS near-field dielectric immunosensor}, series = {The analyst : the analytical journal of the Royal Society of Chemistry}, volume = {140}, journal = {The analyst : the analytical journal of the Royal Society of Chemistry}, number = {9}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {0003-2654}, doi = {10.1039/c4an02194k}, pages = {3019 -- 3027}, year = {2015}, abstract = {In this work we present a CMOS high frequency direct immunosensor operating at 6 GHz (C-band) for label free determination of creatinine. The sensor is fabricated in standard 0.13 mu m SiGe:C BiCMOS process. The report also demonstrates the ability to immobilize creatinine molecules on a Si3N4 passivation layer of the standard BiCMOS/CMOS process, therefore, evading any further need of cumbersome post processing of the fabricated sensor chip. The sensor is based on capacitive detection of the amount of non-creatinine bound antibodies binding to an immobilized creatinine layer on the passivated sensor. The chip bound antibody amount in turn corresponds indirectly to the creatinine concentration used in the incubation phase. The determination of creatinine in the concentration range of 0.88-880 mu M is successfully demonstrated in this work. A sensitivity of 35 MHz/10 fold increase in creatinine concentration (during incubation) at the centre frequency of 6 GHz is gained by the immunosensor. The results are compared with a standard optical measurement technique and the dynamic range and sensitivity is of the order of the established optical indication technique. The C-band immunosensor chip comprising an area of 0.3 mm(2) reduces the sensing area considerably, therefore, requiring a sample volume as low as 2 mu l. The small analyte sample volume and label free approach also reduce the experimental costs in addition to the low fabrication costs offered by the batch fabrication technique of CMOS/BiCMOS process.}, language = {en} } @article{MuellerBochBlaseretal.2015, author = {M{\"u}ller, J{\"o}rg and Boch, Steffen and Blaser, Steffen and Fischer, Markus and Prati, Daniel}, title = {Effects of forest management on bryophyte communities on deadwood}, series = {Nova Hedwigia : Zeitschrift f{\"u}r Kryptogamenkunde}, volume = {100}, journal = {Nova Hedwigia : Zeitschrift f{\"u}r Kryptogamenkunde}, number = {3-4}, publisher = {Cramer}, address = {Stuttgart}, issn = {0029-5035}, doi = {10.1127/nova_hedwigia/2015/0242}, pages = {423 -- 438}, year = {2015}, abstract = {Epixylic bryophytes are important components of forest vegetation but are currently endangered by increment of wood harvest and intensive forest management. In this paper we present a study about the relationship between forest management, deadwood abundance, deadwood attributes and species richness of epixylic bryophytes on 30 plots comprising three forest types (managed coniferous, managed deciduous and unmanaged deciduous forests) in three regions in Germany. Additionally we analyzed the relations between deadwood attributes (wood species, decay, deadwood type, size) and bryophytes on deadwood items (n = 799) and calculated species interaction networks of wood species and bryophytes. Overall, species richness of epixylic bryophytes was positively related to deadwood abundance and diversity. The mean deadwood abundance was lowest in unmanaged forests (9.7 m(3) ha(-1)) compared with 15.0 m(3) ha(-1) in managed deciduous and 25.1 m(3) ha(-1) in managed coniferous forests. Accordingly, epixylic bryophyte species richness per plot increased from 7 species per 400 m(2) in unmanaged, 10 in managed deciduous and 16 in managed coniferous forests. The interaction network provided evidence of importance of tree-species diversity for bryophyte diversity and the relevance of particular wood species for rare bryophytes. Generally, the results demonstrate a considerable lack of deadwood in all forest types, even in unmanaged forests. Species richness of epixylic bryophytes was strongly limited by available substrates within the observed deadwood abundance ranging up to only 60 m(3) ha(-1). Altogether, this suggests a high demand to increase both abundance and diversity of deadwood in forests.}, language = {en} } @article{HeinzeBergmannRilligetal.2015, author = {Heinze, Johannes and Bergmann, Joana and Rillig, Matthias C. and Joshi, Jasmin Radha}, title = {Negative biotic soil-effects enhance biodiversity by restricting potentially dominant plant species in grasslands}, series = {Perspectives in plant ecology, evolution and systematics}, volume = {17}, journal = {Perspectives in plant ecology, evolution and systematics}, number = {3}, publisher = {Elsevier}, address = {Jena}, issn = {1433-8319}, doi = {10.1016/j.ppees.2015.03.002}, pages = {227 -- 235}, year = {2015}, abstract = {Interactions between soil microorganisms and plants can play a vital role for plant fitness and therefore also for plant community composition and biodiversity. However, little is known about how biotic plant soil interactions influence the local dominance and abundance of plant species and whether specific taxonomic or functional groups of plants are differentially affected by such biotic soil-effects. In two greenhouse experiments, we tested the biotic soil-effects of 33 grassland species differing in individual size and local abundance. We hypothesized that large plants that are not locally dominant (despite their size-related competitive advantage enabling them to potentially outshade competitors) are most strongly limited by negative biotic soil-effects. We sampled soils at the opposite ends of a gradient in land-use intensity in temperate grasslands to account for putative modulating effects of land-use intensity on biotic soil-effects. As hypothesized, large, but non-dominant species (especially grasses) experienced more negative biotic soil-effects compared with small and abundant plant species. Land-use intensity had contrasting effects on grasses and herbs resulting in more negative biotic soil-effects for grasses in less intensively managed grasslands. We conclude that biotic soil-effects contribute to the control of potentially dominant plants and hence enable species coexistence and biodiversity especially in species-rich less intensively managed grasslands.}, language = {en} } @article{McKennaLeimkuehlerHerteretal.2015, author = {McKenna, Shane M. and Leimk{\"u}hler, Silke and Herter, Susanne and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Enzyme cascade reactions: synthesis of furandicarboxylic acid (FDCA) and carboxylic acids using oxidases in tandem}, series = {Green chemistry : an international journal and green chemistry resource}, volume = {17}, journal = {Green chemistry : an international journal and green chemistry resource}, number = {6}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9262}, doi = {10.1039/c5gc00707k}, pages = {3271 -- 3275}, year = {2015}, abstract = {A one-pot tandem enzyme reaction using galactose oxidase M3-5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74\% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions.}, language = {en} } @article{SprengerRudackSchudomaetal.2015, author = {Sprenger, Heike and Rudack, Katharina and Schudoma, Christian and Neumann, Arne and Seddig, Sylvia and Peters, Rolf and Zuther, Ellen and Kopka, Joachim and Hincha, Dirk K. and Walther, Dirk and Koehl, Karin}, title = {Assessment of drought tolerance and its potential yield penalty in potato}, series = {Functional plant biology : an international journal of plant function}, volume = {42}, journal = {Functional plant biology : an international journal of plant function}, number = {7}, publisher = {CSIRO}, address = {Clayton}, issn = {1445-4408}, doi = {10.1071/FP15013}, pages = {655 -- 667}, year = {2015}, abstract = {Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied the genetic variance, predictability of field performance and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit of water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial dataset, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified the deviation of relative starch yield from the experimental median (DRYM) as the most efficient index. DRYM corresponded qualitatively to the partial least square model-based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.}, language = {en} } @unpublished{ChattopadhyayChakrabortyGrossartetal.2015, author = {Chattopadhyay, Madhab K. and Chakraborty, Ranadhir and Grossart, Hans-Peter and Reddy, Gundlapally S. and Jagannadham, Medicharla V.}, title = {Antibiotic resistance of bacteria}, series = {BioMed research international}, journal = {BioMed research international}, publisher = {Hindawi Publishing Corp.}, address = {New York}, issn = {2314-6133}, doi = {10.1155/2015/501658}, pages = {2}, year = {2015}, language = {en} } @inproceedings{SpijkermandeCastroGaedke2015, author = {Spijkerman, Elly and de Castro, Francisco and Gaedke, Ursula}, title = {Independent colimitation for Co2 and inorganic phosphorus}, series = {European journal of phycology}, volume = {50}, booktitle = {European journal of phycology}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0967-0262}, pages = {98 -- 99}, year = {2015}, language = {en} } @inproceedings{LachmannSpijkermanMaberly2015, author = {Lachmann, Sabrina C. and Spijkerman, Elly and Maberly, Stephen C.}, title = {Ecology matters: linking inorganic carbon acquisition to ecological preference in four species of microalgae (Chlorophyceae)}, series = {European journal of phycology}, volume = {50}, booktitle = {European journal of phycology}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0967-0262}, pages = {98 -- 98}, year = {2015}, language = {en} } @inproceedings{Wegbrod2015, author = {Wegbrod, Jana}, title = {Influence of interspecific competition on photosynthetic rates of algal communities}, series = {European journal of phycology}, volume = {50}, booktitle = {European journal of phycology}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0967-0262}, pages = {71 -- 72}, year = {2015}, language = {en} } @article{CaronDeFrenneChabrerieetal.2015, author = {Caron, Maria Mercedes and De Frenne, P. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Decocq, G. and Diekmann, M. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, F. and Strimbeck, G. R. and Wulf, M. and Verheyen, Kris}, title = {Impacts of warming and changes in precipitation frequency on the regeneration of two Acer species}, series = {Flora : morphology, distribution, functional ecology of plants}, volume = {214}, journal = {Flora : morphology, distribution, functional ecology of plants}, publisher = {Elsevier}, address = {Jena}, issn = {0367-2530}, doi = {10.1016/j.flora.2015.05.005}, pages = {24 -- 33}, year = {2015}, language = {en} } @article{LombardoOttenAbdelilahSeyfried2015, author = {Lombardo, Veronica A. and Otten, Cecile and Abdelilah-Seyfried, Salim}, title = {Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis}, series = {Journal of visualized experiments}, journal = {Journal of visualized experiments}, number = {95}, publisher = {JoVE}, address = {Cambridge}, issn = {1940-087X}, doi = {10.3791/52087}, pages = {7}, year = {2015}, abstract = {The zebrafish embryonic heart is composed of only a few hundred cells, representing only a small fraction of the entire embryo. Therefore, to prevent the cardiac transcriptome from being masked by the global embryonic transcriptome, it is necessary to collect sufficient numbers of hearts for further analyses. Furthermore, as zebrafish cardiac development proceeds rapidly, heart collection and RNA extraction methods need to be quick in order to ensure homogeneity of the samples. Here, we present a rapid manual dissection protocol for collecting functional/beating hearts from zebrafish embryos. This is an essential prerequisite for subsequent cardiac-specific RNA extraction to determine cardiac-specific gene expression levels by transcriptome analyses, such as quantitative real-time polymerase chain reaction (RT-qPCR). The method is based on differential adhesive properties of the zebrafish embryonic heart compared with other tissues; this allows for the rapid physical separation of cardiac from extracardiac tissue by a combination of fluidic shear force disruption, stepwise filtration and manual collection of transgenic fluorescently labeled hearts.}, language = {en} } @article{DiekmannMuellerHeinkenetal.2015, author = {Diekmann, Martin and M{\"u}ller, Josef and Heinken, Thilo and Dupre, Cecilia}, title = {Survey and statistical analysis of plant reintroductions in Germany}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, number = {35}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, pages = {249 -- 265}, year = {2015}, abstract = {Aim - Plant reintroductions and other forms of targeted species translocations will in the future gain growing importance for nature conservation. In fragmented habitats, species reintroductions offer one of the most efficient tools for preserving or restoring plant diversity. In our study, we have compiled available data about plant reintroduction projects in Germany to answer the following questions: (1) What are the characteristics, habitat preferences and ecological strategies of species considered in plant reintroduction trials, and are these representative of the entire class of threatened species in Germany? (2) Is the judgment of the success or failure of plant reintroductions biased by the choice of species used in the experiments? (3) Do reintroduction efforts focus on those species for which Germany has a particularly high responsibility for conservation? Methods - Information about reintroduction projects in Germany were obtained from published and internet sources as well as unpublished reports. In our search we focused on single-species trials in the framework of scientific or conservation projects. For all threatened species included in our database, we compiled information on their systematics, life form, ecological strategies and habitat preferences. A list of all species being threatened nationally or regionally, comprising both reintroduced and not reintroduced species, served as a reference for statistical analysis. Results - The list of vascular plants used in conservation-oriented reintroductions consisted of 196 taxa. Species of families with large and conspicuous, mostly insect-pollinated flowers (for example, Orchidaceae) were over-represented among the reintroduced species compared to those threatened species not included in reintroduction trials. Species considered were also more often than expected found in semi-natural open habitats such as heathlands and grasslands. Notably, many projects focused on calcareous grasslands, characterized by dry, high-pH and infertile soils. In contrast, species of more near-natural vegetation (alpine and rocky formations, forests) were under-represented. About 25\% of the species that were reintroduced are not threatened on the national scale. Out of 150 species for which Germany has a particularly high responsibility for conservation, only 14 (9.3\%) were reintroduced. For only about 1/3 of all reintroduction attempts, success or failure were documented; whereas the success rate appears to be relatively low in nutrient-poor environments, trials with nutrient-demanding and competitive species were more successful. Conclusions - We conclude that conservation-oriented reintroduction attempts should focus more on species for which the country or a region has a particular high responsibility. Reintroductions, to a larger extent than at present, also need to consider the different chances of success in different habitat types and environments.}, language = {de} } @article{BudzikZuwalaKupferetal.2015, author = {Budzik, Karolina A. and Zuwala, Krystyna and Kupfer, Alexander and Gower, David J. and Wilkinson, Mark}, title = {Diverse anatomy of the tongue and taste organs in five species of caecilian (Amphibia: Gymnophiona)}, series = {Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography}, volume = {257}, journal = {Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography}, publisher = {Elsevier}, address = {Jena}, issn = {0044-5231}, doi = {10.1016/j.jcz.2015.04.007}, pages = {103 -- 109}, year = {2015}, abstract = {Limited previous studies on caecilian taste organs have demonstrated the presence of very few taste buds in the oral epithelium, while providing somewhat contradictory reports of their distribution within the oropharynx and across taxa. Here we report on the gross morphology of the tongue and explore the distribution, number and morphology of taste organs of five caecilian species representing five families, focusing upon variation within the group and investigating whether larvae and adults have the same type of taste organs. We find that taste buds are widespread in the oropharynx of caecilians and that they occur both in adults and larvae of a species with a biphasic life history. Thus Gymnophiona differ substantially from Batriachia, which have distinct larval and adult taste organs.}, language = {en} } @article{CornoSalkaPohlmannetal.2015, author = {Corno, Gianluca and Salka, Ivette and Pohlmann, Kirsten and Hall, Alex R. and Grossart, Hans-Peter}, title = {Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms}, series = {Aquatic microbial ecology : international journal}, volume = {76}, journal = {Aquatic microbial ecology : international journal}, number = {1}, publisher = {Institute of Mathematical Statistics}, address = {Oldendorf Luhe}, issn = {0948-3055}, doi = {10.3354/ame01765}, pages = {27 -- +}, year = {2015}, abstract = {Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems.}, language = {en} } @article{BhaskarMaLendleinetal.2015, author = {Bhaskar, Thanga Bhuvanesh Vijaya and Ma, Nan and Lendlein, Andreas and Roch, Toralf}, title = {The interaction of human macrophage subsets with silicone as a biomaterial}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {61}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-151991}, pages = {119 -- 133}, year = {2015}, abstract = {Silicones are widely used as biomaterials for medical devices such as extracorporeal equipments. However, there is often conflicting evidence about their supposed cell-and histocompatibility. Macrophages could mediate silicone-induced adverse responses such as foreign body reaction and fibrous encapsulation. The polarization behaviour of macrophages could determine the clinical outcome after implantation of biomaterials. Induction of classically activated macrophages (CAM) may induce and support uncontrolled inflammatory responses and undesired material degradation. In contrast, polarization into alternatively activated macrophages (AAM) is assumed to support healing processes and implant integration. This study compared the interaction of non-polarized macrophages (M0), CAM, and AAM with commercially available tissue culture polystyrene (TCP) and a medical grade silicone-based biomaterial, regarding the secretion of inflammatory mediators such as cytokines and chemokines. Firstly, by using the Limulus amoebocyte lysate (LAL) test the silicone films were shown to be free of soluble endotoxins, which is the prerequisite to investigate their interaction with primary immune cells. Primary human monocyte-derived macrophages (M0) were polarized into CAM and AAM by addition of suitable differentiation factors. These macrophage subsets were incubated on the materials for 24 hours and their viability and cytokine secretion was assessed. In comparison to TCP, cell adhesion was lower on silicone after 24 hours for all three macrophage subsets. However, compared to TCP, silicone induced higher levels of certain inflammatory and chemotactic cytokines in M0, CAM, and AAM macrophage subsets. Conclusively, it was shown that silicone has the ability to induce a pro-inflammatory state to different magnitudes dependent on the macrophage subsets. This priming of the macrophage phenotype by silicone could explain the incidence of severe foreign body complications observed in vivo.}, language = {en} } @article{TasiorBaldDeperasinskaetal.2015, author = {Tasior, Mariusz and Bald, Ilko and Deperasinska, Irena and Cywinski, Piotr J. and Gryko, Daniel T.}, title = {An internal charge transfer-dependent solvent effect in V-shaped azacyanines}, series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, volume = {13}, journal = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1477-0520}, doi = {10.1039/c5ob01633a}, pages = {11714 -- 11720}, year = {2015}, language = {en} } @article{PatheNeuschaeferRubeNeuschaeferRubeGenzetal.2015, author = {Pathe-Neuschaefer-Rube, Andrea and Neuschaefer-Rube, Frank and Genz, Lara and P{\"u}schel, Gerhard Paul}, title = {Botulinum Neurotoxin Dose-Dependently Inhibits Release of Neurosecretory Vesicle-Targeted Luciferase from Neuronal Cells}, series = {Alternatives to animal experimentation : ALTEX ; a journal for new paths in biomedical science}, volume = {32}, journal = {Alternatives to animal experimentation : ALTEX ; a journal for new paths in biomedical science}, number = {4}, publisher = {Springer}, address = {Heidelberg}, issn = {1868-596X}, pages = {297 -- 306}, year = {2015}, abstract = {Botulinum toxin is a bacterial toxin that inhibits neurotransmitter release from neurons and thereby causes a flaccid paralysis. It is used as drug to treat a number of serious ailments and, more frequently, for aesthetic medical interventions. Botulinum toxin for pharmacological applications is isolated from bacterial cultures. Due to partial denaturation of the protein, the specific activity of these preparations shows large variations. Because of its extreme potential toxicity, pharmacological preparations must be carefully tested for their activity. For the current gold standard, the mouse lethality assay, several hundred thousand mice are killed per year. Alternative methods have been developed that suffer from one or more of the following deficits: In vitro enzyme assays test only the activity of the catalytic subunit of the toxin. Enzymatic and cell based immunological assays are specific for just one of the different serotypes. The current study takes a completely different approach that overcomes these limitations: Neuronal cell lines were stably transfected with plasmids coding for luciferases of different species, which were N-terminally tagged with leader sequences that redirect the luciferase into neuro-secretory vesicles. From these vesicles, luciferases were released upon depolarization of the cells. The depolarization-dependent release was efficiently inhibited by botulinum toxin in a concentration range (1 to 100 pM) that is used in pharmacological preparations. The new assay might thus be an alternative to the mouse lethality assay and the immunological assays already in use.}, language = {en} } @article{TeasdalevanDoornFiddymentetal.2015, author = {Teasdale, Matthew David and van Doorn, N. L. and Fiddyment, S. and Webb, C. C. and Hofreiter, Michael and Collins, Matthew J. and Bradley, Daniel G.}, title = {Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0379}, pages = {7}, year = {2015}, abstract = {Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4\% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5\%. Over 45\% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7\% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.}, language = {en} } @article{LudwigReissmannBeneckeetal.2015, author = {Ludwig, Arne and Reissmann, Monika and Benecke, Norbert and Bellone, Rebecca and Sandoval-Castellanos, Edson and Cieslak, Michael and Gonz{\´a}lez-Fortes, Gloria M. and Morales-Muniz, Arturo and Hofreiter, Michael and Pruvost, Melanie}, title = {Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0386}, pages = {7}, year = {2015}, abstract = {Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.}, language = {en} } @unpublished{HagelbergHofreiterKeyser2015, author = {Hagelberg, Erika and Hofreiter, Michael and Keyser, Christine}, title = {Ancient DNA: the first three decades}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0371}, pages = {6}, year = {2015}, language = {en} } @article{NowakRussoSchlapbachetal.2015, author = {Nowak, Michael D. and Russo, Giancarlo and Schlapbach, Ralph and Cuong Nguyen Huu, and Lenhard, Michael and Conti, Elena}, title = {The draft genome of Primula veris yields insights into the molecular basis of heterostyly}, series = {Genome biology : biology for the post-genomic era}, volume = {16}, journal = {Genome biology : biology for the post-genomic era}, publisher = {BioMed Central}, address = {London}, issn = {1465-6906}, doi = {10.1186/s13059-014-0567-z}, pages = {16}, year = {2015}, abstract = {Background: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63\% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.}, language = {en} } @article{RenzOttenFaurobertetal.2015, author = {Renz, Marc and Otten, Cecile and Faurobert, Eva and Rudolph, Franziska and Zhu, Yuan and Boulday, Gwenola and Duchene, Johan and Mickoleit, Michaela and Dietrich, Ann-Christin and Ramspacher, Caroline and Steed, Emily and Manet-Dupe, Sandra and Benz, Alexander and Hassel, David and Vermot, Julien and Huisken, Jan and Tournier-Lasserve, Elisabeth and Felbor, Ute and Sure, Ulrich and Albiges-Rizo, Corinne and Abdelilah-Seyfried, Salim}, title = {Regulation of beta 1 Integrin-Klf2-Mediated angiogenesis by CCM proteins}, series = {Developmental cell}, volume = {32}, journal = {Developmental cell}, number = {2}, publisher = {Cell Press}, address = {Cambridge}, issn = {1534-5807}, doi = {10.1016/j.devcel.2014.12.016}, pages = {181 -- 190}, year = {2015}, abstract = {Mechanotransduction pathways are activated in response to biophysical stimuli during the development or homeostasis of organs and tissues. In zebrafish, the blood-flow-sensitive transcription factor Klf2a promotes VEGF-dependent angiogenesis. However, the means by which the Klf2a mechanotransduction pathway is regulated to prevent continuous angiogenesis remain unknown. Here we report that the upregulation of klf2 mRNA causes enhanced egfl7 expression and angiogenesis signaling, which underlies cardiovascular defects associated with the loss of cerebral cavernous malformation (CCM) proteins in the zebrafish embryo. Using CCM-protein-depleted human umbilical vein endothelial cells, we show that the misexpression of KLF2 mRNA requires the extracellular matrix-binding receptor beta 1 integrin and occurs in the absence of blood flow. Downregulation of beta 1 integrin rescues ccm mutant cardiovascular malformations in zebrafish. Our work reveals a beta 1 integrin-Klf2-Egfl7-signaling pathway that is tightly regulated by CCM proteins. This regulation prevents angiogenic overgrowth and ensures the quiescence of endothelial cells.}, language = {en} } @article{ProostVanBelVaneechoutteetal.2015, author = {Proost, Sebastian and Van Bel, Michiel and Vaneechoutte, Dries and Van de Peer, Yves and Inze, Dirk and M{\"u}ller-R{\"o}ber, Bernd and Vandepoele, Klaas}, title = {PLAZA 3.0: an access point for plant comparative genomics}, series = {Nucleic acids research}, volume = {43}, journal = {Nucleic acids research}, number = {D1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gku986}, pages = {D974 -- D981}, year = {2015}, abstract = {Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.}, language = {en} } @article{ImholtReilEccardetal.2015, author = {Imholt, Christian and Reil, Daniela and Eccard, Jana and Jacob, Daniela and Hempelmann, Nils and Jacob, Jens}, title = {Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus)}, series = {Pest management science}, volume = {71}, journal = {Pest management science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1526-498X}, doi = {10.1002/ps.3838}, pages = {166 -- 172}, year = {2015}, abstract = {BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry}, language = {en} } @misc{KirchnerIgnatova2015, author = {Kirchner, Sebastian and Ignatova, Zoya}, title = {Emerging roles of tRNA in adaptive translation, signalling dynamics and disease}, series = {Nature reviews}, volume = {16}, journal = {Nature reviews}, number = {2}, publisher = {Nature Publ. Group}, address = {London}, issn = {1471-0056}, doi = {10.1038/nrg3861}, pages = {98 -- 112}, year = {2015}, abstract = {tRNAs, nexus molecules between mRNAs and proteins, have a central role in translation. Recent discoveries have revealed unprecedented complexity of tRNA biosynthesis, modification patterns, regulation and function. In this Review, we present emerging concepts regarding how tRNA abundance is dynamically regulated and how tRNAs (and their nucleolytic fragments) are centrally involved in stress signalling and adaptive translation, operating across a wide range of timescales. Mutations in tRNAs or in genes affecting tRNA biogenesis are also linked to complex human diseases with surprising heterogeneity in tissue vulnerability, and we highlight cell-specific aspects that modulate the disease penetrance of tRNA-based pathologies.}, language = {en} } @misc{BeninaRibeiroGechevetal.2015, author = {Benina, Maria and Ribeiro, Dimas Mendes and Gechev, Tsanko S. and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M.}, title = {A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {38}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.12355}, pages = {349 -- 363}, year = {2015}, abstract = {Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels.}, language = {en} } @article{AttermeyerTittelAllgaieretal.2015, author = {Attermeyer, Katrin and Tittel, Joerg and Allgaier, Martin and Frindte, Katharina and Wurzbacher, Christian and Hilt, Sabine and Kamjunke, Norbert and Grossart, Hans-Peter}, title = {Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition}, series = {Microbial ecology}, volume = {69}, journal = {Microbial ecology}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0095-3628}, doi = {10.1007/s00248-014-0549-4}, pages = {361 -- 371}, year = {2015}, abstract = {The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties.}, language = {en} } @misc{WarrenSimberloffRicklefsetal.2015, author = {Warren, Ben H. and Simberloff, Daniel and Ricklefs, Robert E. and Aguilee, Robin and Condamine, Fabien L. and Gravel, Dominique and Morlon, Helene and Mouquet, Nicolas and Rosindell, James and Casquet, Juliane and Conti, Elena and Cornuault, Josselin and Maria Fernandez-Palacios, Jose and Hengl, Tomislav and Norder, Sietze J. and Rijsdijk, Kenneth F. and Sanmartin, Isabel and Strasberg, Dominique and Triantis, Kostas A. and Valente, Luis M. and Whittaker, Robert J. and Gillespie, Rosemary G. and Emerson, Brent C. and Thebaud, Christophe}, title = {Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson}, series = {Ecology letters}, volume = {18}, journal = {Ecology letters}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.12398}, pages = {200 -- 217}, year = {2015}, abstract = {The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, An equilibrium theory of insular zoogeography', was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re-assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution - understanding ecosystem functioning, speciation and diversification - frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future.}, language = {en} } @article{StillmanRailsbackGiskeetal.2015, author = {Stillman, Richard A. and Railsback, Steven Floyd and Giske, Jarl and Berger, Uta and Grimm, Volker}, title = {Making Predictions in a Changing World: The Benefits of Individual-Based Ecology}, series = {Bioscience}, volume = {65}, journal = {Bioscience}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0006-3568}, doi = {10.1093/biosci/biu192}, pages = {140 -- 150}, year = {2015}, abstract = {Ecologists urgently need a better ability to predict how environmental change affects biodiversity. We examine individual-based ecology (IBE), a research paradigm that promises better a predictive ability by using individual-based models (IBMs) to represent ecological dynamics as arising from how individuals interact with their environment and with each other. A key advantage of IBMs is that the basis for predictions-fitness maximization by individual organisms-is more general and reliable than the empirical relationships that other models depend on. Case studies illustrate the usefulness and predictive success of long-term IBE programs. The pioneering programs had three phases: conceptualization, implementation, and diversification. Continued validation of models runs throughout these phases. The breakthroughs that make IBE more productive include standards for describing and validating IBMs, improved and standardized theory for individual traits and behavior, software tools, and generalized instead of system-specific IBMs. We provide guidelines for pursuing IBE and a vision for future IBE research.}, language = {en} } @article{ReinhardRennerKupfer2015, author = {Reinhard, Sandy and Renner, Sandra and Kupfer, Alexander}, title = {Sexual dimorphism and age of Mediterranean salamanders}, series = {Zoology}, volume = {118}, journal = {Zoology}, number = {1}, publisher = {Elsevier}, address = {Jena}, issn = {0944-2006}, doi = {10.1016/j.zool.2014.08.002}, pages = {19 -- 26}, year = {2015}, abstract = {We analysed sexual size dimorphism (SSD) for two Mediterranean species of the "true" salamander clade possessing distinct life histories (Salamandra algira and Mertensiella caucasica) and equilibrated the morphometric approach to individual age by using skeletochronology. For species that have a short breeding season and live at high altitudes, such as Mediterranean amphibians, the fecundity advantage hypothesis predicts female-biased SSD to maximise reproductive success. Our results showed no SSD in either species; however, morphometric data indicated a male-biased dimorphism in limb (arm and leg) dimensions in both species when compared to body size. Limb dimorphisms are likely related to the particular mating system, which involves an amplexus during spermatophore transfer. Arm length appeared sexually dimorphic during ontogeny both in viviparous Salamandra algira and oviparous Mertensiella caucasica. A review on SSD indicated monomorphy of body size as a common lineage-specific pattern among the "true" salamander clade, but also the common presence of other traits such as sexually dimorphic limb proportions. (C) 2014 Elsevier GmbH. All rights reserved.}, language = {en} } @article{GermonpreSablinLaznickovaGaletovaetal.2015, author = {Germonpre, Mietje and Sablin, Mikhail V. and Laznickova-Galetova, Martina and Despres, Viviane and Stevens, Rhiannon E. and Stiller, Mathias and Hofreiter, Michael}, title = {Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014)}, series = {Journal of archaeological science}, volume = {54}, journal = {Journal of archaeological science}, publisher = {Elsevier}, address = {London}, issn = {0305-4403}, doi = {10.1016/j.jas.2014.11.035}, pages = {210 -- 216}, year = {2015}, abstract = {This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{HornHempelRistowetal.2015, author = {Horn, Sebastian and Hempel, Stefan and Ristow, Michael and Rillig, Matthias C. and Kowarik, Ingo and Caruso, Tancredi}, title = {Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland}, series = {Acta oecologica : international journal of ecology}, volume = {63}, journal = {Acta oecologica : international journal of ecology}, publisher = {Elsevier}, address = {Paris}, issn = {1146-609X}, doi = {10.1016/j.actao.2015.01.004}, pages = {56 -- 62}, year = {2015}, abstract = {Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18\% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14\% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved.}, language = {en} } @article{vanGervenBredervelddeKleinetal.2015, author = {van Gerven, Luuk P. A. and Brederveld, Robert J. and de Klein, Jeroen J. M. and DeAngelis, Don L. and Downing, Andrea S. and Faber, Michiel and Gerla, Daan J. and Janse, Jan H. and Janssen, Annette B. G. and Jeuken, Michel and Kooi, Bob W. and Kuiper, Jan J. and Lischke, Betty and Liu, Sien and Petzoldt, Thomas and Schep, Sebastiaan A. and Teurlincx, Sven and Thiange, Christophe and Trolle, Dennis and van Nes, Egbert H. and Mooij, Wolf M.}, title = {Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach}, series = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, volume = {186}, journal = {Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology}, number = {1-2}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {1863-9135}, doi = {10.1127/fal/2015/0631}, pages = {5 -- 20}, year = {2015}, abstract = {Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.}, language = {en} } @article{RobertGrunewaldSaueretal.2015, author = {Robert, Helene S. and Grunewald, Wim and Sauer, Michael and Cannoot, Bernard and Soriano, Mercedes and Swarup, Ranjan and Weijers, Dolf and Bennett, Malcolm and Boutilier, Kim and Friml, Jiri}, title = {Plant embryogenesis requires AUX/LAX-mediated auxin influx}, series = {Development : Company of Biologists}, volume = {142}, journal = {Development : Company of Biologists}, number = {4}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.115832}, pages = {702 -- 711}, year = {2015}, abstract = {The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop between MONOPTEROS-(ARF5)dependent auxin signalling and auxin transport. This MONOPTEROS dependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.}, language = {en} } @misc{PetrovHilleMuellerRoeberetal.2015, author = {Petrov, Veselin and Hille, Jacques and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.}, title = {ROS-mediated abiotic stress-induced programmed cell death in plants}, series = {Frontiers in plant science}, volume = {6}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2015.00069}, pages = {16}, year = {2015}, abstract = {During the course of their ontogenesis plants are continuously exposed to a large variety of abiotic stress factors which can damage tissues and jeopardize the survival of the organism unless properly countered. While animals can simply escape and thus evade stressors, plants as sessile organisms have developed complex strategies to withstand them. When the intensity of a detrimental factor is high, one of the defense programs employed by plants is the induction of programmed cell death (PCD). This is an active, genetically controlled process which is initiated to isolate and remove damaged tissues thereby ensuring the survival of the organism. The mechanism of PCD induction usually includes an increase in the levels of reactive oxygen species (ROS) which are utilized as mediators of the stress signal. Abiotic stress-induced PCD is not only a process of fundamental biological importance, but also of considerable interest to agricultural practice as it has the potential to significantly influence crop yield. Therefore, numerous scientific enterprises have focused on elucidating the mechanisms leading to and controlling PCD in response to adverse conditions in plants. This knowledge may help develop novel strategies to obtain more resilient crop varieties with improved tolerance and enhanced productivity. The aim of the present review is to summarize the recent advances in research on ROS-induced PCD related to abiotic stress and the role of the organelles in the process.}, language = {en} } @article{GeisslerPoyarkovGrismeretal.2015, author = {Geissler, Peter and Poyarkov, Nikolay A. and Grismer, Lee and Nguyen, Truong Q. and An, Hang T. and Neang, Thy and Kupfer, Alexander and Ziegler, Thomas and B{\"o}hme, Wolfgang and M{\"u}ller, Hendrik}, title = {New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969}, series = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik}, volume = {15}, journal = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1439-6092}, doi = {10.1007/s13127-014-0190-6}, pages = {143 -- 174}, year = {2015}, abstract = {Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided.}, language = {en} } @article{PietraLangGrebe2015, author = {Pietra, Stefano and Lang, Patricia and Grebe, Markus}, title = {SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana}, series = {Physiologia plantarum}, volume = {153}, journal = {Physiologia plantarum}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0031-9317}, doi = {10.1111/ppl.12257}, pages = {440 -- 453}, year = {2015}, abstract = {Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning.}, language = {en} } @article{HofreiterPaijmansGoodchildetal.2015, author = {Hofreiter, Michael and Paijmans, Johanna L. A. and Goodchild, Helen and Speller, Camilla F. and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Thomas, Jessica A. and Ludwig, Arne and Collins, Matthew J.}, title = {The future of ancient DNA: Technical advances and conceptual shifts}, series = {Bioessays : ideas that push the boundaries}, volume = {37}, journal = {Bioessays : ideas that push the boundaries}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0265-9247}, doi = {10.1002/bies.201400160}, pages = {284 -- 293}, year = {2015}, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, language = {en} } @article{SchwarteWegnerHavensteinetal.2015, author = {Schwarte, Sandra and Wegner, Fanny and Havenstein, Katja and Groth, Detlef and Steup, Martin and Tiedemann, Ralph}, title = {Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana}, series = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, volume = {87}, journal = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, number = {4-5}, publisher = {Springer}, address = {Dordrecht}, issn = {0167-4412}, doi = {10.1007/s11103-015-0293-2}, pages = {489 -- 519}, year = {2015}, abstract = {Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.}, language = {en} } @article{ZurellEggersKaatzetal.2015, author = {Zurell, Damaris and Eggers, Ute and Kaatz, Michael and Rotics, Shay and Sapir, Nir and Wikelski, Martin and Nathan, Ran and Jeltsch, Florian}, title = {Individual-based modelling of resource competition to predict density-dependent population dynamics: a case study with white storks}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.01294}, pages = {319 -- 330}, year = {2015}, abstract = {Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual-based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine-scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density-dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions.}, language = {en} } @misc{MendelLeimkuehler2015, author = {Mendel, Ralf R. and Leimk{\"u}hler, Silke}, title = {The biosynthesis of the molybdenum cofactors}, series = {Journal of biological inorganic chemistry}, volume = {20}, journal = {Journal of biological inorganic chemistry}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0949-8257}, doi = {10.1007/s00775-014-1173-y}, pages = {337 -- 347}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactors (Moco) is an ancient, ubiquitous, and highly conserved pathway leading to the biochemical activation of molybdenum. Moco is the essential component of a group of redox enzymes, which are diverse in terms of their phylogenetic distribution and their architectures, both at the overall level and in their catalytic geometry. A wide variety of transformations are catalyzed by these enzymes at carbon, sulfur and nitrogen atoms, which include the transfer of an oxo group or two electrons to or from the substrate. More than 50 molybdoenzymes were identified to date. In all molybdoenzymes except nitrogenase, molybdenum is coordinated to a dithiolene group on the 6-alkyl side chain of a pterin called molybdopterin (MPT). The biosynthesis of Moco can be divided into three general steps, with a fourth one present only in bacteria and archaea: (1) formation of the cyclic pyranopterin monophosphate, (2) formation of MPT, (3) insertion of molybdenum into molybdopterin to form Moco, and (4) additional modification of Moco in bacteria with the attachment of a nucleotide to the phosphate group of MPT, forming the dinucleotide variant of Moco. This review will focus on the biosynthesis of Moco in bacteria, humans and plants.}, language = {en} } @article{KoesslHechavarriaVossetal.2015, author = {K{\"o}ssl, Manfred and Hechavarria, Julio and Voss, Cornelia and Schaefer, Markus and Vater, Marianne}, title = {Bat auditory cortex - model for general mammalian auditory computation or special design solution for active time perception?}, series = {European journal of neuroscience}, volume = {41}, journal = {European journal of neuroscience}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0953-816X}, doi = {10.1111/ejn.12801}, pages = {518 -- 532}, year = {2015}, abstract = {Audition in bats serves passive orientation, alerting functions and communication as it does in other vertebrates. In addition, bats have evolved echolocation for orientation and prey detection and capture. This put a selective pressure on the auditory system in regard to echolocation-relevant temporal computation and frequency analysis. The present review attempts to evaluate in which respect the processing modules of bat auditory cortex (AC) are a model for typical mammalian AC function or are designed for echolocation-unique purposes. We conclude that, while cortical area arrangement and cortical frequency processing does not deviate greatly from that of other mammals, the echo delay time-sensitive dorsal cortex regions contain special designs for very powerful time perception. Different bat species have either a unique chronotopic cortex topography or a distributed salt-and-pepper representation of echo delay. The two designs seem to enable similar behavioural performance.}, language = {en} } @article{ZhangHankeGogokhiaJiangetal.2015, author = {Zhang, Houbin and Hanke-Gogokhia, Christin and Jiang, Li and Li, Xiaobo and Wang, Pu and Gerstner, Cecilia D. and Frederick, Jeanne M. and Yang, Zhenglin and Baehr, Wolfgang}, title = {Mistrafficking of prenylated proteins causes retinitis pigmentosa 2}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {29}, journal = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, number = {3}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, doi = {10.1096/fj.14-257915}, pages = {932 -- 942}, year = {2015}, abstract = {The retinitis pigmentosa 2 polypeptide (RP2) functions as a GTPase-activating protein (GAP) for ARL3 (Arf-like protein 3), a small GTPase. ARL3 is an effector of phosphodiesterase 6 Delta (PDE6D), a prenyl-binding protein and chaperone of prenylated protein in photoreceptors. Mutations in the human RP2 gene cause X-linked retinitis pigmentosa (XLRP) and cone-rod dystrophy (XL-CORD). To study mechanisms causing XLRP, we generated an RP2 knockout mouse. The RP2h(-/-) mice exhibited a slowly progressing rod-cone dystrophy simulating the human disease. RP2h(-/-) scotopic a-wave and photopic b-wave amplitudes declined at 1 mo of age and continued to decline over the next 6 mo. Prenylated PDE6 subunits and G-protein coupled receptor kinase 1 (GRK1) were unable to traffic effectively to the RP2h(-/-) outer segments. Mechanistically, absence of RP2 GAP activity increases ARL3-GTP levels, forcing PDE6D to assume a predominantly "closed" conformation that impedes binding of lipids. Lack of interaction disrupts trafficking of PDE6 and GRK1 to their destination, the photoreceptor outer segments. We propose that hyperactivity of ARL3-GTP in RP2 knockout mice and human patients with RP2 null alleles leads to XLRP resembling recessive rod-cone dystrophy.}, language = {en} } @article{CastelliniPaltrinieriManca2015, author = {Castellini, Alberto and Paltrinieri, Daniele and Manca, Vincenzo}, title = {MP-GeneticSynth: inferring biological network regulations from time series}, series = {Bioinformatics}, volume = {31}, journal = {Bioinformatics}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btu694}, pages = {785 -- 787}, year = {2015}, abstract = {MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis.}, language = {en} } @article{DammhahnRakotondramananaGoodman2015, author = {Dammhahn, Melanie and Rakotondramanana, Claude Fabienne and Goodman, Steven M.}, title = {Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar: stable isotopes reveal fine-grained niche differentiation among cryptic species}, series = {Journal of tropical ecology}, volume = {31}, journal = {Journal of tropical ecology}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0266-4674}, doi = {10.1017/S0266467414000741}, pages = {153 -- 164}, year = {2015}, abstract = {Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0\% in delta N-15, i.e. two trophic levels, and 4.2\% in delta C-13 with a community mean of 11.3\% in delta N-15 and - 21.0\% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4\%, delta C-13: 1.0\%) with a community mean of 8.0\% delta N-15 and - 21.7\% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa.}, language = {en} } @article{AlseekhTohgeWendenbergetal.2015, author = {Alseekh, Saleh and Tohge, Takayuki and Wendenberg, Regina and Scossa, Federico and Omranian, Nooshin and Li, Jie and Kleessen, Sabrina and Giavalisco, Patrick and Pleban, Tzili and M{\"u}ller-R{\"o}ber, Bernd and Zamir, Dani and Nikoloski, Zoran and Fernie, Alisdair R.}, title = {Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato}, series = {The plant cell}, volume = {27}, journal = {The plant cell}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.132266}, pages = {485 -- 512}, year = {2015}, abstract = {A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.}, language = {en} } @misc{KnappLaluezaFoxHofreiter2015, author = {Knapp, Michael and Lalueza-Fox, Carles and Hofreiter, Michael}, title = {Re-inventing ancient human DNA}, series = {Investigative Genetics}, volume = {6}, journal = {Investigative Genetics}, publisher = {BioMed Central}, address = {London}, issn = {2041-2223}, doi = {10.1186/s13323-015-0020-4}, pages = {11}, year = {2015}, abstract = {For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next-or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.}, language = {en} } @article{GorochowskiIgnatovaBovenbergetal.2015, author = {Gorochowski, Thomas E. and Ignatova, Zoya and Bovenberg, Roel A. L. and Roubos, Johannes A.}, title = {Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate}, series = {Nucleic acids research}, volume = {43}, journal = {Nucleic acids research}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkv199}, pages = {3022 -- 3032}, year = {2015}, abstract = {Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.}, language = {en} } @article{PechouskovaDammhahnBrameieretal.2015, author = {Pechouskova, Eva and Dammhahn, Melanie and Brameier, Markus and Fichtel, Claudia and Kappeler, Peter M. and Huchard, Elise}, title = {MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener}, series = {Immunogenetics}, volume = {67}, journal = {Immunogenetics}, number = {4}, publisher = {Springer}, address = {New York}, issn = {0093-7711}, doi = {10.1007/s00251-015-0827-4}, pages = {229 -- 245}, year = {2015}, abstract = {The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe's mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB.}, language = {en} } @article{KoeslinFindekleeRiziBeckeretal.2015, author = {K{\"o}slin-Findeklee, Fabian and Rizi, Vajiheh Safavi and Becker, Martin A. and Parra-Londono, Sebastian and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Kunze, Reinhard and Horst, Walter J.}, title = {Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.)}, series = {Plant science : an international journal of experimental plant biology}, volume = {233}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier}, address = {Clare}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2014.11.018}, pages = {174 -- 185}, year = {2015}, abstract = {High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved.}, language = {en} } @article{AlterMeyerPostetal.2015, author = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael}, title = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100}, series = {Molecular ecology}, volume = {24}, journal = {Molecular ecology}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13121}, pages = {1510 -- 1522}, year = {2015}, abstract = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.}, language = {en} } @article{PaulMamonekeneVateretal.2015, author = {Paul, Christiane and Mamonekene, Victor and Vater, Marianne and Feulner, Philine G. D. and Engelmann, Jacob and Tiedemann, Ralph and Kirschbaum, Frank}, title = {Comparative histology of the adult electric organ among four species of the genus Campylomormyrus (Teleostei: Mormyridae)}, series = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {201}, journal = {Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology}, number = {4}, publisher = {Springer}, address = {New York}, issn = {0340-7594}, doi = {10.1007/s00359-015-0995-6}, pages = {357 -- 374}, year = {2015}, abstract = {The electric organ (EO) of weakly electric mormyrids consists of flat, disk-shaped electrocytes with distinct anterior and posterior faces. There are multiple species-characteristic patterns in the geometry of the electrocytes and their innervation. To further correlate electric organ discharge (EOD) with EO anatomy, we examined four species of the mormyrid genus Campylomormyrus possessing clearly distinct EODs. In C. compressirostris, C. numenius, and C. tshokwe, all of which display biphasic EODs, the posterior face of the electrocytes forms evaginations merging to a stalk system receiving the innervation. In C. tamandua that emits a triphasic EOD, the small stalks of the electrocyte penetrate the electrocyte anteriorly before merging on the anterior side to receive the innervation. Additional differences in electrocyte anatomy among the former three species with the same EO geometry could be associated with further characteristics of their EODs. Furthermore, in C. numenius, ontogenetic changes in EO anatomy correlate with profound changes in the EOD. In the juvenile the anterior face of the electrocyte is smooth, whereas in the adult it exhibits pronounced surface foldings. This anatomical difference, together with disparities in the degree of stalk furcation, probably contributes to the about 12 times longer EOD in the adult.}, language = {en} } @article{WeithoffRochaGaedke2015, author = {Weithoff, Guntram and Rocha, Marcia R. and Gaedke, Ursula}, title = {Comparing seasonal dynamics of functional and taxonomic diversity reveals the driving forces underlying phytoplankton community structure}, series = {Freshwater biology}, volume = {60}, journal = {Freshwater biology}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/fwb.12527}, pages = {758 -- 767}, year = {2015}, abstract = {In most biodiversity studies, taxonomic diversity is the measure for the multiplicity of species and is often considered to represent functional diversity. However, trends in taxonomic diversity and functional diversity may differ, for example, when many functionally similar but taxonomically different species co-occur in a community. The differences between these diversity measures are of particular interest in diversity research for understanding diversity patterns and their underlying mechanisms. We analysed a temporally highly resolved 20-year time series of lake phytoplankton to determine whether taxonomic diversity and functional diversity exhibit similar or contrasting seasonal patterns. We also calculated the functional mean of the community in n-dimensional trait space for each sampling day to gain further insights into the seasonal dynamics of the functional properties of the community. We found an overall weak positive relationship between taxonomic diversity and functional diversity with a distinct seasonal pattern. The two diversity measures showed synchronous behaviour from early spring to mid-summer and a more complex and diverging relationship from autumn to late winter. The functional mean of the community exhibited a recurrent annual pattern with the most prominent changes before and after the clear-water phase. From late autumn to winter, the functional mean of the community and functional diversity were relatively constant while taxonomic diversity declined, suggesting competitive exclusion during this period. A further decline in taxonomic diversity concomitant with increasing functional diversity in late winter to early spring is seen as a result of niche diversification together with competitive exclusion. Under these conditions, several different sets of traits are suitable to thrive, but within one set of functional traits only one, or very few, morphotypes can persist. Taxonomic diversity alone is a weak descriptor of trait diversity in phytoplankton. However, the combined analysis of taxonomic diversity and functional diversity, along with the functional mean of the community, allows for deeper insights into temporal patterns of community assembly and niche diversification.}, language = {en} } @article{CochardEdwardsWeber2015, author = {Cochard, Roland and Edwards, Peter J. and Weber, Ewald}, title = {Post-ranching tree-grass interactions in secondary Acacia zanzibarica woodlands in coastal Tanzania - an experimental study}, series = {Applied vegetation science : official organ of the International Association for Vegetation Science}, volume = {18}, journal = {Applied vegetation science : official organ of the International Association for Vegetation Science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1402-2001}, doi = {10.1111/avsc.12134}, pages = {297 -- 310}, year = {2015}, abstract = {Questions: We studied a humid savanna rangeland., abandoned in 2000, where intensive cattle grazing had led to widespread encroachment by Acacia zanzibarica. We asked whether the acacia trees were able to regenerate in the absence of domesJic livestock, either beneath acacia canopies or in artificial clearings. Location: Tropical coastal Tanzania (former Mkwaja Ranch, now in Saadani National Park). Methods: We set out a total of 48 plots on four sites in November 2001, and assigned them to three treatments: trees felled (FN), trees felled and the stumps poisoned (FP) with Triclopyr, and no intervention (controls, NN). We analysed soils of plots for texture and nutrients. In two wet (July 2002 and 2003) and one dry (February 2003) seasons we assessed grass and tree leaf biomass and transpiration rates, and counted acacia seedlings and resprouts. The effects of treatments (controlled for site and other co-variables) on grass growth and acacia rectaiitment were determined statistically using general linear models (GLM). Results: Acacia leaves had a much higher stomatal conductance than grasses, with the consequence that total evapotranspiration in woodland was higher than in clearings. In the wet seasons, grass biomass and seedling densities were significantly higher in clearings than in control plots, which we attributed to more.favourable moisture conditions, In the dry season, by contrast, we found no differences, and all seedlings had died. On FN plots, 71\% of stumps, and on FP plots, 11\% resprouted (coppicing), but only a quarter of these shoots survived until July 2003. Root suckering occurred spontaneously at low densities. No root suckers or resprouts grew beyond the grass layer. Conclusions: Acacia woodlands do not regenerate in the absence of cattle grazing, and tree cutting in combination with appropriate fire management could potentially accelerate re-establishment of open grassland. However, regeneration might occur in the future due to the increasing wildlife populations within the new national park.}, language = {en} } @article{ContinFrascaVivekananthanetal.2015, author = {Contin, Andrea and Frasca, Stefano and Vivekananthan, Jeevanthi and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Plumere, Nicolas and Schuhmann, Wolfgang}, title = {A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {27}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {4}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400621}, pages = {938 -- 944}, year = {2015}, abstract = {The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation.}, language = {en} } @article{HoenickeBlissMoritz2015, author = {H{\"o}nicke, Christiane and Bliss, Peter and Moritz, Robin F. A.}, title = {Effect of density on traffic and velocity on trunk trails of Formica pratensis}, series = {The science of nature}, volume = {102}, journal = {The science of nature}, number = {3-4}, publisher = {Springer}, address = {Heidelberg}, issn = {0028-1042}, doi = {10.1007/s00114-015-1267-6}, pages = {9}, year = {2015}, abstract = {The allocation of large numbers of workers facilitates the swift intake of locally available resources which is essential for ant colony survival. To organise the traffic between nest and food source, the black-meadow ant Formica pratensis establishes permanent trunk trails, which are maintained by the ants. To unravel the ant organisation and potential traffic rules on these trails, we analysed velocity and lane segregation under various densities by experimentally changing feeding regimes. Even under the highest ant densities achieved, we never observed any traffic jams. On the contrary, velocity increased after supplementary feeding despite an enhanced density. Furthermore, inbound ants returning to the nest had a higher velocity than those leaving the colony. Whilst at low and medium density the ants used the centre of the trail, they used the full width of the trail at high density. Outbound ants also showed some degree of lane segregation which contributes to traffic organisation.}, language = {en} } @inproceedings{DonohueSmithBroekeretal.2015, author = {Donohue, Patrick and Smith, Mychal Daijon and Br{\"o}ker, Nina Kristin and Doering, Carolin and Mattos, Carla and Barbirz, Stefanie}, title = {Multiple Solvent Crystal Structures of phage P22 tailspike protein: An analysis of binding site hot spots and surface hydration}, series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, volume = {29}, booktitle = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology}, publisher = {Federation of American Societies for Experimental Biology}, address = {Bethesda}, issn = {0892-6638}, pages = {1}, year = {2015}, language = {en} } @article{RoethleinMiettinenIgnatova2015, author = {R{\"o}thlein, Christoph and Miettinen, Markus S. and Ignatova, Zoya}, title = {A flexible approach to assess fluorescence decay functions in complex energy transfer systems}, series = {BMC biophysics}, volume = {8}, journal = {BMC biophysics}, publisher = {BioMed Central}, address = {London}, issn = {2046-1682}, doi = {10.1186/s13628-015-0020-z}, pages = {10}, year = {2015}, abstract = {Background: Time-correlated Forster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions. Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems. Conclusion: This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.}, language = {en} } @article{SchrapersHartmannKositzkietal.2015, author = {Schrapers, Peer and Hartmann, Tobias and Kositzki, Ramona and Dau, Holger and Reschke, Stefan and Schulzke, Carola and Leimk{\"u}hler, Silke and Haumann, Michael}, title = {'Sulfido and Cysteine Ligation Changes at the Molybdenum Cofactor during Substrate Conversion by Formate Dehydrogenase (FDH) from Rhodobacter capsulatus}, series = {Inorganic chemistry}, volume = {54}, journal = {Inorganic chemistry}, number = {7}, publisher = {American Chemical Society}, address = {Washington}, issn = {0020-1669}, doi = {10.1021/ic502880y}, pages = {3260 -- 3271}, year = {2015}, abstract = {Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO-) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Moligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH.}, language = {en} } @article{ZengPankratovFalketal.2015, author = {Zeng, Ting and Pankratov, Dmitry and Falk, Magnus and Leimk{\"u}hler, Silke and Shleev, Sergey and Wollenberger, Ursula}, title = {Miniature direct electron transfer based sulphite/oxygen enzymatic fuel cells}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {66}, 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.2014.10.080}, pages = {39 -- 42}, year = {2015}, abstract = {A direct electron transfer (DET) based sulphite/oxygen biofuel cell is reported that utilises human sulphite oxidase (hSOx) and Myrothecium verrucaria bilirubin oxidase (MvBOx) and nanostructured gold electrodes. For bioanode construction, the nanostructured gold microelectrodes were further modified with 3,3'-dithiodipropionic acid di(N-hydroxysuccinimide ester) to which polyethylene imine was covalently attached. hSOx was adsorbed onto this chemically modified nanostructured electrode with high surface loading of electroactive enzyme and in presence of sulphite high anodic bioelectrocatalytic currents were generated with an onset potential of 0.05 V vs. NHE. The biocathode contained MyBOx directly adsorbed to the deposited gold nanoparticles for cathodic oxygen reduction starting at 0.71 V vs. NHE. Both enzyme electrodes were integrated to a DET-type biofuel cell. Power densities of 8 and 1 mu W cm(-2) were achieved at 0.15 V and 0.45 V of cell voltages, respectively, with the membrane based biodevices under aerobic conditions. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{CaronDeFrenneBrunetetal.2015, author = {Caron, Maria Mercedes and De Frenne, Pieter and Brunet, J{\"o}rg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Diekmann, Martin and Graae, Bente Jessen and Heinken, Thilo and Kolb, Annette and Lenoir, Jonathan and Naaf, Tobias and Plue, Jan and Selvi, Federico and Wulf, Monika and Verheyen, Kris}, title = {Divergent regeneration responses of two closely related tree species to direct abiotic and indirect biotic effects of climate change}, series = {Forest ecology and management}, volume = {342}, journal = {Forest ecology and management}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-1127}, doi = {10.1016/j.foreco.2015.01.003}, pages = {21 -- 29}, year = {2015}, abstract = {Changing temperature and precipitation can strongly influence plant reproduction. However, also biotic interactions might indirectly affect the reproduction and recruitment success of plants in the context of climate change. Information about the interactive effects of changes in abiotic and biotic factors is essential, but still largely lacking, to better understand the potential effects of a changing climate on plant populations. Here we analyze the regeneration from seeds of Acer platanoides and Acer pseudoplatanus, two currently secondary forest tree species from seven regions along a 2200 km-wide latitudinal gradient in Europe. We assessed the germination, seedling survival and growth during two years in a common garden experiment where temperature, precipitation and competition with the understory vegetation were manipulated. A. platanoides was more sensitive to changes in biotic conditions while A. pseudoplatanus was affected by both abiotic and biotic changes. In general, competition reduced (in A. platanoides) and warming enhanced (in A. pseudoplatanus) germination and survival, respectively. Reduced competition strongly increased the growth of A. platanoides seedlings. Seedling responses were independent of the conditions experienced by the mother tree during seed production and maturation. Our results indicate that, due to the negative effects of competition on the regeneration of A. platanoides, it is likely that under stronger competition (projected under future climatic conditions) this species will be negatively affected in terms of germination, survival and seedling biomass. Climate-change experiments including both abiotic and biotic factors constitute a key step forward to better understand the response of tree species' regeneration to climate change. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @misc{XiangHofreiterZhao2015, author = {Xiang, Hai and Hofreiter, Michael and Zhao, Xingbo}, title = {Reply to Peng et al.: Archaeological contexts should not be ignored for early chicken domestication}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {16}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1502207112}, pages = {E1972 -- E1973}, year = {2015}, language = {en} } @article{ReinhardRennerKupfer2015, author = {Reinhard, Sandy and Renner, Sandra and Kupfer, Alexander}, title = {Age and fecundity in Salamandra algira (Caudata: Salamandridae)}, series = {Salamandra : German journal of herpetology}, volume = {51}, journal = {Salamandra : German journal of herpetology}, number = {1}, publisher = {Deutsche Gesellschaft f{\"u}r Herpetologie und Terrarienkunde}, address = {Darmstadt}, issn = {0036-3375}, pages = {19 -- 24}, year = {2015}, abstract = {Amphibians are characterised by potentially indefinite growth. Their body size reflects a trade-off between growth and reproduction. Consequently, growth decreases or even ceases after maturation. Furthermore, the sexes often mature at different ages (sexual bimaturity). We examined fecundity patterns of the terrestrial salamander Salamandra algira (Salamandridae) and tested if age, body size and the fecundity of both sexes are connected and how these reproductive traits interact. We revealed positive correlations for female size, age and fecundity traits, i.e., egg number and volume. The male number of testes lobes was also positively correlated with age. Our study provides basic data on a rarely studied terrestrial salamandrid. Further collection-based research is needed to obtain additional data aiding the understanding of life history evolution of the Salamandridae.}, language = {en} } @article{HuettlHettrichRiedeletal.2015, author = {H{\"u}ttl, Christine and Hettrich, Cornelia and Riedel, Melanie and Henklein, Petra and Rawel, Harshadrai Manilal and Bier, Frank Fabian}, title = {Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition}, series = {Chemical biology \& drug design}, volume = {85}, journal = {Chemical biology \& drug design}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1747-0277}, doi = {10.1111/cbdd.12444}, pages = {565 -- 573}, year = {2015}, abstract = {A straightforward synthesis strategy to multimerize a peptide mimotopes for antibody B13-DE1 recognition is described based on lysine dendrons as multivalent scaffolds. Lysine dendrons that possess N-terminal alkyne residues at the periphery were quantitative functionalized with azido peptides using click chemistry. The solid-phase peptide synthesis (SPPS) allows preparing the peptide dendron in high purity and establishing the possibility of automation. The presented peptide dendron is a promising candidate as multivalent ligand and was used for antibody B13-DE1 recognition. The binding affinity increases with higher dendron generation without loss of specificity. The analysis of biospecific interaction between the synthesized peptide dendron and the antibody was done via surface plasmon resonance (SPR) technique. The presented results show a promising tool for investigations of antigen-antibody reactions.}, language = {en} } @article{LiesenjohannLiesenjohannTrebatickaetal.2015, author = {Liesenjohann, Thilo and Liesenjohann, Monique and Trebaticka, Lenka and Sundell, Janne and Haapakoski, Marko and Ylonen, Hannu and Eccard, Jana}, title = {State-dependent foraging: lactating voles adjust their foraging behavior according to the presence of a potential nest predator and season}, series = {Behavioral ecology and sociobiology}, volume = {69}, journal = {Behavioral ecology and sociobiology}, number = {5}, publisher = {Springer}, address = {New York}, issn = {0340-5443}, doi = {10.1007/s00265-015-1889-x}, pages = {747 -- 754}, year = {2015}, abstract = {Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors "shrew presence" and "season." We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother's foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision.}, language = {en} } @article{HuVoellerSussmuthetal.2015, author = {Hu, Chenlin and V{\"o}ller, Ginka and Sussmuth, Roderich and Dittmann-Th{\"u}nemann, Elke and Kehr, Jan-Christoph}, title = {Functional assessment of mycosporine-like amino acids in Microcystis aeruginosa strain PCC 7806}, series = {Environmental microbiology}, volume = {17}, journal = {Environmental microbiology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.12577}, pages = {1548 -- 1559}, year = {2015}, abstract = {The biological role of the widespread mycosporine-like amino acids (MAAs) in cyanobacteria is under debate. Here, we have constructed and characterized two mutants impaired in MAA biosynthesis in the bloom-forming cyanobacterium Microcystis aeruginosaPCC 7806. We could identify shinorine as the sole MAA type of the strain, which is exclusively located in the extracellular matrix. Bioinformatic studies as wells as polymerase chain reaction screening revealed that the ability to produce MAAs is sporadically distributed within the genus. Growth experiments and reactive oxygen species quantification with wild-type and mutant strains did not support a role of shinorine in protection against UV or other stress conditions in M.aeruginosaPCC 7806. The shinorine content per dry weight of cells as well as transcription of the mys gene cluster was not significantly elevated in response to UV-A, UV-B or any other stress condition tested. Remarkably, both mutants exhibited pronounced morphological changes compared with the wild type. We observed an increased accumulation and an enhanced hydrophobicity of the extracellular matrix. Our study suggests that MAAs in Microcystis play a negligible role in protection against UV radiation but might be a strain-specific trait involved in extracellular matrix formation and cell-cell interaction.}, language = {en} } @article{MeissnerSteinhauserDittmannThuenemann2015, author = {Meissner, Sven and Steinhauser, Dirk and Dittmann-Th{\"u}nemann, Elke}, title = {Metabolomic analysis indicates a pivotal role of the hepatotoxin microcystin in high light adaptation of Microcystis}, series = {Environmental microbiology}, volume = {17}, journal = {Environmental microbiology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.12565}, pages = {1497 -- 1509}, year = {2015}, abstract = {Microcystis is a freshwater cyanobacterium frequently forming nuisance blooms in the summer months. The genus belongs to the predominant producers of the potent hepatotoxin microcystin. The success of Microcystis and its remarkable resistance to high light conditions are not well understood. Here, we have compared the metabolic response of Microcystis aeruginosaPCC7806, its microcystin-deficient mcyB mutant (Mut) and the cyanobacterial model organism SynechocystisPCC6803 to high light exposure of 250molphotonsm(-2)s(-1) using GC/MS-based metabolomics. Microcystis wild type and Mut show pronounced differences in their metabolic reprogramming upon high light. Seventeen percent of the detected metabolites showed significant differences between the two genotypes after high light exposure. Whereas the microcystin-producing wild type shows a faster accumulation of glycolate upon high light illumination, loss of microcystin leads to an accumulation of general stress markers such as trehalose and sucrose. The study further uncovers differences in the high light adaptation of the bloom-forming cyanobacterium Microcystis and the model cyanobacterium Synechocystis. Most notably, Microcystis invests more into carbon reserves such as glycogen after high light exposure. Our data shed new light on the lifestyle of bloom-forming cyanobacteria, the role of the widespread toxin microcystin and the metabolic diversity of cyanobacteria.}, language = {en} } @article{ChoiKlostermanKummeretal.2015, author = {Choi, Young-Joon and Klosterman, Steven J. and Kummer, Volker and Voglmayr, Hermann and Shin, Hyeon-Dong and Thines, Marco}, title = {Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach}, series = {Molecular phylogenetics and evolution}, volume = {86}, journal = {Molecular phylogenetics and evolution}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2015.03.003}, pages = {24 -- 34}, year = {2015}, abstract = {Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. (C) 2015 Elsevier Inc. All rights reserved.}, language = {en} } @article{ApeltBreuerNikoloskietal.2015, author = {Apelt, Federico and Breuer, David and Nikoloski, Zoran and Stitt, Mark and Kragler, Friedrich}, title = {Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth}, series = {The plant journal}, volume = {82}, journal = {The plant journal}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12833}, pages = {693 -- 706}, year = {2015}, abstract = {Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge.}, language = {en} } @article{VenailGrossOakleyetal.2015, author = {Venail, Patrick and Gross, Kevin and Oakley, Todd H. and Narwani, Anita and Allan, Eric and Flombaum, Pedro and Isbell, Forest and Joshi, Jasmin Radha and Reich, Peter B. and Tilman, David and van Ruijven, Jasper and Cardinale, Bradley J.}, title = {Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies}, series = {Functional ecology : an official journal of the British Ecological Society}, volume = {29}, journal = {Functional ecology : an official journal of the British Ecological Society}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0269-8463}, doi = {10.1111/1365-2435.12432}, pages = {615 -- 626}, year = {2015}, abstract = {Hundreds of experiments have now manipulated species richness (SR) of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity (PD) among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than SR because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we reanalyse data from 16 experiments that have manipulated plant SR in grassland ecosystems and examined the impact on above-ground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the PD of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses, we show that, after statistically controlling for variation in SR, PD (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for SR, PD was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. In contrast to the non-significant relationships between PD, biomass and stability, our analyses show that SR per se tends to increase the mean biomass production of plant communities, after controlling for PD. The relationship between SR and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with SR, independently of PD, always led to increased stability. These results suggest that PD is no better as a predictor of ecosystem functioning than SR.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate PD to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of SR as a way to maintain productive and stable communities under changing environmental conditions.}, language = {en} } @misc{OmranianKleessenTohgeetal.2015, author = {Omranian, Nooshin and Kleessen, Sabrina and Tohge, Takayuki and Klie, Sebastian and Basler, Georg and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Differential metabolic and coexpression networks of plant metabolism}, series = {Trends in plant science}, volume = {20}, journal = {Trends in plant science}, number = {5}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2015.02.002}, pages = {266 -- 268}, year = {2015}, abstract = {Recent analyses have demonstrated that plant metabolic networks do not differ in their structural properties and that genes involved in basic metabolic processes show smaller coexpression than genes involved in specialized metabolism. By contrast, our analysis reveals differences in the structure of plant metabolic networks and patterns of coexpression for genes in (non)specialized metabolism. Here we caution that conclusions concerning the organization of plant metabolism based on network-driven analyses strongly depend on the computational approaches used.}, language = {en} } @article{WannickeFrindteGustetal.2015, author = {Wannicke, Nicola and Frindte, Katharina and Gust, Giselher and Liskow, Iris and Wacker, Alexander and Meyer, Andreas and Grossart, Hans-Peter}, title = {Measuring bacterial activity and community composition at high hydrostatic pressure using a novel experimental approach: a pilot study}, series = {FEMS microbiology ecology}, volume = {91}, journal = {FEMS microbiology ecology}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0168-6496}, doi = {10.1093/femsec/fiv036}, pages = {15}, year = {2015}, abstract = {In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 +/- 1.4 and 3.9 +/- 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 +/- 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 +/- 1.5 and 2.9 +/- 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump.}, language = {en} } @article{SchwarzenbergerWacker2015, author = {Schwarzenberger, Anke and Wacker, Alexander}, title = {Melatonin synthesis follows a daily cycle in Daphnia}, series = {Journal of plankton research}, volume = {37}, journal = {Journal of plankton research}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbv029}, pages = {636 -- 644}, year = {2015}, abstract = {In freshwater systems, Daphnia has been demonstrated to show adaptive responses following the light-dark cycle. The adjustment of these responses to the change of day and night is probably transmitted via the hormone melatonin. The rate-limiting enzyme in melatonin synthesis is the arylalkylamine N-transferase (AANAT). We identified three genes coding for insect-like AANATs in Daphnia, of which we measured the gene expression in an ecologically relevant light-dark cycle. We demonstrated that Daphnia's insect-like AANAT gene expression oscillated in a daily manner, and that the highest peak of expression after the onset of darkness was followed by a peak of melatonin production at midnight. Moreover, we could show an oscillation of endogenous melatonin synthesis in Daphnia. In most organisms, melatonin synthesis is due to rhythmic expression of genes of the circadian clock, since transcription of aanats is directly linked to a circadian transcription factor. We could demonstrate that putative clock genes and insect-like AANAT genes of Daphnia were equally expressed. Therefore, we propose that melatonin synthesis is coupled to the expression of Daphnia clock genes, and that insect-like AANATs of crustaceans have a similar function as AANATs of vertebrates: The initiation of melatonin synthesis. In future studies with Daphnia, it will be necessary to take the time of day into account since melatonin concentrations might influence stress responses.}, language = {en} } @inproceedings{HofreiterBarlowPaijmansetal.2015, author = {Hofreiter, Michael and Barlow, Axel and Paijmans, Johanna L. A. and Westbury, Michael V.}, title = {Genomic analyses from highly degraded DNA}, series = {Genome}, volume = {58}, booktitle = {Genome}, number = {5}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {0831-2796}, pages = {228 -- 228}, year = {2015}, language = {en} } @article{GroeneveldJohstKawaguchietal.2015, author = {Groeneveld, J{\"u}rgen and Johst, Karin and Kawaguchi, So and Meyer, Bettina and Teschke, Mathias and Grimm, Volker}, title = {How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {303}, 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.2015.02.009}, pages = {78 -- 86}, year = {2015}, abstract = {The Southern Ocean ecosystem is characterized by extreme seasonal changes in environmental factors such as day length, sea ice extent and food availability. The key species Antarctic krill (Euphausia superba) has evolved metabolic and behavioural seasonal rhythms to cope with these seasonal changes. We investigate the switch between a physiological less active and active period for adult krill, a rhythm which seems to be controlled by internal biological clocks. These biological clocks can be synchronized by environmental triggers such as day length and food availability. They have evolved for particular environmental regimes to synchronize predictable seasonal environmental changes with important life cycle functions of the species. In a changing environment the time when krill is metabolically active and the time of peak food availability may not overlap if krill's seasonal activity is solely determined by photoperiod (day length). This is especially true for the Atlantic sector of the Southern Ocean where the spatio-temporal ice cover dynamics are changing substantially with rising average temperatures. We developed an individual-based model for krill to explore the impact of photoperiod and food availability on the growth and demographics of krill. We simulated dynamics of local krill populations (with no movement of krill assumed) along a south-north gradient for different triggers of metabolic activity and different levels of food availability below the ice. We also observed the fate of larval krill which cannot switch to low metabolism and therefore are likely to overwinter under ice. Krill could only occupy the southern end of the gradient, where algae bloom only lasts for a short time, when alternative food supply under the ice was high and metabolic activity was triggered by photoperiod. The northern distribution was limited by lack of overwintering habitat for krill larvae due to short duration of sea ice cover even for high food content under the ice. The variability of the krill's length-frequency distributions varied for different triggers of metabolic activity, but did not depend on the sea ice extent. Our findings suggest a southward shift of krill populations due to reduction in the spatial sea ice extent, which is consistent with field observations. Overall, our results highlight the importance of the explicit consideration of spatio-temporal sea ice dynamics especially for larval krill together with temporal synchronization through internal clocks, triggered by environmental factors (photoperiod and food) in adult krill for the population modelling of krill. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @article{WeissJeltsch2015, author = {Weiß, Lina and Jeltsch, Florian}, title = {The response of simulated grassland communities to the cessation of grazing}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {303}, 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.2015.02.002}, pages = {1 -- 11}, year = {2015}, abstract = {Changes in land-use are supposed to be among the severest prospective threats to plant diversity worldwide. In semi-natural temperate grasslands, the cessation of traditional land use like livestock grazing is considered to be one of the most important drivers of the diversity loss witnessed within the last decades. Despite of the enormous number of studies on successional pathways following grazing abandonment there is no general pattern of how grassland communities are affected in terms of diversity, trait composition and pace of succession. To gain a comprehensive picture is difficult given the heterogeneity of environments and the time and effort needed for long-term investigations. We here use a proven individual- and trait-based grassland community model to analyze short- and long-term consequences of grazing abandonment under different assumptions of resource availability, pre-abandonment grazing intensity and regional isolation of communities. Grazing abandonment led to a decrease of plant functional type (PFT) diversity in all but two scenarios in the long-term. In short-term we also found an increase or no change in Shannon diversity for several scenarios. With grazing abandonment we overall found an increase in maximum plant mass, clonal integration and longer lateral spread, a decrease in rosette plant types and in stress tolerant plants, as well as an increase in grazing tolerant and a decrease in grazing avoiding plant types. Observed changes were highly dependent on the regional configuration of communities, prevalent resource conditions and land use intensity before abandonment. While long-term changes took around 10-20 years in resource rich conditions, new equilibria established in resource poor conditions only after 30-40 years. Our results confirm the potential threats caused by recent land-use changes and the assumption that oligotrophic communities are more resistant than mesotrophic communities also for long-term abandonment. Moreover, results revealed that species-rich systems are not per se more resistant than species-poor grasslands. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @article{PengUteschYarmanetal.2015, author = {Peng, Lei and Utesch, Tillmann and Yarman, Aysu and Jeoung, Jae-Hun and Steinborn, Silke and Dobbek, Holger and Mroginski, Maria Andrea and Tanne, Johannes and Wollenberger, Ursula and Scheller, Frieder W.}, title = {Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein}, series = {Chemistry - a European journal}, volume = {21}, journal = {Chemistry - a European journal}, number = {20}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201405932}, pages = {7596 -- 7602}, year = {2015}, abstract = {Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant k(s) values between 0.93 and 2.86 s(-1) and apparent formal potentials E-app(0)' between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH.}, language = {en} } @misc{XiangGaoYuetal.2015, author = {Xiang, Hai and Gao, Jianqiang and Yu, Baoquan and Hofreiter, Michael and Zhao, Xingbo}, title = {Reply to Peters et al.: Further discussions confirm early Holocene chicken domestication in northern China}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {19}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1503956112}, pages = {E2416 -- E2416}, year = {2015}, language = {en} } @article{HessSaffertLiebetonetal.2015, author = {Hess, Anne-Katrin and Saffert, Paul and Liebeton, Klaus and Ignatova, Zoya}, title = {Optimization of Translation Profiles Enhances Protein Expression and Solubility}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0127039}, pages = {14}, year = {2015}, abstract = {mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.}, language = {en} } @article{KanzleiterJaehnertSchulzeetal.2015, author = {Kanzleiter, Timo and Jaehnert, Markus and Schulze, Gunnar and Selbig, Joachim and Hallahan, Nicole and Schwenk, Robert Wolfgang and Sch{\"u}rmann, Annette}, title = {Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice}, series = {American journal of physiology : Endocrinology and metabolism}, volume = {308}, journal = {American journal of physiology : Endocrinology and metabolism}, number = {10}, publisher = {American Chemical Society}, address = {Bethesda}, issn = {0193-1849}, doi = {10.1152/ajpendo.00289.2014}, pages = {E912 -- E920}, year = {2015}, abstract = {The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice (n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs (P < 0.05, meth diff >5\%, coverage > 10) in their putative promoter regions. Alignment with gene expression data (n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors (Plexin A2) as well as genes that participate in muscle hypertrophy (Igfbp4) and motor neuron innervation (Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training.}, language = {en} } @article{SynodinosTietjenJeltsch2015, author = {Synodinos, Alexios D. and Tietjen, Britta and Jeltsch, Florian}, title = {Facilitation in drylands: Modeling a neglected driver of savanna dynamics}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {304}, 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.2015.02.015}, pages = {11 -- 21}, year = {2015}, abstract = {Our current understanding regarding the functioning of the savanna ecosystem describes savannas as either competition- or disturbance-dependent. Within this generalized view, the role and importance of facilitation have been mostly neglected. This study presents a mathematical model of savannas with coupled soil moisture-vegetation dynamics, which includes interspecific competition and environmental disturbance. We find that there exist environmental and climatic conditions where grass facilitation toward trees plays an important role in supporting tree cover and by extension preserving the savanna biome. We, therefore, argue that our theoretical results in combination with the first empirical studies on the subject should stimulate further research into the role of facilitation in the savanna ecosystem, particularly when analyzing the impact of past and projected climatic changes on it. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @misc{YokoyamaLeimkuehler2015, author = {Yokoyama, Kenichi and Leimk{\"u}hler, Silke}, title = {The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria}, series = {Biochimica et biophysica acta : Molecular cell research}, volume = {1853}, journal = {Biochimica et biophysica acta : Molecular cell research}, number = {6}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-4889}, doi = {10.1016/j.bbamcr.2014.09.021}, pages = {1335 -- 1349}, year = {2015}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{IshidaNozakiGrossartetal.2015, author = {Ishida, Seiji and Nozaki, Daiki and Grossart, Hans-Peter and Kagami, Maiko}, title = {Novel basal, fungal lineages from freshwater phytoplankton and lake samples}, series = {Environmental microbiology reports}, volume = {7}, journal = {Environmental microbiology reports}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12268}, pages = {435 -- 441}, year = {2015}, abstract = {Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.}, language = {en} } @article{DiGiacomoDiGiacomoKligeretal.2015, author = {Di Giacomo, Adrian S. and Di Giacomo, Alejandro G. and Kliger, Rafi and Reboreda, Juan C. and Tiedemann, Ralph and Mahler, Bettina}, title = {No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed Tyrant Alectrurus risora, an endangered grassland species}, series = {Bird conservation international}, volume = {25}, journal = {Bird conservation international}, number = {2}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0959-2709}, doi = {10.1017/S0959270914000203}, pages = {127 -- 138}, year = {2015}, abstract = {The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90\% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Ibera wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (Phi(ST) = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations.}, language = {en} } @article{CuiLvChenetal.2015, author = {Cui, Xiao and Lv, Yang and Chen, Miaolin and Nikoloski, Zoran and Twell, David and Zhang, Dabing}, title = {Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome}, series = {Molecular plant}, volume = {8}, journal = {Molecular plant}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2014.12.008}, pages = {935 -- 945}, year = {2015}, abstract = {The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens.}, language = {en} } @article{SeifertWeithoffVos2015, author = {Seifert, Linda I. and Weithoff, Guntram and Vos, Matthijs}, title = {Extreme heat changes post-heat wave community reassembly}, series = {Ecology and evolution}, volume = {5}, journal = {Ecology and evolution}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.1490}, pages = {2140 -- 2148}, year = {2015}, abstract = {Climate forecasts project further increases in extremely high-temperature events. These present threats to biodiversity, as they promote population declines and local species extinctions. This implies that ecological communities will need to rely more strongly on recovery processes, such as recolonization from a meta-community context. It is poorly understood how differences in extreme event intensity change the outcome of subsequent community reassembly and if such extremes modify the biotic environment in ways that would prevent the successful re-establishment of lost species. We studied replicated aquatic communities consisting of algae and herbivorous rotifers in a design that involved a control and two different heat wave intensity treatments (29 degrees C and 39 degrees C). Animal species that suffered heat-induced extinction were subsequently re-introduced at the same time and density, in each of the two treatments. The 39 degrees C treatment led to community closure in all replicates, meaning that a previously successful herbivore species could not re-establish itself in the postheat wave community. In contrast, such closure never occurred after a 29 degrees C event. Heat wave intensity determined the number of herbivore extinctions and strongly affected algal relative abundances. Re-introduced herbivore species were thus confronted with significantly different food environments. This ecological legacy generated by heat wave intensity led to differences in the failure or success of herbivore species re-introductions. Reassembly was significantly more variable, and hence less predictable, after an extreme heat wave, and was more canalized after a moderate one. Our results pertain to relatively simple communities, but they suggest that ecological legacies introduced by extremely high-temperature events may change subsequent ecological recovery and even prevent the successful re-establishment of lost species. Knowing the processes promoting and preventing ecological recovery is crucial to the success of species re-introduction programs and to our ability to restore ecosystems damaged by environmental extremes.}, language = {en} } @article{ThieleGrimm2015, author = {Thiele, Jan C. and Grimm, Volker}, title = {Replicating and breaking models: good for you and good for ecology}, series = {Oikos}, volume = {124}, journal = {Oikos}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.02170}, pages = {691 -- 696}, year = {2015}, abstract = {There are two major limitations to the potential of computational models in ecology for producing general insights: their design is path-dependent, reflecting different underlying questions, assumptions, and data, and there is too little robustness analysis exploring where the model mechanisms explaining certain observations break down. We here argue that both limitations could be overcome if modellers in ecology would more often replicate existing models, try to break the models, and explore modifications. Replication comprises the re-implementation of an existing model and the replication of its results. Breaking models means to identify under what conditions the mechanisms represented in a model can no longer explain observed phenomena. The benefits of replication include less effort being spent to enter the iterative stage of model development and having more time for systematic robustness analysis. A culture of replication would lead to increased credibility, coherence and efficiency of computational modelling and thereby facilitate theory development.}, language = {en} } @article{ManningGossnerBossdorfetal.2015, author = {Manning, Pete and Gossner, Martin M. and Bossdorf, Oliver and Allan, Eric and Zhang, Yuan-Ye and Prati, Daniel and Bl{\"u}thgen, Nico and Boch, Steffen and B{\"o}hm, Stefan and B{\"o}rschig, Carmen and H{\"o}lzel, Norbert and Jung, Kirsten and Klaus, Valentin H. and Klein, Alexandra Maria and Kleinebecker, Till and Krauss, Jochen and Lange, Markus and M{\"u}ller, J{\"o}rg and Pasalic, Esther and Socher, Stephanie A. and Tschapka, Marco and T{\"u}rke, Manfred and Weiner, Christiane and Werner, Michael and Gockel, Sonja and Hemp, Andreas and Renner, Swen C. and Wells, Konstans and Buscot, Francois and Kalko, Elisabeth K. V. and Linsenmair, Karl Eduard and Weisser, Wolfgang W. and Fischer, Markus}, title = {Grassland management intensification weakens the associations among the diversities of multiple plant and animal taxa}, series = {Ecology : a publication of the Ecological Society of America}, volume = {96}, journal = {Ecology : a publication of the Ecological Society of America}, number = {6}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, doi = {10.1890/14-1307.1}, pages = {1492 -- 1501}, year = {2015}, abstract = {Land-use intensification is a key driver of biodiversity change. However, little is known about how it alters relationships between the diversities of different taxonomic groups, which are often correlated due to shared environmental drivers and trophic interactions. Using data from 150 grassland sites, we examined how land-use intensification (increased fertilization, higher livestock densities, and increased mowing frequency) altered correlations between the species richness of 15 plant, invertebrate, and vertebrate taxa. We found that 54\% of pairwise correlations between taxonomic groups were significant and positive among all grasslands, while only one was negative. Higher land-use intensity substantially weakened these correlations(35\% decrease in rand 43\% fewer significant pairwise correlations at high intensity), a pattern which may emerge as a result of biodiversity declines and the breakdown of specialized relationships in these conditions. Nevertheless, some groups (Coleoptera, Heteroptera, Hymenoptera and Orthoptera) were consistently correlated with multidiversity, an aggregate measure of total biodiversity comprised of the standardized diversities of multiple taxa, at both high and lowland-use intensity. The form of intensification was also important; increased fertilization and mowing frequency typically weakened plant-plant and plant-primary consumer correlations, whereas grazing intensification did not. This may reflect decreased habitat heterogeneity under mowing and fertilization and increased habitat heterogeneity under grazing. While these results urge caution in using certain taxonomic groups to monitor impacts of agricultural management on biodiversity, they also suggest that the diversities of some groups are reasonably robust indicators of total biodiversity across a range of conditions.}, language = {en} } @article{YildirimSemerciBenayahuAdamovskietal.2015, author = {Yildirim-Semerci, Cigdem and Benayahu, Dafna and Adamovski, Miriam and Wollenberger, Ursula}, title = {An Electrochemical Assay for Monitoring Differentiation of the Osteoblastic Cell Line (MBA-15) on the Sensor Chip}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {27}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {6}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400684}, pages = {1350 -- 1358}, year = {2015}, abstract = {An electrochemical assay for the indication of the activity of the cell bound differentiation marker alkaline phosphatase (ALP) is proposed using voltammetry on an in-vitro cell culture. The basis of the assay is cultivation of cells on gold microelectrodes in wells of a microplate, catalytic hydrolysis of p-aminophenyl phosphate by ALP and indication of p-aminophenol oxidation by square wave voltammetry (SWV) with the sensors onto which the cells attached. The morphology of the bone marrow stromal cell line (MBA-15) on the electrode surface was investigated and it exhibited in vitro osteogenic characteristics. Since ALP is expressed on the cell surface in early differentiation stage of osteoblastic cells, its activity was followed after different culture times over a period of 144 h by recording repetitive voltammograms at different time points upon addition of the substrate p-aminophenyl phosphate. The ALP activity was estimated from the signal increase related to formation rate of p-aminophenol and the number of cells. The highest value was measured at 120 h, when the cells reached confluence. The results of the electrochemical activity assay are consistent with the colorimetric acquired value from p-nitrophenol formation rate.}, language = {en} } @article{GraefBatsiosMeyer2015, author = {Gr{\"a}f, Ralph and Batsios, Petros and Meyer, Irene}, title = {Evolution of centrosomes and the nuclear lamina: Amoebozoan assets}, series = {European journal of cell biology}, volume = {94}, journal = {European journal of cell biology}, number = {6}, publisher = {Elsevier}, address = {Jena}, issn = {0171-9335}, doi = {10.1016/j.ejcb.2015.04.004}, pages = {249 -- 256}, year = {2015}, abstract = {The current eukaryotic tree of life groups most eukaryotes into one of five supergroups, the Opisthokonta, Amoebozoa, Archaeplastida, Excavata and SAR (Stramenopile, Alveolata, Rhizaria). Molecular and comparative morphological analyses revealed that the last eukaryotic common ancestor (LECA) already contained a rather sophisticated equipment of organelles including a mitochondrion, an endomembrane system, a nucleus with a lamina, a microtubule-organizing center (MTOC), and a flagellar apparatus. Recent studies of MTOCs, basal bodies/centrioles, and nuclear envelope organization of organisms in different supergroups have clarified our picture of how the nucleus and MTOCs co-evolved from LECA to extant eukaryotes. In this review we summarize these findings with special emphasis on valuable contributions of research on a lamin-like protein, nuclear envelope proteins, and the MTOC in the amoebozoan model organism Dictyostelium discoideum. (C) 2015 Elsevier GmbH. All rights reserved.}, language = {en} } @article{CamargodosReisRiccardiTeixeiraRibeiroetal.2015, author = {Camargo, Rodolfo Gonzalez and dos Reis Riccardi, Daniela Mendes and Teixeira Ribeiro, Henrique Quintas and Carnevali Junior, Luiz Carlos and de Matos-Neto, Emidio Marques and Enjiu, Lucas and Neves, Rodrigo Xavier and Carola Correia Lima, Joanna Darck and Figueredo, Raquel Galvao and Martins de Alcantara, Paulo Sergio and Maximiano, Linda and Otoch, Jose and Batista Jr., Miguel Luiz and P{\"u}schel, Gerhard Paul and Seelaender, Marilia}, title = {NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients}, series = {Nutrients}, volume = {7}, journal = {Nutrients}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu7064465}, pages = {4465 -- 4479}, year = {2015}, abstract = {Cancer cachexia, of which the most notable symptom is severe and rapid weight loss, is present in the majority of patients with advanced cancer. Inflammatory mediators play an important role in the development of cachexia, envisaged as a chronic inflammatory syndrome. The white adipose tissue (WAT) is one of the first compartments affected in cancer cachexia and suffers a high rate of lipolysis. It secretes several cytokines capable of directly regulating intermediate metabolism. A common pathway in the regulation of the expression of pro-inflammatory cytokines in WAT is the activation of the nuclear transcription factor kappa-B (NF-B). We have examined the gene expression of the subunits NF-Bp65 and NF-Bp50, as well as NF-Bp65 and NF-Bp50 binding, the gene expression of pro-inflammatory mediators under NF-B control (IL-1, IL-6, INF-, TNF-, MCP-1), and its inhibitory protein, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IB-). The observational study involved 35 patients (control group, n = 12 and cancer group, n = 23, further divided into cachectic and non-cachectic). NF-Bp65 and its target genes expression (TNF-, IL-1, MCP-1 and IB-) were significantly higher in cachectic cancer patients. Moreover, NF-Bp65 gene expression correlated positively with the expression of its target genes. The results strongly suggest that the NF-B pathway plays a role in the promotion of WAT inflammation during cachexia.}, language = {en} } @inproceedings{HankeGogokhiaFrederickZhangetal.2015, author = {Hanke-Gogokhia, Christin and Frederick, Jeanne M. and Zhang, Houbin and Baehr, Wolfgang}, title = {ARL3 regulates transport of prenylated and acylated proteins to photoreceptor outer segment in mouse retina}, series = {Investigative ophthalmology \& visual science}, volume = {56}, booktitle = {Investigative ophthalmology \& visual science}, number = {7}, publisher = {Association for Research in Vision and Opthalmology}, address = {Rockville}, issn = {0146-0404}, pages = {2}, year = {2015}, language = {en} } @article{AdamlaIgnatova2015, author = {Adamla, Frauke and Ignatova, Zoya}, title = {Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10692}, pages = {10}, year = {2015}, abstract = {Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.}, language = {en} } @article{TedderCarleialGolebiewskaetal.2015, author = {Tedder, Andrew and Carleial, Samuel and Golebiewska, Martyna and Kappel, Christian and Shimizu, Kentaro K. and Stift, Marc}, title = {Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0126618}, pages = {17}, year = {2015}, abstract = {Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.}, language = {en} } @article{AllhoffRitterskampRalletal.2015, author = {Allhoff, Korinna Theresa and Ritterskamp, Daniel and Rall, Bj{\"o}rn C. and Drossel, Barbara and Guill, Christian}, title = {Evolutionary food web model based on body masses gives realistic networks with permanent species turnover}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep10955}, pages = {12}, year = {2015}, abstract = {The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50\% of the network are not observed.}, language = {en} } @article{PinhasiFernandesSiraketal.2015, author = {Pinhasi, Ron and Fernandes, Daniel and Sirak, Kendra and Novak, Mario and Connell, Sarah and Alpaslan-Roodenberg, Songul and Gerritsen, Fokke and Moiseyev, Vyacheslav and Gromov, Andrey and Raczky, Pal and Anders, Alexandra and Pietrusewsky, Michael and Rollefson, Gary and Jovanovic, Marija and Trinhhoang, Hiep and Bar-Oz, Guy and Oxenham, Marc and Matsumura, Hirofumi and Hofreiter, Michael}, title = {Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0129102}, pages = {13}, year = {2015}, abstract = {The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1\% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1\% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.}, language = {en} }