@article{DevosGraefField2014, author = {Devos, Damien P. and Gr{\"a}f, Ralph and Field, Mark C.}, title = {Evolution of the nucleus}, series = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, volume = {28}, journal = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, publisher = {Elsevier}, address = {London}, issn = {0955-0674}, doi = {10.1016/j.ceb.2014.01.004}, pages = {8 -- 15}, year = {2014}, abstract = {The nucleus represents a major evolutionary transition. As a consequence of separating translation from transcription many new functions arose, which likely contributed to the remarkable success of eukaryotic cells. Here we will consider what has recently emerged on the evolutionary histories of several key aspects of nuclear biology; the nuclear pore complex, the lamina, centrosomes and evidence for prokaryotic origins of relevant players.}, language = {en} } @article{KelmLenskiKelmetal.2014, author = {Kelm, Detlev H. and Lenski, Johannes and Kelm, Volker and Toelch, Ulf and Dziock, Frank}, title = {Seasonal bat activity in relation to distance to hedgerows in an agricultural landscape in central Europe and implications for wind energy development}, series = {Acta chiropterologica : international journal of bat biology}, volume = {16}, journal = {Acta chiropterologica : international journal of bat biology}, number = {1}, publisher = {Museum and Institute of Zoology, Polish Academy of Sciences}, address = {Warsaw}, issn = {1508-1109}, doi = {10.3161/150811014X683273}, pages = {65 -- 73}, year = {2014}, abstract = {Bat activity is often concentrated near linear and edge landscape structures such as hedgerows, but information about seasonal and species-specific bat activity near hedges is scarce despite their abundance in the cultural landscapes of central Europe. Exact knowledge on animals' habitat use, however, is key to effective landscape planning to avoid human-wildlife-conflicts, such as the construction of wind turbines in areas with high bat activity that may result in bat fatalities. We measured bat activity in relation to distance to hedgerows in an agricultural landscape in northeastern Germany. We recorded bat echolocation calls at ground level at 0, 50, 100 and 200 m distances from hedges at five sites during three nights in spring (April to June) and three nights in summer (July to October) at each site. For all bat species we found the overall activity to be similar between seasons, with the highest activity near the hedges, but with considerable variation in species-specific spatial activity patterns between spring and summer. While the genus Myotis and Pipistrellus pipistrellus were mostly active close to the hedges at a similar intensity over the entire study period (i.e. 84\% and 86\% of all bat passes, respectively), Nyctalus noctula and Pipistrellus nathusii showed generally less pronounced concentration of activity near the hedges, and increased activity away from the hedges in summer. Similarly, Pipistrellus pygmaeus showed decreased activity away from the hedges during both seasons, but with reduced activity near the hedges in summer. The observed behavioural changes in activity in relation to distance to hedgerows are likely due to migration or the bats foraging for different prey between seasons. Our findings are highly relevant for landscape planning and distance recommendations for the construction of wind turbines linked to their potential threat for bats.}, language = {en} } @article{MettlerMuehlhausHemmeetal.2014, author = {Mettler, Tabea and M{\"u}hlhaus, Timo and Hemme, Dorothea and Sch{\"o}ttler, Mark Aurel and Rupprecht, Jens and Idoine, Adam and Veyel, Daniel and Pal, Sunil Kumar and Yaneva-Roder, Liliya and Winck, Flavia Vischi and Sommer, Frederik and Vosloh, Daniel and Seiwert, Bettina and Erban, Alexander and Burgos, Asdrubal and Arvidsson, Samuel Janne and Schoenfelder, Stephanie and Arnold, Anne and Guenther, Manuela and Krause, Ursula and Lohse, Marc and Kopka, Joachim and Nikoloski, Zoran and M{\"u}ller-R{\"o}ber, Bernd and Willmitzer, Lothar and Bock, Ralph and Schroda, Michael and Stitt, Mark}, title = {Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {6}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.124537}, pages = {2310 -- 2350}, year = {2014}, abstract = {We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.}, language = {en} } @article{ValenteEtiennePhillimore2014, author = {Valente, Luis M. and Etienne, Rampal S. and Phillimore, Albert B.}, title = {The effects of island ontogeny on species diversity and phylogeny}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {281}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1784}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2013.3227}, pages = {9}, year = {2014}, abstract = {A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological time-scales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.}, language = {en} } @article{DeyAdamovskiFriebeetal.2014, author = {Dey, Pradip and Adamovski, Miriam and Friebe, Simon and Badalyan, Artavazd and Mutihac, Radu-Cristian and Paulus, Florian and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Haag, Rainer}, title = {Dendritic polyglycerol-poly(ethylene glycol)-based polymer networks for biosensing application}, series = {ACS applied materials \& interfaces}, volume = {6}, journal = {ACS applied materials \& interfaces}, number = {12}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/am502018x}, pages = {8937 -- 8941}, year = {2014}, abstract = {This work describes the formation of a new dendritic polyglycerol-poly(ethylene glycol)-based 3D polymer network as a matrix for immobilization of the redox enzyme periplasmatic aldehyde oxidoreductase to create an electrochemical biosensor. The novel network is built directly on the gold surface, where it simultaneously stabilizes the enzyme for up to 4 days. The prepared biosensors can be used for amperometric detection of benzaldehyde in the range of 0.8-400 mu M.}, language = {en} } @article{HahnReschkeLeimkuehleretal.2014, author = {Hahn, Aaron and Reschke, Stefan and Leimk{\"u}hler, Silke and Risse, Thomas}, title = {Ketoxime coupling of p-Acetylphenylalanine at neutral pH for site-directed spin labeling of human sulfite oxidase}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {118}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {25}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp503471j}, pages = {7077 -- 7084}, year = {2014}, abstract = {Site-directed spin labeling of the unnatural amino acid p-acetylphenylalanine (p-AcPhe) using oxime based coupling chemistry is successfully applied to investigate human sulfite oxidase (hSO), a protein containing an essential cysteine residue, which impedes the use of thiol based coupling chemistry. The protein was found to be sensitive toward typical reaction conditions of oxime coupling, namely, acidic reaction conditions and elevated temperatures. Thus, coupling at neutral pH and room temperature is mandatory. Three catalysts described in the literature to accelerate the reaction rate have been tested. Best spin labeling efficiencies were observed for p-methoxyaniline, while the other catalysts described in the literature to have even better performance for oxime coupling at neutral pH were substantially less active or led to precipitation of the protein. A clear correlation of spin labeling efficiency with the local environment of the residue is found, shedding some light on the importance of the sterically demanding reaction complex between p-AcPhe, the aniline catalyst, and the spin label for the reaction rate. The analysis of the line shape has shown that its interpretation in terms of local environment is more challenging as compared to the well-established spin labels based on cysteine chemistry. To this end the results presented here indicate that the larger steric demand of the spin labeled p-AcPhe can induce structural effects instead of reporting on them.}, language = {en} } @article{MahlowHejaziKuhnertetal.2014, author = {Mahlow, Sebastian and Hejazi, Mahdi and Kuhnert, Franziska and Garz, Andreas and Brust, Henrike and Baumann, Otto and Fettke, J{\"o}rg}, title = {Phosphorylation of transitory starch by -glucan, water dikinase during starch turnover affects the surface properties and morphology of starch granules}, series = {New phytologist : international journal of plant science}, volume = {203}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.12801}, pages = {495 -- 507}, year = {2014}, abstract = {Glucan, water dikinase (GWD) is a key enzyme of starch metabolism but the physico-chemical properties of starches isolated from GWD-deficient plants and their implications for starch metabolism have so far not been described. Transgenic Arabidopsis thaliana plants with reduced or no GWD activity were used to investigate the properties of starch granules. In addition, using various in vitro assays, the action of recombinant GWD, -amylase, isoamylase and starch synthase 1 on the surface of native starch granules was analysed. The internal structure of granules isolated from GWD mutant plants is unaffected, as thermal stability, allomorph, chain length distribution and density of starch granules were similar to wild-type. However, short glucan chain residues located at the granule surface dominate in starches of transgenic plants and impede GWD activity. A similarly reduced rate of phosphorylation by GWD was also observed in potato tuber starch fractions that differ in the proportion of accessible glucan chain residues at the granule surface. A model is proposed to explain the characteristic morphology of starch granules observed in GWD transgenic plants. The model postulates that the occupancy rate of single glucan chains at the granule surface limits accessibility to starch-related enzymes.}, language = {en} } @article{MummSchefflerHermanussen2014, author = {Mumm, Rebekka and Scheffler, Christiane and Hermanussen, Michael}, title = {Developing differential height, weight and body mass index references for girls that reflect the impact of the menarche}, series = {Acta paediatrica : nurturing the child}, volume = {103}, journal = {Acta paediatrica : nurturing the child}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0803-5253}, doi = {10.1111/apa.12625}, pages = {e312 -- e316}, year = {2014}, abstract = {Aim Growth is both a matter of amplitude and tempo. We aimed to develop references for body height, body weight and body mass index (BMI) with respect to tempo of maturity. Methods Data obtained from the German KiGGS study (2003-2006) on body height, body weight and presence or absence of the menarche were re-analysed in 3776 girls, aged 10-17years. We developed smoothed centiles for BMI-, body-height- and body-weight-for-age using the LMS method for premenarcheal and postmenarcheal girls. Results Body height, body weight and BMI differed significantly between premenarcheal and postmenarcheal girls. On average, postmenarcheal girls aged 11-17years were 5.3cm taller and 9.7kg heavier, and their BMI was 2.9kg/m2 higher than in premenarcheal girls of the same calendar age. Conclusion Adolescent BMI rises with calendar age and biological age. New reference charts for adolescent girls aged 10-18years were generated to be inserted into the currently used references to avoid misclassifying underweight and overweight pubertal girls.}, language = {en} } @article{RottstockJoshiKummeretal.2014, author = {Rottstock, Tanja and Joshi, Jasmin Radha and Kummer, Volker and Fischer, Markus}, title = {Higher plant diversity promotes higher diversity of fungal pathogens, while it decreases pathogen infection per plant}, series = {Ecology : a publication of the Ecological Society of America}, volume = {95}, journal = {Ecology : a publication of the Ecological Society of America}, number = {7}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {1907 -- 1917}, year = {2014}, abstract = {Fungal plant pathogens are common in natural communities where they affect plant physiology, plant survival, and biomass production. Conversely, pathogen transmission and infection may be regulated by plant community characteristics such as plant species diversity and functional composition that favor pathogen diversity through increases in host diversity while simultaneously reducing pathogen infection via increased variability in host density and spatial heterogeneity. Therefore, a comprehensive understanding of multi-host multi-pathogen interactions is of high significance in the context of biodiversity-ecosystem functioning. We investigated the relationship between plant diversity and aboveground obligate parasitic fungal pathogen ("pathogens" hereafter) diversity and infection in grasslands of a long-term, large-scale, biodiversity experiment with varying plant species (1-60 species) and plant functional group diversity (1-4 groups). To estimate pathogen infection of the plant communities, we visually assessed pathogen-group presence (i.e., rusts, powdery mildews, downy mildews, smuts, and leaf-spot diseases) and overall infection levels (combining incidence and severity of each pathogen group) in 82 experimental plots on all aboveground organs of all plant species per plot during four surveys in 2006. Pathogen diversity, assessed as the cumulative number of pathogen groups on all plant species per plot, increased log-linearly with plant species diversity. However, pathogen incidence and severity, and hence overall infection, decreased with increasing plant species diversity. In addition, co-infection of plant individuals by two or more pathogen groups was less likely with increasing plant community diversity. We conclude that plant community diversity promotes pathogen-community diversity while at the same time reducing pathogen infection levels of plant individuals.}, language = {en} } @article{CortesAvizandaJovaniAntonioDonazaretal.2014, author = {Cortes-Avizanda, Ainara and Jovani, Roger and Antonio Donazar, Jose and Grimm, Volker}, title = {Bird sky networks: How do avian scavengers use social information to find carrion?}, series = {Ecology : a publication of the Ecological Society of America}, volume = {95}, journal = {Ecology : a publication of the Ecological Society of America}, number = {7}, publisher = {Wiley}, address = {Washington}, issn = {0012-9658}, pages = {1799 -- 1808}, year = {2014}, abstract = {The relative contribution of personal and social information to explain individual and collective behavior in different species and contexts is an open question in animal ecology. In particular, there is a major lack of studies combining theoretical and empirical approaches to test the relative relevance of different hypothesized individual behaviors to predict empirical collective patterns. We used an individual-based model to confront three hypotheses about the information transfer between social scavengers (Griffon Vultures, Gyps fulvus) when searching for carrion: (1) Vultures only use personal information during foraging ("nonsocial" hypothesis); (2) they create long chains of vultures by following both other vultures that are flying towards carcasses and vultures that are following other vultures that are flying towards carcasses ("chains of vultures" hypothesis); and (3) vultures are only attracted by other vultures that are sinking vertically to a carcass ("local enhancement" hypothesis). The chains of vultures hypothesis has been used in existing models, but never been confronted with field data. Testing is important, though, because these hypotheses could have different management implications. The model was parameterized to mimic the behavior and the densities of both Griffon Vultures and carcasses in a 10 000-km(2) study area in northeastern Spain. We compared the number of vultures attending simulated carcasses with those attending 25 continuously monitored experimental carcasses in the field. Social hypotheses outperformed the nonsocial hypothesis. The chains of vultures hypothesis overestimated the number of vultures feeding on carcasses; the local enhancement hypothesis fitted closely to the empirical data. Supported by our results, we discuss mechanistic and adaptive considerations that reveal that local enhancement may be the key social mechanism behind collective foraging in this and likely other avian scavengers and/or social birds. It also highlights the current need for more studies confronting alternative models of key behaviors with empirical patterns in order to understand how collective behavior emerges in animal societies.}, language = {en} } @article{ZulawskiSchulzeBraginetsetal.2014, author = {Zulawski, Monika and Schulze, Gunnar and Braginets, Rostyslav and Hartmann, Stefanie and Schulze, Waltraud X.}, title = {The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification}, series = {BMC genomics}, volume = {15}, journal = {BMC genomics}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-548}, pages = {14}, year = {2014}, abstract = {Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.}, language = {en} } @article{AlluSojaWuetal.2014, author = {Allu, Annapurna Devi and Soja, Aleksandra Maria and Wu, Anhui and Szymanski, Jedrzej and Balazadeh, Salma}, title = {Salt stress and senescence: identification of cross-talk regulatory components}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru173}, pages = {3993 -- 4008}, year = {2014}, abstract = {Leaf senescence is an active process with a pivotal impact on plant productivity. It results from extensive signalling cross-talk coordinating environmental factors with intrinsic age-related mechanisms. Although many studies have shown that leaf senescence is affected by a range of external parameters, knowledge about the regulatory systems that govern the interplay between developmental programmes and environmental stress is still vague. Salinity is one of the most important environmental stresses that promote leaf senescence and thus affect crop yield. Improving salt tolerance by avoiding or delaying senescence under stress will therefore play an important role in maintaining high agricultural productivity. Experimental evidence suggests that hydrogen peroxide (H2O2) functions as a common signalling molecule in both developmental and salt-induced leaf senescence. In this study, microarray-based gene expression profiling on Arabidopsis thaliana plants subjected to long-term salinity stress to induce leaf senescence was performed, together with co-expression network analysis for H2O2-responsive genes that are mutually up-regulated by salt induced-and developmental leaf senescence. Promoter analysis of tightly co-expressed genes led to the identification of seven cis-regulatory motifs, three of which were known previously, namely CACGTGT and AAGTCAA, which are associated with reactive oxygen species (ROS)-responsive genes, and CCGCGT, described as a stress-responsive regulatory motif, while the others, namely ACGCGGT, AGCMGNC, GMCACGT, and TCSTYGACG were not characterized previously. These motifs are proposed to be novel elements involved in the H2O2-mediated control of gene expression during salinity stress-triggered and developmental senescence, acting through upstream transcription factors that bind to these sites.}, language = {en} } @article{BalazadehSchildhauerAraujoetal.2014, author = {Balazadeh, Salma and Schildhauer, Joerg and Araujo, Wagner L. and Munne-Bosch, Sergi and Fernie, Alisdair and Proost, Sebastian and Humbeck, Klaus and M{\"u}ller-R{\"o}ber, Bernd}, title = {Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru119}, pages = {3975 -- 3992}, year = {2014}, abstract = {Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.}, language = {en} } @article{BrothersKoehlerAttermeyeretal.2014, author = {Brothers, Soren M. and Koehler, J. and Attermeyer, Katrin and Grossart, Hans-Peter and Mehner, T. and Meyer, N. and Scharnweber, Inga Kristin and Hilt, Sabine}, title = {A feedback loop links brownification and anoxia in a temperate, shallow lake}, series = {Limnology and oceanography}, volume = {59}, journal = {Limnology and oceanography}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.4319/lo.2014.59.4.1388}, pages = {1388 -- 1398}, year = {2014}, abstract = {This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.}, language = {en} } @article{BehrensFrankRaweletal.2014, author = {Behrens, Maik and Frank, Oliver and Rawel, Harshadrai Manilal and Ahuja, Gaurav and Potting, Christoph and Hofmann, Thomas and Meyerhof, Wolfgang and Korsching, Sigrun}, title = {ORA1, a Zebrafish Olfactory Receptor Ancestral to All Mammalian V1R Genes, Recognizes 4-Hydroxyphenylacetic Acid, a Putative Reproductive Pheromone}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {28}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.573162}, pages = {19778 -- 19788}, year = {2014}, abstract = {The teleost v1r-related ora genes are a small, highly conserved olfactory receptor gene family of only six genes, whose direct orthologues can be identified in lineages as far as that of cartilaginous fish. However, no ligands for fish olfactory receptor class A related genes (ORA) had been uncovered so far. Here we have deorphanized the ORA1 receptor using heterologous expression and calcium imaging. We report that zebrafish ORA1 recognizes with high specificity and sensitivity 4-hydroxyphenylacetic acid. The carboxyl group of this compound is required in a particular distance from the aromatic ring, whereas the hydroxyl group in the para-position is not essential, but strongly enhances the binding efficacy. Low concentrations of 4-hydroxyphenylacetic acid elicit increases in oviposition frequency in zebrafish mating pairs. This effect is abolished by naris closure. We hypothesize that 4-hydroxyphenylacetic acid might function as a pheromone for reproductive behavior in zebrafish. ORA1 is ancestral to mammalian V1Rs, and its putative function as pheromone receptor is reminiscent of the role of several mammalian V1Rs as pheromone receptors.}, language = {en} } @article{BrustLehmannFettke2014, author = {Brust, Henrike and Lehmann, Tanja and Fettke, J{\"o}rg}, title = {Analysis of the functional interaction of arabidopsis starch synthase and branching enzyme isoforms reveals that the cooperative action of SSI and BEs results in glucans with polymodal chain length distribution similar to amylopectin}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0102364}, pages = {14}, year = {2014}, abstract = {Starch synthase (SS) and branching enzyme (BE) establish the two glycosidic linkages existing in starch. Both enzymes exist as several isoforms. Enzymes derived from several species were studied extensively both in vivo and in vitro over the last years, however, analyses of a functional interaction of SS and BE isoforms are missing so far. Here, we present data from in vitro studies including both interaction of leaf derived and heterologously expressed SS and BE isoforms. We found that SSI activity in native PAGE without addition of glucans was dependent on at least one of the two BE isoforms active in Arabidopsis leaves. This interaction is most likely not based on a physical association of the enzymes, as demonstrated by immunodetection and native PAGE mobility analysis of SSI, BE2, and BE3. The glucans formed by the action of SSI/BEs were analysed using leaf protein extracts from wild type and be single mutants (Atbe2 and Atbe3 mutant lines) and by different combinations of recombinant proteins. Chain length distribution (CLD) patterns of the formed glucans were irrespective of SSI and BE isoforms origin and still independent of assay conditions. Furthermore, we show that all SS isoforms (SSI-SSIV) were able to interact with BEs and form branched glucans. However, only SSI/BEs generated a polymodal distribution of glucans which was similar to CLD pattern detected in amylopectin of Arabidopsis leaf starch. We discuss the impact of the SSI/BEs interplay for the CLD pattern of amylopectin.}, language = {en} } @article{DongYangLehnkuehleretal.2014, author = {Dong, Chao and Yang, Jing and Lehnkuehler, Silke and Kirk, Martin L.}, title = {Pyranopterin dithiolene distortions relevant to electron transfer in xanthine oxidase/dehydrogenase}, series = {Inorganic chemistry}, volume = {53}, journal = {Inorganic chemistry}, number = {14}, publisher = {American Chemical Society}, address = {Washington}, issn = {0020-1669}, doi = {10.1021/ic500873y}, pages = {7077 -- 7079}, year = {2014}, abstract = {The reducing substrates 4-thiolumazine and 2,4-dithiolumazine have been used to form Mo-IV-product complexes with xanthine oxidase (XO) and xanthine dehydrogenase. These Mo-IV-product complexes display an intense metal-to-ligand charge-transfer (MLCT) band in the near-infrared region of the spectrum. Optical pumping into this MLCT band yields resonance Raman spectra of the Mo site that are devoid of contributions from the highly absorbing FAD and 2Fe2S clusters in the protein. The resonance Raman spectra reveal in-plane bending modes of the bound product and low-frequency molybdenum dithiolene and pyranopterin dithiolene vibrational modes. This work provides keen insight into the role of the pyranopterin dithiolene in electron-transfer reactivity.}, language = {en} } @article{McNairNakagawaGrimm2014, author = {McNair, Alistair Senior and Nakagawa, Shinichi and Grimm, Volker}, title = {The evolutionary consequences of disrupted male mating signals: An agent-based modelling exploration of endocrine disrupting chemicals in the guppy}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0103100}, pages = {9}, year = {2014}, abstract = {Females may select a mate based on signalling traits that are believed to accurately correlate with heritable aspects of male quality. Anthropogenic actions, in particular chemicals released into the environment, are now disrupting the accuracy of mating signals to convey information about male quality. The long-term prediction for disrupted mating signals is most commonly loss of female preference. Yet, this prediction has rarely been tested using quantitative models. We use agent-based models to explore the effects of rapid disruption of mating signals. In our model, a gene determines survival. Males signal their level of genetic quality via a signal trait, which females use to select a mate. We allowed this system of sexual selection to become established, before introducing a disruption between the male signal trait and quality, which was similar in nature to that induced by exogenous chemicals. Finally, we assessed the capacity of the system to recover from this disruption. We found that within a relatively short time frame, disruption of mating signals led to a lasting loss of female preference. Decreases in mean viability at the population-level were also observed, because sexual-selection acting against newly arising deleterious mutations was relaxed. The ability of the population to recover from disrupted mating signals was strongly influenced by the mechanisms that promoted or maintained genetic diversity in traits under sexual selection. Our simple model demonstrates that environmental perturbations to the accuracy of male mating signals can result in a long-term loss of female preference for those signals within a few generations. What is more, the loss of this preference can have knock-on consequences for mean population fitness.}, language = {en} } @article{BiancoKetmaier2014, author = {Bianco, Pier Giorgio and Ketmaier, Valerio}, title = {A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae)}, series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, volume = {3841}, journal = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, number = {3}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1175-5326}, pages = {379 -- 402}, year = {2014}, abstract = {By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre-Messinian time, in the Lago Mare, entered the Mediterranean area during the Messinian Lago Mare phase of the Mediterranean Sea and survived only in the Tuscany-Latium district. This genus differs from Leucos in having large pearl organs on the central part of head and body scales in mature males and for the habitat preference, being a riverine-adapted species. It differs from Rutilus in pharyngeal teeth formula (5-5 in Sarmarutilus and 6-5 in Rutilus), size (small in Sarmarutilus and large in Rutilus) and for the preferential habitat (riverine vs. still water). Finally, lectotypes for Leucos basak, Leucos aula, and Sarmarutilus rubilio are designated.}, language = {en} } @article{LohmannTietjenBlaumetal.2014, author = {Lohmann, Dirk and Tietjen, Britta and Blaum, Niels and Joubert, David Francois and Jeltsch, Florian}, title = {Prescribed fire as a tool for managing shrub encroachment in semi-arid savanna rangelands}, series = {Journal of arid environments}, volume = {107}, journal = {Journal of arid environments}, publisher = {Elsevier}, address = {London}, issn = {0140-1963}, doi = {10.1016/j.jaridenv.2014.04.003}, pages = {49 -- 56}, year = {2014}, abstract = {Savanna rangelands worldwide are threatened by shrub encroachment, i.e. the increase of woody plant species at the cost of perennial grasses, causing a strong decline in the productivity of domestic livestock production. Although recent studies indicate that fire might be of great importance for semi-arid and arid savanna dynamics, it is largely not applied in the management of semi-arid rangelands especially with regard to woody plant control. We used the eco-hydrological savanna model EcoHyD to simulate the effects of different fire management strategies on semi-arid savanna vegetation and to assess their longterm suitability for semi-arid rangeland management. Simulation results show that prescribed fires, timed to kill tree seedlings prevented shrub encroachment for a broad range of livestock densities while the possible maximum long-term cattle densities on the simulated semi-arid rangeland in Namibia increased by more than 30\%. However, when grazing intensity was too high, fire management failed in preventing shrub encroachment. Our findings indicate that with regard to fire management a clear distinction between mesic and more arid savannas is necessary: While the frequency of fires is of relevance for mesic savannas, we recommend a fire management focussing on the timing of fire for semi-arid and arid savannas. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{StoofLeichsenringBernhardtPestryakovaetal.2014, author = {Stoof-Leichsenring, Kathleen Rosemarie and Bernhardt, Nadine and Pestryakova, Luidmila Agafyevna and Epp, Laura Saskia and Herzschuh, Ulrike and Tiedemann, Ralph}, title = {A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect}, series = {Journal of paleolimnolog}, volume = {52}, journal = {Journal of paleolimnolog}, number = {1-2}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-014-9779-1}, pages = {77 -- 93}, year = {2014}, abstract = {Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools for tracking differences between diatom lineages that are not visible in their morphologies. These markers revealed putatively high genetic diversity within the Staurosira/Staurosirella species complex, at a finer scale than is possible to resolve by microscopic determination. The rbcL markers may provide additional reliable information on the diversity of barely distinguishable minute benthic fragilarioids. Environmental sequencing may thus allow the tracking of spatial and temporal diversification in Siberian lakes, especially in the context of diatom responses to recent environmental changes, which remains a matter of controversy.}, language = {en} } @article{GraccevaHerdeGroothuisetal.2014, author = {Gracceva, Giulia and Herde, Antje and Groothuis, Ton G. G. and Koolhaas, Jaap M. and Palme, Rupert and Eccard, Jana}, title = {Turning shy on a winter's day: Effects of season on personality and stress response in Microtus arvalis}, series = {Ethology}, volume = {120}, journal = {Ethology}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0179-1613}, doi = {10.1111/eth.12246}, pages = {753 -- 767}, year = {2014}, abstract = {Animal personalities are by definition stable over time, but to what extent they may change during development and in adulthood to adjust to environmental change is unclear. Animals of temperate environments have evolved physiological and behavioural adaptations to cope with the cyclic seasonal changes. This may also result in changes in personality: suites of behavioural and physiological traits that vary consistently among individuals. Winter, typically the adverse season challenging survival, may require individuals to have shy/cautious personality, whereas during summer, energetically favourable to reproduction, individuals may benefit from a bold/risk-taking personality. To test the effects of seasonal changes in early life and in adulthood on behaviours (activity, exploration and anxiety), body mass and stress response, we manipulated the photoperiod and quality of food in two experiments to simulate the conditions of winter and summer. We used the common voles (Microtus arvalis) as they have been shown to display personality based on behavioural consistency over time and contexts. Summer-born voles allocated to winter conditions at weaning had lower body mass, a higher corticosterone increase after stress and a less active, more cautious behavioural phenotype in adulthood compared to voles born in and allocated to summer conditions. In contrast, adult females only showed plasticity in stress-induced corticosterone levels, which were higher in the animals that were transferred to the winter conditions than to those staying in summer conditions. These results suggest a sensitive period for season-related behavioural plasticity in which juveniles shift over the bold-shy axis.}, language = {en} } @article{GuoFuJuerchottetal.2014, author = {Guo, Ke-Tai and Fu, Peng and Juerchott, Kathrin and Motaln, Helena and Selbig, Joachim and Lah, Tamara T. and Tonn, J{\"o}rg-Christian and Schichor, Christian}, title = {The expression of Wnt-inhibitor DKK1 (Dickkopf 1) is determined by intercellular crosstalk and hypoxia in human malignant gliomas}, series = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, volume = {140}, journal = {Journal of cancer research and clinical oncology : official organ of the Deutsche Krebsgesellschaft}, number = {8}, publisher = {Springer}, address = {New York}, issn = {0171-5216}, doi = {10.1007/s00432-014-1642-2}, pages = {1261 -- 1270}, year = {2014}, abstract = {Objective Wnt signalling pathways regulate proliferation, motility and survival in a variety of human cell types. Dickkopf 1 (DKK1) gene codes for a secreted Wnt inhibitory factor. It functions as tumour suppressor gene in breast cancer and as a pro-apoptotic factor in glioma cells. In this study, we aimed to demonstrate whether the different expression of DKK1 in human glioma-derived cells is dependent on microenvironmental factors like hypoxia and regulated by the intercellular crosstalk with bone-marrow-derived mesenchymal stem cells (bmMSCs). Methods Glioma cell line U87-MG, three cell lines from human glioblastoma grade IV (glioma-derived mesenchymal stem cells) and three bmMSCs were selected for the experiment. The expression of DKK1 in cell lines under normoxic/hypoxic environment or co-culture condition was measured using real-time PCR and enzyme-linked immunoadsorbent assay. The effect of DKK1 on cell migration and proliferation was evaluated by in vitro wound healing assays and sulphorhodamine assays, respectively. Results Glioma-derived cells U87-MG displayed lower DKK1 expression compared with bmMSCs. Hypoxia led to an overexpression of DKK1 in bmMSCs and U87-MG when compared to normoxic environment, whereas co-culture of U87-MG with bmMSCs induced the expression of DKK1 in both cell lines. Exogenous recombinant DKK1 inhibited cell migration on all cell lines, but did not have a significant effect on cell proliferation of bmMSCs and glioma cell lines. Conclusion In this study, we showed for the first time that the expression of DKK1 was hypoxia dependent in human malignant glioma cell lines. The induction of DKK1 by intracellular crosstalk or hypoxia stimuli sheds light on the intense adaption of glial tumour cells to environmental alterations.}, language = {en} } @article{CaronDeFrenneBrunetetal.2014, author = {Caron, Maria Mercedes and De Frenne, P. and Brunet, J. and Chabrerie, Olivier and Cousins, S. A. O. and De Backer, L. and Diekmann, M. and Graae, B. J. and Heinken, Thilo and Kolb, A. and Naaf, T. and Plue, J. and Selvi, F. and Strimbeck, G. R. and Wulf, Monika and Verheyen, Kris}, title = {Latitudinal variation in seeds characteristics of Acer platanoides and A. pseudoplatanus}, series = {Plant ecology : an international journal}, volume = {215}, journal = {Plant ecology : an international journal}, number = {8}, publisher = {Springer}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-014-0343-x}, pages = {911 -- 925}, year = {2014}, abstract = {Climate change will likely affect population dynamics of numerous plant species by modifying several aspects of the life cycle. Because plant regeneration from seeds may be particularly vulnerable, here we assess the possible effects of climate change on seed characteristics and present an integrated analysis of seven seed traits (nutrient concentrations, samara mass, seed mass, wing length, seed viability, germination percentage, and seedling biomass) of Acer platanoides and A. pseudoplatanus seeds collected along a wide latitudinal gradient from Italy to Norway. Seed traits were analyzed in relation to the environmental conditions experienced by the mother trees along the latitudinal gradient. We found that seed traits of A. platanoides were more influenced by the climatic conditions than those of A. pseudoplatanus. Additionally, seed viability, germination percentage, and seedling biomass of A. platanoides were strongly related to the seed mass and nutrient concentration. While A. platanoides seeds were more influenced by the environmental conditions (generally negatively affected by rising temperatures), compared to A. pseudoplatanus, A. platanoides still showed higher germination percentage and seedling biomass than A. pseudoplatanus. Thus, further research on subsequent life-history stages of both species is needed. The variation in seed quality observed along the climatic gradient highlights the importance of studying the possible impact of climate change on seed production and species demography.}, language = {en} } @article{FilipBauerHillebrandetal.2014, author = {Filip, Joanna and Bauer, Barbara and Hillebrand, Helmut and Beniermann, Anna and Gaedke, Ursula and Moorthi, Stefanie D.}, title = {Multitrophic diversity effects depend on consumer specialization and species-specific growth and grazing rates}, series = {Oikos}, volume = {123}, journal = {Oikos}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0030-1299}, doi = {10.1111/oik.01219}, pages = {912 -- 922}, year = {2014}, abstract = {Ecosystem functioning is affected by horizontal (within trophic groups) and vertical (across trophic levels) biodiversity. Theory predicts that the effects of vertical biodiversity depend on consumer specialization. In a microcosm experiment, we investigated ciliate consumer diversity and specialization effects on algal prey biovolume, evenness and composition, and on ciliate biovolume production. The experimental data was complemented by a process-based model further analyzing the ecological mechanisms behind the observed diversity effects. Overall, increasing consumer diversity had no significant effect on prey biovolume or evenness. However, consumer specialization affected the prey community. Specialist consumers showed a stronger negative impact on prey biovolume and evenness than generalists. The model confirmed that this pattern was mainly driven by a single specialist with a high per capita grazing rate, consuming the two most productive prey species. When these were suppressed, the prey assemblage became dominated by a less productive species, consequently decreasing prey biovolume and evenness. Consumer diversity increased consumer biovolume, which was stronger for generalists than for specialists and highest in mixed combinations, indicating that consumer functional diversity, i.e. more diverse feeding strategies, increased resource use efficiency. Overall, our results indicate that consumer diversity effects on prey and consumers strongly depend on species-specific growth and grazing rates, which may be at least equally important as consumer specialization in driving consumer diversity effects across trophic levels.}, language = {en} } @article{PagelAndersonCrameretal.2014, author = {Pagel, J{\"o}rn and Anderson, Barbara J. and Cramer, Wolfgang and Fox, Richard and Jeltsch, Florian and Roy, David B. and Thomas, Chris D. and Schurr, Frank Martin}, title = {Quantifying range-wide variation in population trends from local abundance surveys and widespread opportunistic occurrence records}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {5}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, doi = {10.1111/2041-210X.12221}, pages = {751 -- 760}, year = {2014}, abstract = {2. We present a hierarchical model that integrates observations from multiple sources to estimate spatio-temporal abundance trends. The model links annual population densities on a spatial grid to both long-term count data and to opportunistic occurrence records from a citizen science programme. Specific observation models for both data types explicitly account for differences in data structure and quality. 3. We test this novel method in a virtual study with simulated data and apply it to the estimation of abundance dynamics across the range of a butterfly species (Pyronia tithonus) in Great Britain between 1985 and 2004. The application to simulated and real data demonstrates how the hierarchical model structure accommodates various sources of uncertainty which occur at different stages of the link between observational data and the modelled abundance, thereby it accounts for these uncertainties in the inference of abundance variations. 4. We show that by using hierarchical observation models that integrate different types of commonly available data sources, we can improve the estimates of variation in species abundances across space and time. This will improve our ability to detect regional trends and can also enhance the empirical basis for understanding range dynamics.}, language = {en} } @article{KabelitzKappelHennebergeretal.2014, author = {Kabelitz, Tina and Kappel, Christian and Henneberger, Kirstin and Benke, Eileen and Noeh, Christiane and B{\"a}urle, Isabel}, title = {eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in thee arabidopsis lineage}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {8}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.128512}, pages = {3261 -- 3271}, year = {2014}, abstract = {Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 39 end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 39 untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3' end of genes.}, language = {en} } @article{PavlovaNabeNielsenDietzetal.2014, author = {Pavlova, Viola and Nabe-Nielsen, Jacob and Dietz, Rune and Svenning, Jens-Christian and Vorkamp, Katrin and Riget, Frank Farso and Sonne, Christian and Letcher, Robert J. and Grimm, Volker}, title = {Field metabolic rate and PCB adipose tissue deposition efficiency in East Greenland polar bears derived from contaminant monitoring data}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0104037}, pages = {10}, year = {2014}, abstract = {Climate change will increasingly affect the natural habitat and diet of polar bears (Ursus maritimus). Understanding the energetic needs of polar bears is therefore important. We developed a theoretical method for estimating polar bear food consumption based on using the highly recalcitrant polychlorinated biphenyl (PCB) congener, 2,2',4,4',55-hexaCB (CB153) in bear adipose tissue as an indicator of food intake. By comparing the CB153 tissue concentrations in wild polar bears with estimates from a purposely designed individual-based model, we identified the possible combinations of field metabolic rates (FMR) and CB153 deposition efficiencies in East Greenland polar bears. Our simulations indicate that if 30\% of the CB153 consumed by polar bear individuals were deposited into their adipose tissue, the corresponding FMR would be only two times the basal metabolic rate. In contrast, if the modelled CB153 deposition efficiency were 10\%, adult polar bears would require six times more energy than that needed to cover basal metabolism. This is considerably higher than what has been assumed for polar bears in previous studies though it is similar to FMRs found in other marine mammals. An implication of this result is that even relatively small reductions in future feeding opportunities could impact the survival of East Greenland polar bears.}, language = {en} } @article{GossnerPasalicLangeetal.2014, author = {Gossner, Martin M. and Pasalic, Esther and Lange, Markus and Lange, Patricia and Boch, Steffen and Hessenm{\"o}ller, Dominik and M{\"u}ller, J{\"o}rg and Socher, Stephanie A. and Fischer, Markus and Schulze, Ernst-Detlef and Weisser, Wolfgang W.}, title = {Differential responses of herbivores and herbivory to management in temperate Eeuropean beech}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0104876}, pages = {16}, year = {2014}, abstract = {Forest management not only affects biodiversity but also might alter ecosystem processes mediated by the organisms, i.e. herbivory the removal of plant biomass by plant-eating insects and other arthropod groups. Aiming at revealing general relationships between forest management and herbivory we investigated aboveground arthropod herbivory in 105 plots dominated by European beech in three different regions in Germany in the sun-exposed canopy of mature beech trees and on beech saplings in the understorey. We separately assessed damage by different guilds of herbivores, i.e. chewing, sucking and scraping herbivores, gall-forming insects and mites, and leaf-mining insects. We asked whether herbivory differs among different forest management regimes (unmanaged, uneven-aged managed, even-aged managed) and among age-classes within even-aged forests. We further tested for consistency of relationships between regions, strata and herbivore guilds. On average, almost 80\% of beech leaves showed herbivory damage, and about 6\% of leaf area was consumed. Chewing damage was most common, whereas leaf sucking and scraping damage were very rare. Damage was generally greater in the canopy than in the understorey, in particular for chewing and scraping damage, and the occurrence of mines. There was little difference in herbivory among differently managed forests and the effects of management on damage differed among regions, strata and damage types. Covariates such as wood volume, tree density and plant diversity weakly influenced herbivory, and effects differed between herbivory types. We conclude that despite of the relatively low number of species attacking beech; arthropod herbivory on beech is generally high. We further conclude that responses of herbivory to forest management are multifaceted and environmental factors such as forest structure variables affecting in particular microclimatic conditions are more likely to explain the variability in herbivory among beech forest plots.}, language = {en} } @article{DechtriratGajovicEichelmannWojciketal.2014, author = {Dechtrirat, Decha and Gajovic-Eichelmann, Nenad and Wojcik, Felix and Hartmann, Laura and Bier, Frank Fabian and Scheller, Frieder W.}, title = {Electrochemical displacement sensor based on ferrocene boronic acid tracer and immobilized glycan for saccharide binding proteins and E. coli}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {58}, journal = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2014.02.028}, pages = {1 -- 8}, year = {2014}, abstract = {Pathogens such as viruses and bacteria use their envelope proteins and their adhesin lectins to recognize the glycan residues presented on the cell surface of the target tissues. This principle of recognition is used in a new electrochemical displacement sensor for the protein concanavalin A (ConA). A gold electrode was first modified with a self-assembled monolayer of a thiolated mannose/OEG conjugate and a ferrocene boroxol derivative was pre-assembled as reporter molecule onto the mannose surface. The novel tracer molecule based on a 2-hydroxymethyl phenyl boronic acid derivative binds even at neutral pH to the saccharides which could expand the application towards biological samples (i.e., urine and feces). Upon the binding of ConA, the tracer was displaced and washed away from the sensor surface leading to a decrease in the electrochemical signal. Using square wave voltammetry (SWV), the concentration of ConA in the sample solution could be determined in the dynamic concentration range established from 38 nmol L-1 to 5.76 mu mol L-1 with a reproducible detection limit of 1 mu g mL(-1) (38 nmol L-1) based on the signal-to-noise ratio (S/N=3) with fast response of 15 min. The new reporter molecule showed a reduced non-specific displacement by BSA and ribonuclease A. The sensor was also successfully transferred to the first proof of principle for the detection of Escherichia coli exhibiting a detection limit of approximately 6 x 102 cells/mL Specificity of the displacement by target protein ConA and E. coli was demonstrated since the control proteins (i.e., BSA and RNaseA) and the control E. coli strain, which lack of type 1 fimbriae, were ineffective. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{SicardThammMaronaetal.2014, author = {Sicard, Adrien and Thamm, Anna and Marona, Cindy and Lee, Young Wha and Wahl, Vanessa and Stinchcombe, John R. and Wright, Stephen I. and Kappel, Christian and Lenhard, Michael}, title = {Repeated evolutionary changes of leaf morphology caused by mutations to a homeobox gene}, series = {Current biology}, volume = {24}, journal = {Current biology}, number = {16}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2014.06.061}, pages = {1880 -- 1886}, year = {2014}, abstract = {Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology [1-3]. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation [4-6]. In animals, changes to "hot spot" genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions [4-8]. By contrast, only few such genes have been identified from plants [8-11], limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus [12] underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin [12], suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection.}, language = {en} } @article{DietrichLombardoAbdelilahSeyfried2014, author = {Dietrich, Ann-Christin and Lombardo, Veronica A. and Abdelilah-Seyfried, Salim}, title = {Blood flow and Bmp signaling control endocardial chamber morphogenesis}, series = {Developmental cell}, volume = {30}, journal = {Developmental cell}, number = {4}, publisher = {Cell Press}, address = {Cambridge}, issn = {1534-5807}, doi = {10.1016/j.devcel.2014.06.020}, pages = {367 -- 377}, year = {2014}, abstract = {During heart development, the onset of heartbeat and blood flow coincides with a ballooning of the cardiac chambers. Here, we have used the zebrafish as a vertebrate model to characterize chamber ballooning morphogenesis of the endocardium, a specialized population of endothelial cells that line the interior of the heart. By combining functional manipulations, fate mapping studies, and high-resolution imaging, we show that endocardial growth occurs without an influx of external cells. Instead, endocardial cell proliferation is regulated, both by blood flow and by Bmp signaling, in a manner independent of vascular endothelial growth factor (VEGF) signaling. Similar to myocardial cells, endocardial cells obtain distinct chamber-specific and inner- versus outer-curvature-specific surface area sizes. We find that the hemodynamic-sensitive transcription factor Klf2a is involved in regulating endocardial cell morphology. These findings establish the endocardium as the flow-sensitive tissue in the heart with a key role in adapting chamber growth in response to the mechanical stimulus of blood flow.}, language = {en} } @article{SpijkermanStojkovicBeardall2014, author = {Spijkerman, Elly and Stojkovic, Slobodanka and Beardall, John}, title = {CO2 acquisition in Chlamydomonas acidophila is influenced mainly by CO2, not phosphorus, availability}, series = {Photosynthesis research}, volume = {121}, journal = {Photosynthesis research}, number = {2-3}, publisher = {Springer}, address = {Dordrecht}, issn = {0166-8595}, doi = {10.1007/s11120-014-0016-6}, pages = {213 -- 221}, year = {2014}, abstract = {The extremophilic green microalga Chlamydomonas acidophila grows in very acidic waters (pH 2.3-3.4), where CO2 is the sole inorganic carbon source. Previous work has revealed that the species can accumulate inorganic carbon (Ci) and exhibits high affinity CO2 utilization under low-CO2 (air-equilibrium) conditions, similar to organisms with an active CO2 concentrating mechanism (CCM), whereas both processes are down-regulated under high CO2 (4.5 \% CO2) conditions. Responses of this species to phosphorus (Pi)-limited conditions suggested a contrasting regulation of the CCM characteristics. Therefore, we measured external carbonic anhydrase (CA(ext)) activities and protein expression (CAH1), the internal pH, Ci accumulation, and CO2-utilization in cells adapted to high or low CO2 under Pi-replete and Pi-limited conditions. Results reveal that C. acidophila expressed CA(ext) activity and expressed a protein cross-reacting with CAH1 (the CA(ext) from Chlamydomonas reinhardtii). Although the function of this CA remains unclear, CA(ext) activity and high affinity CO2 utilization were the highest under low CO2 conditions. C. acidophila accumulated Ci and expressed the CAH1 protein under all conditions tested, and C. reinhardtii also contained substantial amounts of CAH1 protein under Pi-limitation. In conclusion, Ci utilization is optimized in C. acidophila under ecologically relevant conditions, which may enable optimal survival in its extreme Ci- and Pi-limited habitat. The exact physiological and biochemical acclimation remains to be further studied.}, language = {en} } @article{NiCaoJeltschetal.2014, author = {Ni, Jian and Cao, Xianyong and Jeltsch, Florian and Herzschuh, Ulrike}, title = {Biome distribution over the last 22,000 yr in China}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {409}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2014.04.023}, pages = {33 -- 47}, year = {2014}, abstract = {Patterns of past vegetation changes over time and space can help facilitate better understanding of the interactions among climate, ecosystem, and human impact. Biome changes in China over the last 22,000 yr (calibrated radiocarbon date, a BP) were numerically reconstructed by using a standard approach of pollen-plant functional type-biome assignment (biomization). The biomization procedure involves pollen data from 2434 surface sites and 228 fossil sites with a high quality of pollen count and C-14 dating, 51 natural and three anthropogenic plant functional types (PFTs), as well as 19 natural and one anthropogenic biome. Surface pollen-based reconstruction of modern natural biome patterns is in good agreement (74.4\%) with actual vegetation distribution in China. However, modem large-scale anthropogenic biome reconstruction has not been successful based on the current setup of three anthropogenic PFTs (plantation, secondary, and disturbed PFT) because of the limitation of non-species level pollen identification and the difficulty in the clear assignment of disturbed PFTs. The non-anthropogenic biome distributions of 44 time slices at 500-year intervals show large-scale discrepant and changed vegetation patterns from the last glacial maximum (LGM) to the Holocene throughout China. From 22 ka BP to 19 ka BP, temperate grassland, xerophytic shrubland, and desert dominated northern China, whereas cold or cool forests flourished in central China. Warm-temperate evergreen forests were restricted to far southern China, and tropical forests were absent During 18.5 ka BP to 12 ka BP, cold, cool, and dry biomes extended to some parts of northern, westem, and eastern China. Warm-temperate evergreen and mixed forests gradually expanded to occupy the whole of southern China. A slight northward shift of forest biomes occurred from 15 ka BP to 12 lea BP. During 11.5 ka BP to 9 ka BP, temperate grassland and shrubland gradually stretched to northern and western China. Cold and cool forests widely expanded into northern and central China, as well as in the northern margin of South China along with temperate deciduous forest. Since the early mid-Holocene (approximately 8.5 ka BP to 5.5 ka BP), all forest biomes shifted northward at the expense of herbaceous and shrubby biomes. Simultaneously, cold and cool forest biomes occupied the marginal areas of the Tibetan Plateau and the high mountains in western China. During the middle to late Holocene, from 5 ka to the present, temperate grassland and xerophytic shrubland expanded to the south and east, whereas temperate deciduous forests slightly shifted southward. After 3 lea BP, forest biomes were absent in western China and on the Tibetan plateau surface. Dramatic biome shifts from the LGM to the Holocene were observed in the forest-grassland ecotone and transitional zones between temperate and subtropical climates, between subtropical and tropical regions, and in the mountainous margins of the eastern Tibetan Plateau. Evidence showed more human disturbances during the late Holocene. More pollen records and historical documents are therefore further needed to understand fully the human disturbance-induced large-scale forest changes. In addition, more classifications of anthropogenic biome or land cover, more distinct assignment of pollen taxa to anthropogenic PFTs, and more effective numerical and/or mechanistic techniques in building large-scale human disturbances are required. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{SollySchoeningBochetal.2014, author = {Solly, Emily F. and Sch{\"o}ning, Ingo and Boch, Steffen and Kandeler, Ellen and Marhan, Sven and Michalzik, Beate and M{\"u}ller, J{\"o}rg and Zscheischler, Jakob and Trumbore, Susan E. and Schrumpf, Marion}, title = {Factors controlling decomposition rates of fine root litter in temperate forests and grasslands}, series = {Plant and soil}, volume = {382}, journal = {Plant and soil}, number = {1-2}, publisher = {Springer}, address = {Dordrecht}, issn = {0032-079X}, doi = {10.1007/s11104-014-2151-4}, pages = {203 -- 218}, year = {2014}, abstract = {Fine root decomposition contributes significantly to element cycling in terrestrial ecosystems. However, studies on root decomposition rates and on the factors that potentially influence them are fewer than those on leaf litter decomposition. To study the effects of region and land use intensity on fine root decomposition, we established a large scale study in three German regions with different climate regimes and soil properties. Methods In 150 forest and 150 grassland sites we deployed litterbags (100 mu m mesh size) with standardized litter consisting of fine roots from European beech in forests and from a lowland mesophilous hay meadow in grasslands. In the central study region, we compared decomposition rates of this standardized litter with root litter collected on-site to separate the effect of litter quality from environmental factors. Standardized herbaceous roots in grassland soils decomposed on average significantly faster (24 +/- 6 \% mass loss after 12 months, mean +/- SD) than beech roots in forest soils (12 +/- 4 \%; p < 0.001). Fine root decomposition varied among the three study regions. Land use intensity, in particular N addition, decreased fine root decomposition in grasslands. The initial lignin:N ratio explained 15 \% of the variance in grasslands and 11 \% in forests. Soil moisture, soil temperature, and C:N ratios of soils together explained 34 \% of the variance of the fine root mass loss in grasslands, and 24 \% in forests. Grasslands, which have higher fine root biomass and root turnover compared to forests, also have higher rates of root decomposition. Our results further show that at the regional scale fine root decomposition is influenced by environmental variables such as soil moisture, soil temperature and soil nutrient content. Additional variation is explained by root litter quality.}, language = {en} } @article{SchedinaPfautschHartmannetal.2014, author = {Schedina, Ina-Maria and Pfautsch, Simone and Hartmann, Stefanie and Dolgener, N. and Polgar, Anika and Bianco, Pier Giorgio and Tiedemann, Ralph and Ketmaier, Valerio}, title = {Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data}, series = {Journal of fish biology}, volume = {85}, journal = {Journal of fish biology}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0022-1112}, doi = {10.1111/jfb.12470}, pages = {960 -- 964}, year = {2014}, abstract = {Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0.388 and 0.424 and a mean observed heterozygosity of 0.418 and 0.411, respectively. (C) 2014 The Fisheries Society of the British Isles}, language = {en} } @article{KedrackiChekiniMaronietal.2014, author = {Kedracki, Dawid and Chekini, Mahshid and Maroni, Plinio and Schlaad, Helmut and Nardin, Corinne}, title = {Synthesis and Self-Assembly of a DNA Molecular Brush}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {15}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/bm5008713}, pages = {3375 -- 3382}, year = {2014}, abstract = {We report herein on the polymer-crystallization-assisted thiol-ene photosynthesis of an amphiphilic comb/graft DNA copolymer, or molecular brush, composed of a hydrophobic poly(2-oxazoline) backbone and hydrophilic short single-stranded nucleic acid grafts. Coupling efficiencies are above 60\% and thus higher as compared with the straight solid-phase-supported synthesis of amphiphilic DNA block copolymers. The DNA molecular brushes self-assemble into sub-micron-sized spherical structures in water as evidenced by light scattering as well as atomic force and electron microscopy imaging. The nucleotide sequences remain functional, as assessed by UV and fluorescence spectroscopy subsequent to isoindol synthesis at the surface of the structures. The determination of a vesicular morphology is supported by encapsulation and subsequent spectroscopy monitoring of the release of a water-soluble dye and spectroscopic quantification of the hybridization efficiency (30\% in average) of the functional nucleic acid strands engaged in structure formation: about one-half of the nucleotide sequences are available for hybridization, whereas the other half are hindered within the self-assembled structure. Because speciation between complementary and non complementary sequences in the medium could be ascertained by confocal laser scanning microscopy, the stable self-assembled molecular brushes demonstrate the potential for sensing applications.}, language = {en} } @article{KuekenshoenerHagemannWohlwendetal.2014, author = {Kuekenshoener, Tim and Hagemann, Urs B. and Wohlwend, Daniel and Raeuber, Christina and Baumann, Tobias and Keller, Sandro and Einsle, Oliver and Mueller, Kristian M. and Arndt, Katja Maren}, title = {Analysis of Selected and Designed Chimeric D- and L-alpha-Helix Assemblies}, series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, volume = {15}, journal = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences}, number = {9}, publisher = {American Chemical Society}, address = {Washington}, issn = {1525-7797}, doi = {10.1021/bm5006883}, pages = {3296 -- 3305}, year = {2014}, abstract = {D-Peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.}, language = {en} } @article{PuriWetzelSaffertetal.2014, author = {Puri, Pranav and Wetzel, Collin and Saffert, Paul and Gaston, Kirk W. and Russell, Susan P. and Varela, Juan A. Cordero and van der Vlies, Pieter and Zhang, Gong and Limbach, Patrick A. and Ignatova, Zoya and Poolman, Bert}, title = {Systematic identification of tRNAome and its dynamics in Lactococcus lactis}, series = {Molecular microbiology}, volume = {93}, journal = {Molecular microbiology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0950-382X}, doi = {10.1111/mmi.12710}, pages = {944 -- 956}, year = {2014}, abstract = {Transfer RNAs (tRNAs) through their abundance and modification pattern significantly influence protein translation. Here, we present a systematic analysis of the tRNAome of Lactococcus lactis. Using the next-generation sequencing approach, we identified 40 tRNAs which carry 16 different post-transcriptional modifications as revealed by mass spectrometry analysis. While small modifications are located in the tRNA body, hypermodified nucleotides are mainly present in the anticodon loop, which through wobbling expand the decoding potential of the tRNAs. Using tRNA-based microarrays, we also determined the dynamics in tRNA abundance upon changes in the growth rate and heterologous protein overexpression stress. With a fourfold increase in the growth rate, the relative abundance of tRNAs cognate to low abundance codons decrease, while the tRNAs cognate to major codons remain mostly unchanged. Significant changes in the tRNA abundances are observed upon protein overexpression stress, which does not correlate with the codon usage of the overexpressed gene but rather reflects the altered expression of housekeeping genes.}, language = {en} } @article{SchwahndeSouzaFernieetal.2014, author = {Schwahn, Kevin and de Souza, Leonardo Perez and Fernie, Alisdair and Tohge, Takayuki}, title = {Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade}, series = {Journal of integrative plant biology}, volume = {56}, journal = {Journal of integrative plant biology}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1672-9072}, doi = {10.1111/jipb.12274}, pages = {864 -- 875}, year = {2014}, abstract = {Steroidal glycoalkaloids (SGAs) are nitrogen-containing secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and development on LC/MS techniques for SGA profiling have elucidated the main pathways of SGA metabolism in tomato, the problem of peak annotation still remains due to the vast diversity of chemical structure and similar on overlapping of chemical formula. Here we provide a case study of peak classification and annotation approach by integration of species and tissue specificities of SGA accumulation for provision of comprehensive pathways of SGA biosynthesis. In order to elucidate natural diversity of SGA biosynthesis, a total of 169 putative SGAs found in eight tomato accessions (Solanum lycopersicum, S. pimpinellifolium, S. cheesmaniae, S. chmielewskii, S. neorickii, S. peruvianum, S. habrochaites, S. pennellii) and four tissue types were used for correlation analysis. The results obtained in this study contribute annotation and classification of SGAs as well as detecting putative novel biosynthetic branch points. As such this represents a novel strategy for peak annotation for plant secondary metabolites.}, language = {en} } @article{FujikuraElsaesserBreuningeretal.2014, author = {Fujikura, Ushio and Elsaesser, Lore and Breuninger, Holger and Sanchez-Rodriguez, Clara and Ivakov, Alexander and Laux, Thomas and Findlay, Kim and Persson, Staffan and Lenhard, Michael}, title = {Atkinesin-13A modulates cell-wall synthesis and cell expansion in arabidopsis thaliana via the THESEUS1 pathway}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {10}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {9}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7390}, doi = {10.1371/journal.pgen.1004627}, pages = {15}, year = {2014}, abstract = {Growth of plant organs relies on cell proliferation and expansion. While an increasingly detailed picture about the control of cell proliferation is emerging, our knowledge about the control of cell expansion remains more limited. We demonstrate the internal-motor kinesin AtKINESIN-13A (AtKIN13A) limits cell expansion and cell size in Arabidopsis thaliana, ion atkinl3a mutants forming larger petals with larger cells. The homolog, AtKINESIN-13B, also affects cell expansion and double mutants display growth, gametophytic and early embryonic defects, indicating a redundant role of he two genes. AtKIN13A is known to depolymerize microtubules and influence Golgi motility and distribution. Consistent his function, AtKIN13A interacts genetically with ANGUSTIFOLIA, encoding a regulator of Golgi dynamics. Reduced AtIGN13A activity alters cell wall structure as assessed by Fourier-transformed infrared-spectroscopy and triggers signalling he THESEUS1-dependent cell-wall integrity pathway, which in turn promotes the excess cell expansion in the atkinl3a mutant. Thus, our results indicate that the intracellular activity of AtKIN13A regulates cell expansion and wall architecture via THESEUS1, providing a compelling case of interplay between cell wall integrity sensing and expansion.}, language = {en} } @article{HeindorffBaumann2014, author = {Heindorff, Kristoffer and Baumann, Otto}, title = {Calcineurin is part of a negative feedback loop in the InsP(3)/Ca2+ signalling pathway in blowfly salivary glands}, series = {Cell calcium}, volume = {56}, journal = {Cell calcium}, number = {3}, publisher = {Churchill Livingstone}, address = {Edinburgh}, issn = {0143-4160}, doi = {10.1016/j.ceca.2014.07.009}, pages = {215 -- 224}, year = {2014}, abstract = {The ubiquitous InsP(3)/Ca2+ signalling pathway is modulated by diverse mechanisms, i.e. feedback of Ca2+ and interactions with other signalling pathways. In the salivary glands of the blowfly Calliphora vicina, the hormone serotonin (5-HT) causes a parallel rise in intracellular [Ca2+] and [cAMP] via two types of 5-HT receptors. We have shown recently that cAMP/protein kinase A (PKA) sensitizes InsP(3)-induced Ca2+ release. We have now identified the protein phosphatase that counteracts the effect of PKA on 5-HT-induced InsP(3)/Ca2+ signalling. We demonstrate that (1) tautomycin and okadaic acid, inhibitors of protein phosphatases PP1 and PP2A, have no effect on 5-HT-induced Ca2+ signals; (2) cyclosporin A and FK506, inhibitors of Ca2+/calmodulin-activated protein phosphatase calcineurin, cause an increase in the frequency of 5-HT-induced Ca2+ oscillations; (3) the sensitizing effect of cyclosporin A on 5-HT-induced Ca2+ responses does not involve Ca2+ entry into the cells; (4) cyclosporin A increases InsP(3)-dependent Ca2+ release; (5) inhibition of PKA abolishes the effect of cyclosporin A on the 5-HT-induced Ca2+ responses, indicating that PKA and calcineurin act antagonistically on the InsP(3)/Ca2+ signalling pathway. These findings suggest that calcineurin provides a negative feedback on InsP(3)/Ca2+ signalling in blowfly salivary glands, counteracting the effect of PKA and desensitizing the signalling cascade at higher 5-HT concentrations. (C) 2014 Elsevier Ltd. All rights reserved.}, language = {en} } @article{YarmanSchulzSygmundetal.2014, author = {Yarman, Aysu and Schulz, Christopher and Sygmund, Cristoph and Ludwig, Roland and Gorton, Lo and Wollenberger, Ursula and Scheller, Frieder W.}, title = {Third generation ATP sensor with enzymatic analyte recycling}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {26}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {9}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201400231}, pages = {2043 -- 2048}, year = {2014}, abstract = {For the first time the direct electron transfer of an enzyme - cellobiose dehydrogenase, CDH - has been coupled with the hexokinase catalyzed competition for glucose in a sensor for ATP. To enhance the signal output for ATP, pyruvate kinase was coimmobilized to recycle ADP by the phosphoenolpyruvate driven reaction. The new sensor overcomes the limit of 1:1 stoichiometry of the sequential or competitive conversion of ATP by effective enzymatic recycling of the analyte. The anodic oxidation of the glucose converting CDH proceeds at electrode potentials below 0 mV vs. Ag vertical bar AgCl thus potentially interfering substances like ascorbic acid or catecholamines do not influence the measuring signal. The combination of direct electron transfer of CDH with the enzymatic recycling results in an interference-free and oxygen-independent measurement of ATP in the lower mu molar concentration range with a lower limit of detection of 63.3 nM (S/N=3).}, language = {en} } @article{SchefflerHermanussen2014, author = {Scheffler, Christiane and Hermanussen, Michael}, title = {Is there an influence of modern life style on skeletal build?}, series = {American journal of human biology : the official journal of the Human Biology Council}, volume = {26}, journal = {American journal of human biology : the official journal of the Human Biology Council}, number = {5}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1042-0533}, doi = {10.1002/ajhb.22561}, pages = {590 -- 597}, year = {2014}, abstract = {Objectives: Modern human life style has led to significant decrease in everyday physical activity and bipedal locomotion. It has previously been shown that skeletal robustness (relative elbow breadth) is associated with daily step counts. The aim of the study was to investigate whether also other skeletal measures, particularly pelvic breadth may have changed in recent decades. Methods: We re-analyzed elbow breadth, pelvic breadth (bicristal), and thoracic depth and breadth, of up to 28,975 healthy females and 28,288 healthy males aged 3-18 years from cross-sectional anthropological surveys performed between 1980 and 2012 by the Universities of Potsdam and Berlin, Germany. Results: Relative elbow breadth (Frame index) significantly decreased in both sexes since 1980 (< 0.001). The trend toward slighter built was even more pronounced in absolute and relative pelvic breadth. In contrast, equivalent changes of parts of the skeletal system that are not involved in bipedal locomotion such as thoracic breadth, thoracic depth, and the thoracic index were absent. Conclusions: The present investigation confirms the decline in relative elbow breadth in recent decades. Analogue, but even more pronounced changes were detected in pelvic breadth that coincides with the modern decline in upright locomotion. The findings underscore the phenotypic plasticity of humans while adapting to new environmental conditions. (C) 2014Wiley Periodicals, Inc.}, language = {en} } @article{MartinCreuzburgOexleWacker2014, author = {Martin-Creuzburg, Dominik and Oexle, Sarah and Wacker, Alexander}, title = {Thresholds for sterol-limited growth of Daphnia magna: A comparative approach using 10 different sterols}, series = {Journal of chemical ecology}, volume = {40}, journal = {Journal of chemical ecology}, number = {9}, publisher = {Springer}, address = {Dordrecht}, issn = {0098-0331}, doi = {10.1007/s10886-014-0486-1}, pages = {1039 -- 1050}, year = {2014}, abstract = {Arthropods are incapable of synthesizing sterols de novo and thus require a dietary source to cover their physiological demands. The most prominent sterol in animal tissues is cholesterol, which is an indispensable structural component of cell membranes and serves as precursor for steroid hormones. Instead of cholesterol, plants and algae contain a variety of different phytosterols. Consequently, herbivorous arthropods have to metabolize dietary phytosterols to cholesterol to meet their requirements for growth and reproduction. Here, we investigated sterol-limited growth responses of the freshwater herbivore Daphnia magna by supplementing a sterol-free diet with increasing amounts of 10 different phytosterols and comparing thresholds for sterol-limited growth. In addition, we analyzed the sterol composition of D. magna to explore sterol metabolic constraints and bioconversion capacities. We show that dietary phytosterols strongly differ in their potential to support somatic growth of D. magna. The dietary threshold concentrations obtained by supplementing the different sterols cover a wide range (3.5-34.4 mu g mg C-1) and encompass the one for cholesterol (8.9 mu g mg C-1), indicating that certain phytosterols are more efficient in supporting somatic growth than cholesterol (e.g., fucosterol, brassicasterol) while others are less efficient (e.g., dihydrocholesterol, lathosterol). The dietary sterol concentration gradients revealed that the poor quality of particular sterols can be alleviated partially by increasing dietary concentrations, and that qualitative differences among sterols are most pronounced at low to moderate dietary concentrations. We infer that the dietary sterol composition has to be considered in zooplankton nutritional ecology to accurately assess potential sterol limitations under field conditions.}, language = {en} } @article{SimonsGossnerLewinsohnetal.2014, author = {Simons, Nadja K. and Gossner, Martin M. and Lewinsohn, Thomas M. and Boch, Steffen and Lange, Markus and M{\"u}ller, J{\"o}rg and Pasalic, Esther and Socher, Stephanie A. and T{\"u}rke, Manfred and Fischer, Markus and Weisser, Wolfgang W.}, title = {Resource-mediated indirect effects of grassland management on arthropod diversity}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {9}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0107033}, pages = {12}, year = {2014}, abstract = {Intensive land use is a driving force for biodiversity decline in many ecosystems. In semi-natural grasslands, land-use activities such as mowing, grazing and fertilization affect the diversity of plants and arthropods, but the combined effects of different drivers and the chain of effects are largely unknown. In this study we used structural equation modelling to analyse how the arthropod communities in managed grasslands respond to land use and whether these responses are mediated through changes in resource diversity or resource quantity (biomass). Plants were considered resources for herbivores which themselves were considered resources for predators. Plant and arthropod (herbivores and predators) communities were sampled on 141 meadows, pastures and mown pastures within three regions in Germany in 2008 and 2009. Increasing land-use intensity generally increased plant biomass and decreased plant diversity, mainly through increasing fertilization. Herbivore diversity decreased together with plant diversity but showed no response to changes in plant biomass. Hence, land-use effects on herbivore diversity were mediated through resource diversity rather than quantity. Land-use effects on predator diversity were mediated by both herbivore diversity (resource diversity) and herbivore quantity (herbivore biomass), but indirect effects through resource quantity were stronger. Our findings highlight the importance of assessing both direct and indirect effects of land-use intensity and mode on different trophic levels. In addition to the overall effects, there were subtle differences between the different regions, pointing to the importance of regional land-use specificities. Our study underlines the commonly observed strong effect of grassland land use on biodiversity. It also highlights that mechanistic approaches help us to understand how different land-use modes affect biodiversity.}, language = {en} } @article{HaemaelaeinenDammhahnAujardetal.2014, author = {Haemaelaeinen, Anni and Dammhahn, Melanie and Aujard, Fabienne and Eberle, Manfred and Hardy, Isabelle and Kappeler, Peter M. and Perret, Martine and Schliehe-Diecks, Susanne and Kraus, Cornelia}, title = {Senescence or selective disappearance? Age trajectories of body mass in wild and captive populations of a small-bodied primate}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {281}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1791}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2014.0830}, pages = {10}, year = {2014}, abstract = {Classic theories of ageing consider extrinsic mortality (EM) a major factor in shaping longevity and ageing, yet most studies of functional ageing focus on species with low EM. This bias may cause overestimation of the influence of senescent declines in performance over condition-dependent mortality on demographic processes across taxa. To simultaneously investigate the roles of functional senescence (FS) and intrinsic, extrinsic and condition-dependent mortality in a species with a high predation risk in nature, we compared age trajectories of body mass (BM) in wild and captive grey mouse lemurs (Microcebus murinus) using longitudinal data (853 individuals followed through adulthood). We found evidence of non-random mortality in both settings. In captivity, the oldest animals showed senescence in their ability to regain lost BM, whereas no evidence of FS was found in the wild. Overall, captive animals lived longer, but a reversed sex bias in lifespan was observed between wild and captive populations. We suggest that even moderately condition-dependent EM may lead to negligible FS in the wild. While high EM may act to reduce the average lifespan, this evolutionary process may be counteracted by the increased fitness of the long-lived, high-quality individuals.}, language = {en} } @article{RoethleinMiettinenBorwankaretal.2014, author = {Roethlein, Christoph and Miettinen, Markus S. and Borwankar, Tejas and Buerger, Joerg and Mielke, Thorsten and Kumke, Michael Uwe and Ignatova, Zoya}, title = {Architecture of polyglutamine-containing fibrils from time-resolved fluorescence decay}, series = {The journal of biological chemistry}, volume = {289}, journal = {The journal of biological chemistry}, number = {39}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M114.581991}, pages = {26817 -- 26828}, year = {2014}, abstract = {The disease risk and age of onset of Huntington disease (HD) and nine other repeat disorders strongly depend on the expansion of CAG repeats encoding consecutive polyglutamines (polyQ) in the corresponding disease protein. PolyQ length-dependent misfolding and aggregation are the hallmarks of CAG pathologies. Despite intense effort, the overall structure of these aggregates remains poorly understood. Here, we used sensitive time-dependent fluorescent decay measurements to assess the architecture of mature fibrils of huntingtin (Htt) exon 1 implicated in HD pathology. Varying the position of the fluorescent labels in the Htt monomer with expanded 51Q (Htt51Q) and using structural models of putative fibril structures, we generated distance distributions between donors and acceptors covering all possible distances between the monomers or monomer dimensions within the polyQ amyloid fibril. Using Monte Carlo simulations, we systematically scanned all possible monomer conformations that fit the experimentally measured decay times. Monomers with four-stranded 51Q stretches organized into five-layered beta-sheets with alternating N termini of the monomers perpendicular to the fibril axis gave the best fit to our data. Alternatively, the core structure of the polyQ fibrils might also be a zipper layer with antiparallel four-stranded stretches as this structure showed the next best fit. All other remaining arrangements are clearly excluded by the data. Furthermore, the assessed dimensions of the polyQ stretch of each monomer provide structural evidence for the observed polyQ length threshold in HD pathology. Our approach can be used to validate the effect of pharmacological substances that inhibit or alter amyloid growth and structure.}, language = {en} } @article{LangeTuerkePasalicetal.2014, author = {Lange, Markus and T{\"u}rke, Manfred and Pasalic, Esther and Boch, Steffen and Hessenm{\"o}ller, Dominik and M{\"u}ller, J{\"o}rg and Prati, Daniel and Socher, Stephanie A. and Fischer, Markus and Weisser, Wolfgang W. and Gossner, Martin M.}, title = {Effects of forest management on ground-dwelling beetles (Coleoptera; Carabidae, Staphylinidae) in Central Europe are mainly mediated by changes in forest structure}, series = {Forest ecology and management}, volume = {329}, journal = {Forest ecology and management}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-1127}, doi = {10.1016/j.foreco.2014.06.012}, pages = {166 -- 176}, year = {2014}, abstract = {Forest management is known to influence species diversity of various taxa but inconsistent or even contrasting effects are reported for arthropods. Regional differences in management as well as differences in regional species pools might be responsible for these inconsistencies, but, inter-regional replicated studies that account for regional variability are rare. We investigated the effect of forest type on the abundance, diversity, community structure and composition of two important ground-dwelling beetle families, Carabidae and Staphylinidae, in 149 forest stands distributed over three regions in Germany. In particular we focused on recent forestry history, stand age and dominant tree species, in addition to a number of environmental descriptors. Overall management effects on beetle communities were small and mainly mediated by structural habitat parameters such as the cover of forest canopy or the plant diversity on forest stands. The general response of both beetle taxa to forest management was similar in all regions: abundance and species richness of beetles was higher in older than in younger stands and species richness was lower in unmanaged than in managed stands. The abundance ratio of forest species-to-open habitat species differed between regions, but generally increased from young to old stands, from coniferous to deciduous stands and from managed to unmanaged stands. The response of both beetle families to dominant tree species was variable among regions and staphylinid richness varied in the response to recent forestry history. Our results suggest that current forest management practices change the composition of ground-dwelling beetle communities mainly by favoring generalists and open habitat species. To protect important forest beetle communities and thus the ecosystem functions and services provided by them, we suggest to shelter remaining ancient forests and to develop near-to-nature management strategies by prolonging rotation periods and increasing structural diversity of managed forests. Possible geographic variations in the response of beetle communities need to be considered in conservation-orientated forest management strategies. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @article{BechiHerterMcKennaetal.2014, author = {Bechi, Beatrice and Herter, Susanne and McKenna, Shane and Riley, Christopher and Leimk{\"u}hler, Silke and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Catalytic bio-chemo and bio-bio tandem oxidation reactions for amide and carboxylic acid synthesis}, series = {Green chemistry : an international journal and green chemistry resource}, volume = {16}, journal = {Green chemistry : an international journal and green chemistry resource}, number = {10}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9262}, doi = {10.1039/c4gc01321b}, pages = {4524 -- 4529}, year = {2014}, abstract = {A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or Cul(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.}, language = {en} }