@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} }