@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{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{MazumderBrechunKimetal.2015,
  author    = {Mazumder, Mostafizur and Brechun, Katherine E. and Kim, Yongjoo B. and Hoffmann, Stefan A. and Chen, Yih Yang and Keiski, Carrie-Lynn and Arndt, Katja Maren and McMillen, David R. and Woolley, G. Andrew},
  title     = {An Escherichia coli system for evolving improved light-controlled DNA-binding proteins},
  series = {Protein engineering design \& selection},
  volume    = {28},
  journal   = {Protein engineering design \& selection},
  number    = {9},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1741-0126},
  doi       = {10.1093/protein/gzv033},
  pages     = {293 -- 302},
  year      = {2015},
  abstract  = {Light-switchable proteins offer numerous opportunities as tools for manipulating biological systems with exceptional degrees of spatiotemporal control. Most designed light-switchable proteins currently in use have not been optimised using the randomisation and selection/screening approaches that are widely used in other areas of protein engineering. Here we report an approach for screening light-switchable DNA-binding proteins that relies on light-dependent repression of the transcription of a fluorescent reporter. We demonstrate that the method can be used to recover a known light-switchable DNA-binding protein from a random library.},
  language  = {en}
}
@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{MarcusBochDurkaetal.2015,
  author    = {Marcus, Tamar and Boch, Steffen and Durka, Walter and Fischer, Markus and Gossner, Martin M. and M{\"u}ller, J{\"o}rg and Sch{\"o}ning, Ingo and Weisser, Wolfgang W. and Drees, Claudia and Assmann, Thorsten},
  title     = {Living in Heterogeneous Woodlands - Are Habitat Continuity or Quality Drivers of Genetic Variability in a Flightless Ground Beetle?},
  series = {PLoS one},
  volume    = {10},
  journal   = {PLoS one},
  number    = {12},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0144217},
  pages     = {18},
  year      = {2015},
  abstract  = {Although genetic diversity is one of the key components of biodiversity, its drivers are still not fully understood. While it is known that genetic diversity is affected both by environmental parameters as well as habitat history, these factors are not often tested together. Therefore, we analyzed 14 microsatellite loci in Abax parallelepipedus, a flightless, forest dwelling ground beetle, from 88 plots in two study regions in Germany. We modeled the effects of historical and environmental variables on allelic richness, and found for one of the regions, the Schorfheide-Chorin, a significant effect of the depth of the litter layer, which is a main component of habitat quality, and of the sampling effort, which serves as an inverse proxy for local population size. For the other region, the Schwabische Alb, none of the potential drivers showed a significant effect on allelic richness. We conclude that the genetic diversity in our study species is being driven by current local population sizes via environmental variables and not by historical processes in the studied regions. This is also supported by lack of genetic differentiation between local populations sampled from ancient and from recent woodlands. We suggest that the potential effects of former fragmentation and recolonization processes have been mitigated by the large and stable local populations of Abax parallelepipedus in combination with the proximity of the ancient and recent woodlands in the studied landscapes.},
  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{MakowerSchuurmansGrothetal.2015,
  author    = {Makower, A. Katharina and Schuurmans, J. Merijn and Groth, Detlef and Zilliges, Yvonne and Matthijs, Hans C. P. and Dittmann-Th{\"u}nemann, Elke},
  title     = {Transcriptomics-Aided dissection of the intracellular and extracellular roles of microcystin in microcystis aeruginosa PCC 7806},
  series = {Applied and environmental microbiology},
  volume    = {81},
  journal   = {Applied and environmental microbiology},
  number    = {2},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {0099-2240},
  doi       = {10.1128/AEM.02601-14},
  pages     = {544 -- 554},
  year      = {2015},
  abstract  = {Recent studies have provided evidence for both intracellular and extracellular roles of the potent hepatotoxin microcystin (MC) in the bloom-forming cyanobacterium Microcystis. Here, we surveyed transcriptomes of the wild-type strain M. aeruginosa PCC 7806 and the microcystin-deficient Delta mcyB mutant under low light conditions with and without the addition of external MC of the LR variant (MC-LR). Transcriptomic data acquired by microarray and quantitative PCR revealed substantial differences in the relative expression of genes of the central intermediary metabolism, photosynthesis, and energy metabolism. In particular, the data provide evidence for a lower photosystem I (PSI)-to-photosystem II (PSII) ratio and a more pronounced carbon limitation in the microcystin-deficient mutant. Interestingly, only 6\% of the transcriptional differences could be complemented by external microcystin-LR addition. This MC signaling effect was seen exclusively for genes of the secondary metabolism category. The orphan polyketide synthase gene cluster IPF38-51 was specifically downregulated in response to external MC-LR under low light. Our data suggest a hierarchical and light-dependent cross talk of secondary metabolites and support both an intracellular and an extracellular role of MC in Microcystis.},
  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}
}
@article{LotkowskaTohgeFernieetal.2015,
  author    = {Lotkowska, Magda E. and Tohge, Takayuki and Fernie, Alisdair and Xue, Gang-Ping and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {169},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.15.00605},
  pages     = {1862 -- 1880},
  year      = {2015},
  abstract  = {MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions.},
  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{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{LiCorriganYangetal.2015,
  author    = {Li, Chenhong and Corrigan, Shannon and Yang, Lei and Straube, Nicolas and Harris, Mark and Hofreiter, Michael and White, William T. and Naylor, Gavin J. P.},
  title     = {DNA capture reveals transoceanic gene flow in endangered river sharks},
  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    = {43},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1508735112},
  pages     = {13302 -- 13307},
  year      = {2015},
  abstract  = {For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.},
  language  = {en}
}
@article{LemkeKolbGraaeetal.2015,
  author    = {Lemke, Isgard H. and Kolb, Annette and Graae, Bente J. and De Frenne, Pieter and Acharya, Kamal P. and Blandino, Cristina and Brunet, Jorg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Heinken, Thilo and Hermy, Martin and Liira, Jaan and Schmucki, Reto and Shevtsova, Anna and Verheyen, Kris and Diekmann, Martin},
  title     = {Patterns of phenotypic trait variation in two temperate forest herbs along a broad climatic gradient},
  series = {Plant ecology : an international journal},
  volume    = {216},
  journal   = {Plant ecology : an international journal},
  number    = {11},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1385-0237},
  doi       = {10.1007/s11258-015-0534-0},
  pages     = {1523 -- 1536},
  year      = {2015},
  abstract  = {Phenotypic trait variation plays a major role in the response of plants to global environmental change, particularly in species with low migration capabilities and recruitment success. However, little is known about the variation of functional traits within populations and about differences in this variation on larger spatial scales. In a first approach, we therefore related trait expression to climate and local environmental conditions, studying two temperate forest herbs, Milium effusum and Stachys sylvatica, along a similar to 1800-2500 km latitudinal gradient. Within each of 9-10 regions in six European countries, we collected data from six populations of each species and recorded several variables in each region (temperature, precipitation) and population (light availability, soil parameters). For each plant, we measured height, leaf area, specific leaf area, seed mass and the number of seeds and examined environmental effects on within-population trait variation as well as on trait means. Most importantly, trait variation differed both between and within populations. Species, however, differed in their response. Intrapopulation variation in Milium was consistently positively affected by higher mean temperatures and precipitation as well as by more fertile local soil conditions, suggesting that more productive conditions may select for larger phenotypic variation. In Stachys, particularly light availability positively influenced trait variation, whereas local soil conditions had no consistent effects. Generally, our study emphasises that intra-population variation may differ considerably across larger scales-due to phenotypic plasticity and/or underlying genetic diversity-possibly affecting species response to global environmental change.},
  language  = {en}
}
@article{LeDucRenaudKrishnanetal.2015,
  author    = {Le Duc, Diana and Renaud, Gabriel and Krishnan, Arunkumar and Almen, Markus Sallman and Huynen, Leon and Prohaska, Sonja J. and Ongyerth, Matthias and Bitarello, Barbara D. and Schioth, Helgi B. and Hofreiter, Michael and Stadler, Peter F. and Pr{\"u}fer, Kay and Lambert, David and Kelso, Janet and Sch{\"o}neberg, Torsten},
  title     = {Kiwi genome provides insights into evolution of a nocturnal lifestyle},
  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/s13059-015-0711-4},
  pages     = {15},
  year      = {2015},
  abstract  = {Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.},
  language  = {en}
}
@article{LamannaKirschbaumWauricketal.2015,
  author    = {Lamanna, Francesco and Kirschbaum, Frank and Waurick, Isabelle and Dieterich, Christoph and Tiedemann, Ralph},
  title     = {Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)},
  series = {BMC genomics},
  volume    = {16},
  journal   = {BMC genomics},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-015-1858-9},
  pages     = {17},
  year      = {2015},
  abstract  = {Background: African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results: Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C. tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions: The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ's transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.},
  language  = {en}
}
@article{LamannaKirschbaumWauricketal.2015,
  author    = {Lamanna, Francesco and Kirschbaum, Frank and Waurick, Isabelle and Dieterich, Christoph and Tiedemann, Ralph},
  title     = {Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {668},
  publisher = {Biomed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-015-1858-9},
  year      = {2015},
  abstract  = {Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ's transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.},
  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{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{KraemerRavindranZaqoutetal.2015,
  author    = {Kr{\"a}mer, Nadine and Ravindran, Ethiraj and Zaqout, Sami and Neubert, Gerda and Schindler, Detlev and Ninnemann, Olaf and Gr{\"a}f, Ralph and Seiler, Andrea E. M. and Kaindl, Angela M.},
  title     = {Loss of CDK5RAP2 affects neural but not non-neural mESC differentiation into cardiomyocytes},
  series = {Cell cycle},
  volume    = {14},
  journal   = {Cell cycle},
  number    = {13},
  publisher = {Taylor \& Francis Group},
  address   = {Philadelphia},
  issn      = {1538-4101},
  doi       = {10.1080/15384101.2015.1044169},
  pages     = {2044 -- 2057},
  year      = {2015},
  abstract  = {Biallelic mutations in the gene encoding centrosomal CDK5RAP2 lead to autosomal recessive primary microcephaly (MCPH), a disorder characterized by pronounced reduction in volume of otherwise architectonical normal brains and intellectual deficit. The current model for the microcephaly phenotype in MCPH invokes a premature shift from symmetric to asymmetric neural progenitor-cell divisions with a subsequent depletion of the progenitor pool. The isolated neural phenotype, despite the ubiquitous expression of CDK5RAP2, and reports of progressive microcephaly in individual MCPH cases prompted us to investigate neural and non-neural differentiation of Cdk5rap2-depleted and control murine embryonic stem cells (mESC). We demonstrate an accumulating proliferation defect of neurally differentiating Cdk5rap2-depleted mESC and cell death of proliferative and early postmitotic cells. A similar effect does not occur in non-neural differentiation into beating cardiomyocytes, which is in line with the lack of non-central nervous system features in MCPH patients. Our data suggest that MCPH is not only caused by premature differentiation of progenitors, but also by reduced propagation and survival of neural progenitors.},
  language  = {en}
}
@article{KopyshevLomadzeFeldmannetal.2015,
  author    = {Kopyshev, Alexey and Lomadze, Nino and Feldmann, David and Genzer, Jan and Santer, Svetlana},
  title     = {Making polymer brush photosensitive with azobenzene containing surfactants},
  series = {Polymer : the international journal for the science and technology of polymers},
  volume    = {79},
  journal   = {Polymer : the international journal for the science and technology of polymers},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0032-3861},
  doi       = {10.1016/j.polymer.2015.09.023},
  pages     = {65 -- 72},
  year      = {2015},
  abstract  = {We report on rendering polyelectrolyte brushes photosensitive by loading them with azobenzene-containing cationic surfactants. Planar poly( methacrylic acid) (PMAA) brushes are synthesized using the "grafting from" free-radical polymerization scheme followed by exposure to a solution of photosensitive surfactants consisting of positively-charged head groups and hydrophobic tails into which azobenzene moieties are inserted. In this study the length of the hydrophobic methylene spacer connecting the azobenzene and the charged head group ranges from 4 to 10 CH2 groups. Under irradiation with UV light, the photo-isomerization of azobenzene integrated into a surfactant results in a change in size, geometry, dipole moment and free volume of the whole molecule. When the brush loaded with photosensitive surfactants is exposed to irradiation with UV interference patterns, the topography of the brush deforms following the distribution of the light intensity, exhibiting surface relief gratings (SRG). Since SRG formation is accompanied by a local rupturing of polymer chains in areas from which the polymer material is receding, most of the polymer material is removed from the surface during treatment with good solvent, leaving behind characteristic patterns of lines or dots. The azobenzene molecules still integrated within the polymer film can be removed by washing the brush with water. The remaining nano-structured brush can then be re-used for further functionalization. Although the opto-mechanically induced rupturing occurs for all surfactants, larger species do not penetrate deep enough into the brush such that after rupturing a leftover layer of polymer material remains on the substrate. This indicates that rupturing occurs predominantly in regions of high surfactant density.},
  language  = {en}
}