TY - JOUR A1 - Pechouskova, Eva A1 - Dammhahn, Melanie A1 - Brameier, Markus A1 - Fichtel, Claudia A1 - Kappeler, Peter M. A1 - Huchard, Elise T1 - MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener JF - Immunogenetics N2 - The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe's mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB. KW - Primates KW - Cheirogaleidae KW - Microcebus berthae KW - 454 pyrosequencing Y1 - 2015 U6 - https://doi.org/10.1007/s00251-015-0827-4 SN - 0093-7711 SN - 1432-1211 VL - 67 IS - 4 SP - 229 EP - 245 PB - Springer CY - New York ER - TY - JOUR A1 - Paul, Christiane A1 - Mamonekene, Victor A1 - Vater, Marianne A1 - Feulner, Philine G. D. A1 - Engelmann, Jacob A1 - Tiedemann, Ralph A1 - Kirschbaum, Frank T1 - Comparative histology of the adult electric organ among four species of the genus Campylomormyrus (Teleostei: Mormyridae) JF - Journal of comparative physiology : A, Neuroethology, sensory, neural, and behavioral physiology N2 - The electric organ (EO) of weakly electric mormyrids consists of flat, disk-shaped electrocytes with distinct anterior and posterior faces. There are multiple species-characteristic patterns in the geometry of the electrocytes and their innervation. To further correlate electric organ discharge (EOD) with EO anatomy, we examined four species of the mormyrid genus Campylomormyrus possessing clearly distinct EODs. In C. compressirostris, C. numenius, and C. tshokwe, all of which display biphasic EODs, the posterior face of the electrocytes forms evaginations merging to a stalk system receiving the innervation. In C. tamandua that emits a triphasic EOD, the small stalks of the electrocyte penetrate the electrocyte anteriorly before merging on the anterior side to receive the innervation. Additional differences in electrocyte anatomy among the former three species with the same EO geometry could be associated with further characteristics of their EODs. Furthermore, in C. numenius, ontogenetic changes in EO anatomy correlate with profound changes in the EOD. In the juvenile the anterior face of the electrocyte is smooth, whereas in the adult it exhibits pronounced surface foldings. This anatomical difference, together with disparities in the degree of stalk furcation, probably contributes to the about 12 times longer EOD in the adult. KW - Mormyridae KW - Campylomormyrus KW - Electric organ discharge KW - Electrocyte geometry KW - Electric organ ontogeny Y1 - 2015 U6 - https://doi.org/10.1007/s00359-015-0995-6 SN - 0340-7594 SN - 1432-1351 VL - 201 IS - 4 SP - 357 EP - 374 PB - Springer CY - New York ER - TY - JOUR A1 - Pathe-Neuschaefer-Rube, Andrea A1 - Neuschaefer-Rube, Frank A1 - Genz, Lara A1 - Püschel, Gerhard Paul T1 - Botulinum Neurotoxin Dose-Dependently Inhibits Release of Neurosecretory Vesicle-Targeted Luciferase from Neuronal Cells JF - Alternatives to animal experimentation : ALTEX ; a journal for new paths in biomedical science N2 - Botulinum toxin is a bacterial toxin that inhibits neurotransmitter release from neurons and thereby causes a flaccid paralysis. It is used as drug to treat a number of serious ailments and, more frequently, for aesthetic medical interventions. Botulinum toxin for pharmacological applications is isolated from bacterial cultures. Due to partial denaturation of the protein, the specific activity of these preparations shows large variations. Because of its extreme potential toxicity, pharmacological preparations must be carefully tested for their activity. For the current gold standard, the mouse lethality assay, several hundred thousand mice are killed per year. Alternative methods have been developed that suffer from one or more of the following deficits: In vitro enzyme assays test only the activity of the catalytic subunit of the toxin. Enzymatic and cell based immunological assays are specific for just one of the different serotypes. The current study takes a completely different approach that overcomes these limitations: Neuronal cell lines were stably transfected with plasmids coding for luciferases of different species, which were N-terminally tagged with leader sequences that redirect the luciferase into neuro-secretory vesicles. From these vesicles, luciferases were released upon depolarization of the cells. The depolarization-dependent release was efficiently inhibited by botulinum toxin in a concentration range (1 to 100 pM) that is used in pharmacological preparations. The new assay might thus be an alternative to the mouse lethality assay and the immunological assays already in use. KW - Botulinum toxin KW - cell-based assay KW - mouse lethality assay Y1 - 2015 SN - 1868-596X SN - 1868-8551 VL - 32 IS - 4 SP - 297 EP - 306 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Proost, Sebastian A1 - Fujikura, Ushio A1 - Müller-Röber, Bernd T1 - Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology JF - Molecular plant N2 - Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level. KW - abiotic stress KW - chromatin remodeling KW - flower development KW - growth regulation KW - leaf development KW - miRNA Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2015.01.013 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 7 SP - 998 EP - 1010 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Nowak, Michael D. A1 - Russo, Giancarlo A1 - Schlapbach, Ralph A1 - Cuong Nguyen Huu, A1 - Lenhard, Michael A1 - Conti, Elena T1 - The draft genome of Primula veris yields insights into the molecular basis of heterostyly JF - Genome biology : biology for the post-genomic era N2 - Background: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole. Y1 - 2015 U6 - https://doi.org/10.1186/s13059-014-0567-z SN - 1465-6906 SN - 1474-760X VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Neuschaefer-Rube, Frank A1 - Schraplau, Anne A1 - Schewe, Bettina A1 - Lieske, Stefanie A1 - Kruetzfeldt, Julia-Mignon A1 - Ringel, Sebastian A1 - Henkela, Janin A1 - Birkenfeld, Andreas L. A1 - Püschel, Gerhard Paul T1 - Arylhydrocarbon receptor-dependent mIndy (SIc13a5) induction as possible contributor to benzo[a]pyrene-induced lipid accumulation in hepatocytes JF - Toxicology N2 - Non-alcoholic fatty liver disease is a growing problem in industrialized and developing countries. Hepatic lipid accumulation is the result of an imbalance between fatty acid uptake, fatty acid de novo synthesis, beta-oxidation and secretion of triglyceride-rich lipoproteins from the hepatocyte. A central regulator of hepatic lipid metabolism is cytosolic citrate that can either be derived from the mitochondrium or be taken up from the blood via the plasma membrane sodium citrate transporter NaCT, the product of the mammalian INDY gene (SLC13A5). mINDY ablation protects against diet-induced steatosis whereas mINDY expression is increased in patients with hepatic steatosis. Diet-induced hepatic steatosis is also enhanced by activation of the arylhyrocarbon receptor (AhR) both in humans and animal models. Therefore, the hypothesis was tested whether the mINDY gene might be a target of the AhR. In accordance with such a hypothesis, the AhR activator benzo[a]pyrene induced the mINDY expression in primary cultures of rat hepatocytes in an AhR-dependent manner. This induction resulted in an increased citrate uptake and citrate incorporation into lipids which probably was further enhanced by the benzo[a]pyrene-dependent induction of key enzymes of fatty acid synthesis. A potential AhR binding site was identified in the mINDY promoter that appears to be conserved in the human promoter. Elimination or mutation of this site largely abolished the activation of the mINDY promoter by benzo[a]pyrene. This study thus identified the mINDY as an AhR target gene. AhR-dependent induction of the mINDY gene might contribute to the development of hepatic steatosis. (C) 2015 Elsevier Ireland Ltd. All rights reserved. KW - SLC13A5 KW - Non-alcoholic fatty liver disease KW - NAFLD Y1 - 2015 U6 - https://doi.org/10.1016/j.tox.2015.08.007 SN - 0300-483X VL - 337 SP - 1 EP - 9 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Müller, Jörg A1 - Boch, Steffen A1 - Blaser, Steffen A1 - Fischer, Markus A1 - Prati, Daniel T1 - Effects of forest management on bryophyte communities on deadwood JF - Nova Hedwigia : Zeitschrift für Kryptogamenkunde N2 - Epixylic bryophytes are important components of forest vegetation but are currently endangered by increment of wood harvest and intensive forest management. In this paper we present a study about the relationship between forest management, deadwood abundance, deadwood attributes and species richness of epixylic bryophytes on 30 plots comprising three forest types (managed coniferous, managed deciduous and unmanaged deciduous forests) in three regions in Germany. Additionally we analyzed the relations between deadwood attributes (wood species, decay, deadwood type, size) and bryophytes on deadwood items (n = 799) and calculated species interaction networks of wood species and bryophytes. Overall, species richness of epixylic bryophytes was positively related to deadwood abundance and diversity. The mean deadwood abundance was lowest in unmanaged forests (9.7 m(3) ha(-1)) compared with 15.0 m(3) ha(-1) in managed deciduous and 25.1 m(3) ha(-1) in managed coniferous forests. Accordingly, epixylic bryophyte species richness per plot increased from 7 species per 400 m(2) in unmanaged, 10 in managed deciduous and 16 in managed coniferous forests. The interaction network provided evidence of importance of tree-species diversity for bryophyte diversity and the relevance of particular wood species for rare bryophytes. Generally, the results demonstrate a considerable lack of deadwood in all forest types, even in unmanaged forests. Species richness of epixylic bryophytes was strongly limited by available substrates within the observed deadwood abundance ranging up to only 60 m(3) ha(-1). Altogether, this suggests a high demand to increase both abundance and diversity of deadwood in forests. KW - Coarse woody debris KW - cryptogams KW - deadwood KW - species interaction network KW - wood harvest Y1 - 2015 U6 - https://doi.org/10.1127/nova_hedwigia/2015/0242 SN - 0029-5035 VL - 100 IS - 3-4 SP - 423 EP - 438 PB - Cramer CY - Stuttgart ER - TY - JOUR A1 - Muiño, Jose M. A1 - de Bruijn, Suzanne A1 - Pajoro, Alice A1 - Geuten, Koen A1 - Vingron, Martin A1 - Angenent, Gerco C. A1 - Kaufmann, Kerstin T1 - Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor JF - Molecular biology and evolution : MBE N2 - lower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. KW - MADS-domain transcription factor KW - plant development KW - cis-regulatory evolution Y1 - 2015 U6 - https://doi.org/10.1093/molbev/msv210 SN - 1537-1719 SN - 0737-4038 VL - 33 IS - 1 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Mossbrucker, Alexander Markus A1 - Apriyana, Isabella A1 - Fickel, Jörns A1 - Imron, Muhammad Ali A1 - Pudyatmoko, Satyawan A1 - Sumardi, A1 - Suryadi, Helena T1 - Non-invasive genotyping of Sumatran elephants: implications for conservation JF - Tropical conservation science N2 - Reliable baseline information necessary for the monitoring and conservation of Sumatran elephants is scarce. We here combine non-invasive molecular genetics methods and capture-recapture modeling to estimate elephant population size, distribution, sex ratio, and age structure for the Bukit Tigapuluh landscape in Sumatra, Indonesia. Two separate subpopulations were found, for which we estimated a population size of 99 (95% CI = [86, 125], PCCL = 38.59%) and 44 elephants (95% CI = [37, 56], PCCL = 43.18%), respectively. Low elephant densities are likely the result of patchy habitat usage and anthropogenically increased mortality, the latter assumption being supported by strong skews in both sex ratio and age structure as well as direct evidence of elephant killing. Still, the Bukit Tigapuluh landscape currently holds the largest known population of elephants in central Sumatra, representing one of the most important areas for their conservation in Indonesia. Conservation of both the elephant population and their habitat in this region should thus be of high priority. We identified several threats to the population, including (i) the risk of inbreeding and subsequent loss of genetic diversity, (ii) illegal elephant killing, and (iii) the lack of protected habitat. In order to overcome these challenges we suggest: (i) the implementation of a meta-population management program, (ii) monitoring and safeguarding elephants and improving law enforcement, and (iii) providing sufficient safe habitat to mitigate human-elephant-conflict (HEC) and ensure elephant survival. KW - Elephas maximus sumatranus KW - capture-recapture modeling KW - abundance estimation KW - sex ratio KW - age structure KW - Bukit Tigapuluh Landscape Y1 - 2015 SN - 1940-0829 VL - 8 IS - 3 SP - 745 EP - 759 PB - Mongabay.com CY - Menlo Park ER - TY - JOUR A1 - Metz, Johannes A1 - von Oppen, Jonathan A1 - Tielbörger, Katja T1 - Parental environmental effects due to contrasting watering adapt competitive ability, but not drought tolerance, in offspring of a semi-arid annual Brassicaceae JF - The journal of ecology N2 - Parental effects (PE) can be adaptive and improve offspring performance when parents and offspring experience similar environmental conditions. However, it is unknown whether adaptive PE exist also in habitats where such similarity is unlikely due to strong temporal variation. In particular, we do not know whether PE can adapt offspring to fluctuating levels of neighbour competition in such habitats. Here, we tested for adaptive PE in terms of two key environmental factors in a semi-arid annual system, competition and drought. While rainfall was stochastic in the study site, the competitive environment was partly predictable: higher plant densities followed after favourable (rainy) years due to high seed production. We therefore expected PE to adapt the offspring's competitive ability to these (predictable) fluctuations in plant densities, rather than to adapt the offspring's drought tolerance to the (unpredictable) occurrence of intensified drought. Parental plants of Biscutella didyma, an annual Brassicaceae, were raised under favourable watering and under drought conditions. Offspring performance was then tested under a full-factorial combination of two neighbour regimes and six watering levels in the glasshouse. Offspring of parents grown under favourable conditions were stronger competitors. This was associated with a small shift in phenology but not with higher parental seed provisioning. Offspring from parents grown under drought showed no improved drought tolerance. Moreover, no PE were detectable when offspring were grown without neighbours. Our results suggest a novel path of adaptive PE: higher competitive ability was induced in offspring that were more likely to experience high neighbour densities. Together with the lack of adaptive PE towards drought tolerance, this emphasizes that a correlation between parental and offspring environment is crucial for adaptive PE to evolve. Our results also call for the inclusion of competitive effects in future PE studies.Synthesis. This study demonstrates the important role of adaptive PE for plant fitness (regarding competition) but also their limits (regarding drought) in temporally variable environments, based on the predictability of the respective environmental factor. KW - annual plants KW - Biscutella didyma KW - competition KW - dryland ecosystems KW - maternal environmental effects KW - phenology KW - plant population and community dynamics KW - plant-plant interactions KW - transgenerational plasticity KW - water stress Y1 - 2015 U6 - https://doi.org/10.1111/1365-2745.12411 SN - 0022-0477 SN - 1365-2745 VL - 103 IS - 4 SP - 990 EP - 997 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Meissner, Sven A1 - Steinhauser, Dirk A1 - Dittmann-Thünemann, Elke T1 - Metabolomic analysis indicates a pivotal role of the hepatotoxin microcystin in high light adaptation of Microcystis JF - Environmental microbiology N2 - Microcystis is a freshwater cyanobacterium frequently forming nuisance blooms in the summer months. The genus belongs to the predominant producers of the potent hepatotoxin microcystin. The success of Microcystis and its remarkable resistance to high light conditions are not well understood. Here, we have compared the metabolic response of Microcystis aeruginosaPCC7806, its microcystin-deficient mcyB mutant (Mut) and the cyanobacterial model organism SynechocystisPCC6803 to high light exposure of 250molphotonsm(-2)s(-1) using GC/MS-based metabolomics. Microcystis wild type and Mut show pronounced differences in their metabolic reprogramming upon high light. Seventeen percent of the detected metabolites showed significant differences between the two genotypes after high light exposure. Whereas the microcystin-producing wild type shows a faster accumulation of glycolate upon high light illumination, loss of microcystin leads to an accumulation of general stress markers such as trehalose and sucrose. The study further uncovers differences in the high light adaptation of the bloom-forming cyanobacterium Microcystis and the model cyanobacterium Synechocystis. Most notably, Microcystis invests more into carbon reserves such as glycogen after high light exposure. Our data shed new light on the lifestyle of bloom-forming cyanobacteria, the role of the widespread toxin microcystin and the metabolic diversity of cyanobacteria. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12565 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 5 SP - 1497 EP - 1509 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - McKenna, Shane M. A1 - Leimkühler, Silke A1 - Herter, Susanne A1 - Turner, Nicholas J. A1 - Carnell, Andrew J. T1 - Enzyme cascade reactions: synthesis of furandicarboxylic acid (FDCA) and carboxylic acids using oxidases in tandem JF - Green chemistry : an international journal and green chemistry resource N2 - A one-pot tandem enzyme reaction using galactose oxidase M3-5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions. Y1 - 2015 U6 - https://doi.org/10.1039/c5gc00707k SN - 1463-9262 SN - 1463-9270 VL - 17 IS - 6 SP - 3271 EP - 3275 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Mazumder, Mostafizur A1 - Brechun, Katherine E. A1 - Kim, Yongjoo B. A1 - Hoffmann, Stefan A. A1 - Chen, Yih Yang A1 - Keiski, Carrie-Lynn A1 - Arndt, Katja Maren A1 - McMillen, David R. A1 - Woolley, G. Andrew T1 - An Escherichia coli system for evolving improved light-controlled DNA-binding proteins JF - Protein engineering design & selection N2 - Light-switchable proteins offer numerous opportunities as tools for manipulating biological systems with exceptional degrees of spatiotemporal control. Most designed light-switchable proteins currently in use have not been optimised using the randomisation and selection/screening approaches that are widely used in other areas of protein engineering. Here we report an approach for screening light-switchable DNA-binding proteins that relies on light-dependent repression of the transcription of a fluorescent reporter. We demonstrate that the method can be used to recover a known light-switchable DNA-binding protein from a random library. KW - directed evolution KW - fluorescent reporter KW - optogenetics Y1 - 2015 U6 - https://doi.org/10.1093/protein/gzv033 SN - 1741-0126 SN - 1741-0134 VL - 28 IS - 9 SP - 293 EP - 302 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Massie, Thomas Michael A1 - Weithoff, Guntram A1 - Kucklaender, Nina A1 - Gaedke, Ursula A1 - Blasius, Bernd T1 - Enhanced Moran effect by spatial variation in environmental autocorrelation JF - Nature Communications N2 - Spatial correlations in environmental stochasticity can synchronize populations over wide areas, a phenomenon known as the Moran effect. The Moran effect has been confirmed in field, laboratory and theoretical investigations. Little is known, however, about the Moran effect in a common ecological case, when environmental variation is temporally autocorrelated and this autocorrelation varies spatially. Here we perform chemostat experiments to investigate the temporal response of independent phytoplankton populations to autocorrelated stochastic forcing. In contrast to naive expectation, two populations without direct coupling can be more strongly correlated than their environmental forcing (enhanced Moran effect), if the stochastic variations differ in their autocorrelation. Our experimental findings are in agreement with numerical simulations and analytical calculations. The enhanced Moran effect is robust to changes in population dynamics, noise spectra and different measures of correlation-suggesting that noise-induced synchrony may play a larger role for population dynamics than previously thought. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms6993 SN - 2041-1723 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Marcus, Tamar A1 - Boch, Steffen A1 - Durka, Walter A1 - Fischer, Markus A1 - Gossner, Martin M. A1 - Müller, Jörg A1 - Schöning, Ingo A1 - Weisser, Wolfgang W. A1 - Drees, Claudia A1 - Assmann, Thorsten T1 - Living in Heterogeneous Woodlands - Are Habitat Continuity or Quality Drivers of Genetic Variability in a Flightless Ground Beetle? JF - PLoS one N2 - Although genetic diversity is one of the key components of biodiversity, its drivers are still not fully understood. While it is known that genetic diversity is affected both by environmental parameters as well as habitat history, these factors are not often tested together. Therefore, we analyzed 14 microsatellite loci in Abax parallelepipedus, a flightless, forest dwelling ground beetle, from 88 plots in two study regions in Germany. We modeled the effects of historical and environmental variables on allelic richness, and found for one of the regions, the Schorfheide-Chorin, a significant effect of the depth of the litter layer, which is a main component of habitat quality, and of the sampling effort, which serves as an inverse proxy for local population size. For the other region, the Schwabische Alb, none of the potential drivers showed a significant effect on allelic richness. We conclude that the genetic diversity in our study species is being driven by current local population sizes via environmental variables and not by historical processes in the studied regions. This is also supported by lack of genetic differentiation between local populations sampled from ancient and from recent woodlands. We suggest that the potential effects of former fragmentation and recolonization processes have been mitigated by the large and stable local populations of Abax parallelepipedus in combination with the proximity of the ancient and recent woodlands in the studied landscapes. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0144217 SN - 1932-6203 VL - 10 IS - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Manning, Pete A1 - Gossner, Martin M. A1 - Bossdorf, Oliver A1 - Allan, Eric A1 - Zhang, Yuan-Ye A1 - Prati, Daniel A1 - Blüthgen, Nico A1 - Boch, Steffen A1 - Böhm, Stefan A1 - Börschig, Carmen A1 - Hölzel, Norbert A1 - Jung, Kirsten A1 - Klaus, Valentin H. A1 - Klein, Alexandra-Maria A1 - Kleinebecker, Till A1 - Krauss, Jochen A1 - Lange, Markus A1 - Müller, Jörg A1 - Pasalic, Esther A1 - Socher, Stephanie A. A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Weiner, Christiane A1 - Werner, Michael A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Renner, Swen C. A1 - Wells, Konstans A1 - Buscot, Francois A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, Karl Eduard A1 - Weisser, Wolfgang W. A1 - Fischer, Markus T1 - Grassland management intensification weakens the associations among the diversities of multiple plant and animal taxa JF - Ecology : a publication of the Ecological Society of America N2 - Land-use intensification is a key driver of biodiversity change. However, little is known about how it alters relationships between the diversities of different taxonomic groups, which are often correlated due to shared environmental drivers and trophic interactions. Using data from 150 grassland sites, we examined how land-use intensification (increased fertilization, higher livestock densities, and increased mowing frequency) altered correlations between the species richness of 15 plant, invertebrate, and vertebrate taxa. We found that 54% of pairwise correlations between taxonomic groups were significant and positive among all grasslands, while only one was negative. Higher land-use intensity substantially weakened these correlations(35% decrease in rand 43% fewer significant pairwise correlations at high intensity), a pattern which may emerge as a result of biodiversity declines and the breakdown of specialized relationships in these conditions. Nevertheless, some groups (Coleoptera, Heteroptera, Hymenoptera and Orthoptera) were consistently correlated with multidiversity, an aggregate measure of total biodiversity comprised of the standardized diversities of multiple taxa, at both high and lowland-use intensity. The form of intensification was also important; increased fertilization and mowing frequency typically weakened plant-plant and plant-primary consumer correlations, whereas grazing intensification did not. This may reflect decreased habitat heterogeneity under mowing and fertilization and increased habitat heterogeneity under grazing. While these results urge caution in using certain taxonomic groups to monitor impacts of agricultural management on biodiversity, they also suggest that the diversities of some groups are reasonably robust indicators of total biodiversity across a range of conditions. KW - Biodiversity indicators KW - correlation KW - fertilization KW - grassland management KW - grazing KW - land-use change KW - land-use intensity KW - mowing KW - multidiversity KW - multitrophic interactions Y1 - 2015 U6 - https://doi.org/10.1890/14-1307.1 SN - 0012-9658 SN - 1939-9170 VL - 96 IS - 6 SP - 1492 EP - 1501 PB - Wiley CY - Washington ER - TY - JOUR A1 - Makower, A. Katharina A1 - Schuurmans, J. Merijn A1 - Groth, Detlef A1 - Zilliges, Yvonne A1 - Matthijs, Hans C. P. A1 - Dittmann-Thünemann, Elke T1 - Transcriptomics-Aided dissection of the intracellular and extracellular roles of microcystin in microcystis aeruginosa PCC 7806 JF - Applied and environmental microbiology N2 - Recent studies have provided evidence for both intracellular and extracellular roles of the potent hepatotoxin microcystin (MC) in the bloom-forming cyanobacterium Microcystis. Here, we surveyed transcriptomes of the wild-type strain M. aeruginosa PCC 7806 and the microcystin-deficient Delta mcyB mutant under low light conditions with and without the addition of external MC of the LR variant (MC-LR). Transcriptomic data acquired by microarray and quantitative PCR revealed substantial differences in the relative expression of genes of the central intermediary metabolism, photosynthesis, and energy metabolism. In particular, the data provide evidence for a lower photosystem I (PSI)-to-photosystem II (PSII) ratio and a more pronounced carbon limitation in the microcystin-deficient mutant. Interestingly, only 6% of the transcriptional differences could be complemented by external microcystin-LR addition. This MC signaling effect was seen exclusively for genes of the secondary metabolism category. The orphan polyketide synthase gene cluster IPF38-51 was specifically downregulated in response to external MC-LR under low light. Our data suggest a hierarchical and light-dependent cross talk of secondary metabolites and support both an intracellular and an extracellular role of MC in Microcystis. Y1 - 2015 U6 - https://doi.org/10.1128/AEM.02601-14 SN - 0099-2240 SN - 1098-5336 VL - 81 IS - 2 SP - 544 EP - 554 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Ludwig, Arne A1 - Reissmann, Monika A1 - Benecke, Norbert A1 - Bellone, Rebecca A1 - Sandoval-Castellanos, Edson A1 - Cieslak, Michael A1 - González-Fortes, Gloria M. A1 - Morales-Muniz, Arturo A1 - Hofreiter, Michael A1 - Pruvost, Melanie T1 - Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses JF - Philosophical transactions of the Royal Society of London : B, Biological sciences N2 - Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times. KW - ancient DNA KW - coat colour KW - domestication KW - Equus KW - palaeogenetics KW - population Y1 - 2015 U6 - https://doi.org/10.1098/rstb.2013.0386 SN - 0962-8436 SN - 1471-2970 VL - 370 IS - 1660 PB - Royal Society CY - London ER - TY - JOUR A1 - Lotkowska, Magda E. A1 - Tohge, Takayuki A1 - Fernie, Alisdair A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00605 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 3 SP - 1862 EP - 1880 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Lombardo, Veronica A. A1 - Otten, Cecile A1 - Abdelilah-Seyfried, Salim T1 - Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis JF - Journal of visualized experiments N2 - The zebrafish embryonic heart is composed of only a few hundred cells, representing only a small fraction of the entire embryo. Therefore, to prevent the cardiac transcriptome from being masked by the global embryonic transcriptome, it is necessary to collect sufficient numbers of hearts for further analyses. Furthermore, as zebrafish cardiac development proceeds rapidly, heart collection and RNA extraction methods need to be quick in order to ensure homogeneity of the samples. Here, we present a rapid manual dissection protocol for collecting functional/beating hearts from zebrafish embryos. This is an essential prerequisite for subsequent cardiac-specific RNA extraction to determine cardiac-specific gene expression levels by transcriptome analyses, such as quantitative real-time polymerase chain reaction (RT-qPCR). The method is based on differential adhesive properties of the zebrafish embryonic heart compared with other tissues; this allows for the rapid physical separation of cardiac from extracardiac tissue by a combination of fluidic shear force disruption, stepwise filtration and manual collection of transgenic fluorescently labeled hearts. KW - Developmental Biology KW - Issue 95 KW - zebrafish KW - embryo KW - heart KW - dissection KW - RNA KW - RT-qPCR Y1 - 2015 U6 - https://doi.org/10.3791/52087 SN - 1940-087X IS - 95 PB - JoVE CY - Cambridge ER - TY - JOUR A1 - Liesenjohann, Thilo A1 - Liesenjohann, Monique A1 - Trebaticka, Lenka A1 - Sundell, Janne A1 - Haapakoski, Marko A1 - Ylonen, Hannu A1 - Eccard, Jana T1 - State-dependent foraging: lactating voles adjust their foraging behavior according to the presence of a potential nest predator and season JF - Behavioral ecology and sociobiology N2 - Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors "shrew presence" and "season." We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother's foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision. KW - Myodes glareolus KW - Optimal foraging KW - Sorex araneus KW - Nest protection KW - Seasonality KW - Interference Y1 - 2015 U6 - https://doi.org/10.1007/s00265-015-1889-x SN - 0340-5443 SN - 1432-0762 VL - 69 IS - 5 SP - 747 EP - 754 PB - Springer CY - New York ER - TY - JOUR A1 - Li, Chenhong A1 - Corrigan, Shannon A1 - Yang, Lei A1 - Straube, Nicolas A1 - Harris, Mark A1 - Hofreiter, Michael A1 - White, William T. A1 - Naylor, Gavin J. P. T1 - DNA capture reveals transoceanic gene flow in endangered river sharks JF - Proceedings of the National Academy of Sciences of the United States of America N2 - For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks. KW - freshwater sharks KW - DNA KW - museum specimens Y1 - 2015 U6 - https://doi.org/10.1073/pnas.1508735112 SN - 0027-8424 VL - 112 IS - 43 SP - 13302 EP - 13307 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Lemke, Isgard H. A1 - Kolb, Annette A1 - Graae, Bente J. A1 - De Frenne, Pieter A1 - Acharya, Kamal P. A1 - Blandino, Cristina A1 - Brunet, Jorg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Liira, Jaan A1 - Schmucki, Reto A1 - Shevtsova, Anna A1 - Verheyen, Kris A1 - Diekmann, Martin T1 - Patterns of phenotypic trait variation in two temperate forest herbs along a broad climatic gradient JF - Plant ecology : an international journal N2 - Phenotypic trait variation plays a major role in the response of plants to global environmental change, particularly in species with low migration capabilities and recruitment success. However, little is known about the variation of functional traits within populations and about differences in this variation on larger spatial scales. In a first approach, we therefore related trait expression to climate and local environmental conditions, studying two temperate forest herbs, Milium effusum and Stachys sylvatica, along a similar to 1800-2500 km latitudinal gradient. Within each of 9-10 regions in six European countries, we collected data from six populations of each species and recorded several variables in each region (temperature, precipitation) and population (light availability, soil parameters). For each plant, we measured height, leaf area, specific leaf area, seed mass and the number of seeds and examined environmental effects on within-population trait variation as well as on trait means. Most importantly, trait variation differed both between and within populations. Species, however, differed in their response. Intrapopulation variation in Milium was consistently positively affected by higher mean temperatures and precipitation as well as by more fertile local soil conditions, suggesting that more productive conditions may select for larger phenotypic variation. In Stachys, particularly light availability positively influenced trait variation, whereas local soil conditions had no consistent effects. Generally, our study emphasises that intra-population variation may differ considerably across larger scales-due to phenotypic plasticity and/or underlying genetic diversity-possibly affecting species response to global environmental change. KW - Climate change KW - Global environmental change KW - Milium effusum KW - Phenotypic plasticity KW - Intraspecific variation KW - Stachys sylvatica Y1 - 2015 U6 - https://doi.org/10.1007/s11258-015-0534-0 SN - 1385-0237 SN - 1573-5052 VL - 216 IS - 11 SP - 1523 EP - 1536 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Le Duc, Diana A1 - Renaud, Gabriel A1 - Krishnan, Arunkumar A1 - Almen, Markus Sallman A1 - Huynen, Leon A1 - Prohaska, Sonja J. A1 - Ongyerth, Matthias A1 - Bitarello, Barbara D. A1 - Schioth, Helgi B. A1 - Hofreiter, Michael A1 - Stadler, Peter F. A1 - Prüfer, Kay A1 - Lambert, David A1 - Kelso, Janet A1 - Schöneberg, Torsten T1 - Kiwi genome provides insights into evolution of a nocturnal lifestyle JF - Genome biology : biology for the post-genomic era N2 - Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites. Y1 - 2015 U6 - https://doi.org/10.1186/s13059-015-0711-4 SN - 1465-6906 SN - 1474-760X VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) JF - BMC genomics N2 - Background: African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results: Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C. tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions: The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ's transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1858-9 SN - 1471-2164 VL - 16 PB - BioMed Central CY - London ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) JF - BMC Genomics N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1858-9 SN - 1471-2164 VL - 16 IS - 668 PB - Biomed Central CY - London ER - TY - JOUR A1 - Kössl, Manfred A1 - Hechavarria, Julio A1 - Voss, Cornelia A1 - Schaefer, Markus A1 - Vater, Marianne T1 - Bat auditory cortex - model for general mammalian auditory computation or special design solution for active time perception? JF - European journal of neuroscience N2 - Audition in bats serves passive orientation, alerting functions and communication as it does in other vertebrates. In addition, bats have evolved echolocation for orientation and prey detection and capture. This put a selective pressure on the auditory system in regard to echolocation-relevant temporal computation and frequency analysis. The present review attempts to evaluate in which respect the processing modules of bat auditory cortex (AC) are a model for typical mammalian AC function or are designed for echolocation-unique purposes. We conclude that, while cortical area arrangement and cortical frequency processing does not deviate greatly from that of other mammals, the echo delay time-sensitive dorsal cortex regions contain special designs for very powerful time perception. Different bat species have either a unique chronotopic cortex topography or a distributed salt-and-pepper representation of echo delay. The two designs seem to enable similar behavioural performance. KW - chronotopy KW - echolocation KW - fovea KW - salt-and-pepper KW - target range Y1 - 2015 U6 - https://doi.org/10.1111/ejn.12801 SN - 0953-816X SN - 1460-9568 VL - 41 IS - 5 SP - 518 EP - 532 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Köslin-Findeklee, Fabian A1 - Rizi, Vajiheh Safavi A1 - Becker, Martin A. A1 - Parra-Londono, Sebastian A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Kunze, Reinhard A1 - Horst, Walter J. T1 - Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.) JF - Plant science : an international journal of experimental plant biology N2 - High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved. KW - Brassica napus KW - Genotypic differences KW - Leaf senescence KW - Molecular marker KW - N efficiency KW - Stay-green Y1 - 2015 U6 - https://doi.org/10.1016/j.plantsci.2014.11.018 SN - 0168-9452 VL - 233 SP - 174 EP - 185 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Krämer, Nadine A1 - Ravindran, Ethiraj A1 - Zaqout, Sami A1 - Neubert, Gerda A1 - Schindler, Detlev A1 - Ninnemann, Olaf A1 - Gräf, Ralph A1 - Seiler, Andrea E. M. A1 - Kaindl, Angela M. T1 - Loss of CDK5RAP2 affects neural but not non-neural mESC differentiation into cardiomyocytes JF - Cell cycle N2 - Biallelic mutations in the gene encoding centrosomal CDK5RAP2 lead to autosomal recessive primary microcephaly (MCPH), a disorder characterized by pronounced reduction in volume of otherwise architectonical normal brains and intellectual deficit. The current model for the microcephaly phenotype in MCPH invokes a premature shift from symmetric to asymmetric neural progenitor-cell divisions with a subsequent depletion of the progenitor pool. The isolated neural phenotype, despite the ubiquitous expression of CDK5RAP2, and reports of progressive microcephaly in individual MCPH cases prompted us to investigate neural and non-neural differentiation of Cdk5rap2-depleted and control murine embryonic stem cells (mESC). We demonstrate an accumulating proliferation defect of neurally differentiating Cdk5rap2-depleted mESC and cell death of proliferative and early postmitotic cells. A similar effect does not occur in non-neural differentiation into beating cardiomyocytes, which is in line with the lack of non-central nervous system features in MCPH patients. Our data suggest that MCPH is not only caused by premature differentiation of progenitors, but also by reduced propagation and survival of neural progenitors. KW - CDK5RAP2 KW - MCPH KW - mental retardation KW - neural differentiation KW - primary microcephaly KW - stem cell Y1 - 2015 U6 - https://doi.org/10.1080/15384101.2015.1044169 SN - 1538-4101 SN - 1551-4005 VL - 14 IS - 13 SP - 2044 EP - 2057 PB - Taylor & Francis Group CY - Philadelphia ER - TY - JOUR A1 - Kopyshev, Alexey A1 - Lomadze, Nino A1 - Feldmann, David A1 - Genzer, Jan A1 - Santer, Svetlana T1 - Making polymer brush photosensitive with azobenzene containing surfactants JF - Polymer : the international journal for the science and technology of polymers N2 - We report on rendering polyelectrolyte brushes photosensitive by loading them with azobenzene-containing cationic surfactants. Planar poly( methacrylic acid) (PMAA) brushes are synthesized using the "grafting from" free-radical polymerization scheme followed by exposure to a solution of photosensitive surfactants consisting of positively-charged head groups and hydrophobic tails into which azobenzene moieties are inserted. In this study the length of the hydrophobic methylene spacer connecting the azobenzene and the charged head group ranges from 4 to 10 CH2 groups. Under irradiation with UV light, the photo-isomerization of azobenzene integrated into a surfactant results in a change in size, geometry, dipole moment and free volume of the whole molecule. When the brush loaded with photosensitive surfactants is exposed to irradiation with UV interference patterns, the topography of the brush deforms following the distribution of the light intensity, exhibiting surface relief gratings (SRG). Since SRG formation is accompanied by a local rupturing of polymer chains in areas from which the polymer material is receding, most of the polymer material is removed from the surface during treatment with good solvent, leaving behind characteristic patterns of lines or dots. The azobenzene molecules still integrated within the polymer film can be removed by washing the brush with water. The remaining nano-structured brush can then be re-used for further functionalization. Although the opto-mechanically induced rupturing occurs for all surfactants, larger species do not penetrate deep enough into the brush such that after rupturing a leftover layer of polymer material remains on the substrate. This indicates that rupturing occurs predominantly in regions of high surfactant density. KW - Azobenzene containing cationic surfactants KW - Photosensitive polymer brushes KW - Opto-mechanically induced scission of KW - polymer chains Y1 - 2015 U6 - https://doi.org/10.1016/j.polymer.2015.09.023 SN - 0032-3861 SN - 1873-2291 VL - 79 SP - 65 EP - 72 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Kielb, Patrycja A1 - Sezer, Murat A1 - Katz, Sagie A1 - Lopez, Francesca A1 - Schulz, Christopher A1 - Gorton, Lo A1 - Ludwig, Roland A1 - Wollenberger, Ursula A1 - Zebger, Ingo A1 - Weidinger, Inez M. T1 - Spectroscopic Observation of Calcium-Induced Reorientation of Cellobiose Dehydrogenase Immobilized on Electrodes and its Effect on Electrocatalytic Activity JF - ChemPhysChem : a European journal of chemical physics and physical chemistry N2 - Cellobiose dehydrogenase catalyzes the oxidation of various carbohydrates and is considered as a possible anode catalyst in biofuel cells. It has been shown that the catalytic performance of this enzyme immobilized on electrodes can be increased by presence of calcium ions. To get insight into the Ca2+-induced changes in the immobilized enzyme we employ surface-enhanced vibrational (SERR and SEIRA) spectroscopy together with electrochemistry. Upon addition of Ca2+ ions electrochemical measurements show a shift of the catalytic turnover signal to more negative potentials while SERR measurements reveal an offset between the potential of heme reduction and catalytic current. Comparing SERR and SEIRA data we propose that binding of Ca2+ to the heme induces protein reorientation in a way that the electron transfer pathway of the catalytic FAD center to the electrode can bypass the heme cofactor, resulting in catalytic activity at more negative potentials. KW - cellobiose dehydrogenase KW - electron transfer KW - enzyme catalysis KW - spectroelectrochemistry KW - surface-enhanced vibrational spectroscopy Y1 - 2015 U6 - https://doi.org/10.1002/cphc.201500112 SN - 1439-4235 SN - 1439-7641 VL - 16 IS - 9 SP - 1960 EP - 1968 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Kiefer, Christian S. A1 - Claes, Andrea R. A1 - Nzayisenga, Jean-Claude A1 - Pietra, Stefano A1 - Stanislas, Thomas A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity JF - Development N2 - The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. KW - AIP1 KW - Actin KW - Arabidopsis KW - Patterning KW - Planar polarity Y1 - 2015 UR - http://dev.biologists.org/content/142/1/151.long U6 - https://doi.org/doi: 10.1242/dev.111013 IS - 142 SP - 151 EP - 161 ER - TY - JOUR A1 - Kiefer, Christian S. A1 - Claes, Andrea R. A1 - Nzayisenga, Jean-Claude A1 - Pietra, Stefano A1 - Stanislas, Thomas A1 - Hueser, Anke A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity JF - Development : Company of Biologists N2 - The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. KW - AIP1 KW - Arabidopsis KW - WEREWOLF KW - Actin KW - Patterning KW - Planar polarity Y1 - 2015 U6 - https://doi.org/10.1242/dev.111013 SN - 0950-1991 SN - 1477-9129 VL - 142 IS - 1 SP - 151 EP - 161 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Son Lang A1 - Bispo, Cláudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. KW - messenger-rna polyadenylation KW - differential expression analysis KW - gene-expression KW - tail-length KW - cytoplasmic polyadenylation KW - poly(a)-binding protein KW - translational control KW - comprehensive analysis KW - specificity factor KW - mammalian-cells Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005474 SN - 1553-7390 SN - 1553-7404 VL - 11 IS - 8 PB - Public Library of Science CY - San Francisco ER - TY - JOUR A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Son Lang A1 - Bispo, Claudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005474 SN - 1553-7390 SN - 1553-7404 VL - 11 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Kanzleiter, Timo A1 - Jaehnert, Markus A1 - Schulze, Gunnar A1 - Selbig, Joachim A1 - Hallahan, Nicole A1 - Schwenk, Robert Wolfgang A1 - Schürmann, Annette T1 - Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice JF - American journal of physiology : Endocrinology and metabolism N2 - The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice (n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs (P < 0.05, meth diff >5%, coverage > 10) in their putative promoter regions. Alignment with gene expression data (n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors (Plexin A2) as well as genes that participate in muscle hypertrophy (Igfbp4) and motor neuron innervation (Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training. KW - DNA methylation KW - regular exercise training KW - muscle development Y1 - 2015 U6 - https://doi.org/10.1152/ajpendo.00289.2014 SN - 0193-1849 SN - 1522-1555 VL - 308 IS - 10 SP - E912 EP - E920 PB - American Chemical Society CY - Bethesda ER - TY - JOUR A1 - Kaba, Hani E. J. A1 - Maier, Natalia A1 - Schliebe-Ohler, Nicole A1 - Mayer, Yvonne A1 - Mueller, Peter P. A1 - van den Heuvel, Joop A1 - Schuchhardt, Johannes A1 - Hanack, Katja A1 - Bilitewski, Ursula T1 - Identification of whole pathogenic cells by monoclonal antibodies generated against a specific peptide from an immunogenic cell wall protein JF - Journal of microbiological methods N2 - We selected the immunogenic cell wall beta-(1,3)-glucosyltransferase Bgl2p from Candida albicans as a target protein for the production of antibodies. We identified a unique peptide sequence in the protein and generated monoclonal anti- C. albicans Bgl2p antibodies, which bound in particular to whole C. albicans cells. KW - Candida KW - Diagnostics KW - Flow cytometry KW - Peptides KW - Bgl2p Y1 - 2015 U6 - https://doi.org/10.1016/j.mimet.2014.11.003 SN - 0167-7012 SN - 1872-8359 VL - 108 SP - 61 EP - 69 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Mueller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians JF - Nature Communications N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms9912 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Johnson, Kim L. A1 - Ramm, Sascha A1 - Kappel, Christian A1 - Ward, Sally A1 - Leyser, Ottoline A1 - Sakamoto, Tomoaki A1 - Kurata, Tetsuya A1 - Bevan, Michael W. A1 - Lenhard, Michael T1 - The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis JF - PLoS one N2 - Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0131103 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Jetzschmann, Katharina J. A1 - Jagerszki, Gyula A1 - Dechtrirat, Decha A1 - Yarman, Aysu A1 - Gajovic-Eichelmann, Nenad A1 - Gilsing, Hans-Detlev A1 - Schulz, Burkhard A1 - Gyurcsanyi, Robert E. A1 - Scheller, Frieder W. T1 - Vectorially Imprinted Hybrid Nanofilm for Acetylcholinesterase Recognition JF - Advanced functional materials N2 - Effective recognition of enzymatically active tetrameric acetylcholinesterase (AChE) is accomplished by a hybrid nanofilm composed of a propidium-terminated self-assembled monolayer (Prop-SAM) which binds AChE via its peripheral anionic site (PAS) and an ultrathin electrosynthesized molecularly imprinted polymer (MIP) cover layer of a novel carboxylate-modified derivative of 3,4-propylenedioxythiophene. The rebinding of the AChE to the MIP/Prop-SAM nanofilm covered electrode is detected by measuring in situ the enzymatic activity. The oxidative current of the released thiocholine is dependent on the AChE concentration from approximate to 0.04 x 10(-6) to 0.4 x 10(-6)m. An imprinting factor of 9.9 is obtained for the hybrid MIP, which is among the best values reported for protein imprinting. The dissociation constant characterizing the strength of the MIP-AChE binding is 4.2 x 10(-7)m indicating the dominant role of the PAS-Prop-SAM interaction, while the benefit of the MIP nanofilm covering the Prop-SAM layer is the effective suppression of the cross-reactivity toward competing proteins as compared with the Prop-SAM. The threefold selectivity gain provided by i) the shape-specific MIP filter, ii) the propidium-SAM, iii) signal generation only by the AChE bound to the nanofilm shows promise for assessing AChE activity levels in cerebrospinal fluid. KW - acetylcholinesterase KW - biomimetic sensors KW - molecularly imprinted electropolymers KW - peripheral anionic site KW - propidium Y1 - 2015 U6 - https://doi.org/10.1002/adfm.201501900 SN - 1616-301X SN - 1616-3028 VL - 25 IS - 32 SP - 5178 EP - 5183 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Ishida, Seiji A1 - Nozaki, Daiki A1 - Grossart, Hans-Peter A1 - Kagami, Maiko T1 - Novel basal, fungal lineages from freshwater phytoplankton and lake samples JF - Environmental microbiology reports N2 - Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems. Y1 - 2015 U6 - https://doi.org/10.1111/1758-2229.12268 SN - 1758-2229 VL - 7 IS - 3 SP - 435 EP - 441 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Ionescu, Danny A1 - Bizic-Ionescu, Mina A1 - Khalili, Arzhang A1 - Malekmohammadi, Reza A1 - Morad, Reza Mohammad A1 - de Beer, Dirk A1 - Grossart, Hans-Peter T1 - A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect JF - Scientific reports N2 - Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods. Y1 - 2015 U6 - https://doi.org/10.1038/srep14706 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Imholt, Christian A1 - Reil, Daniela A1 - Eccard, Jana A1 - Jacob, Daniela A1 - Hempelmann, Nils A1 - Jacob, Jens T1 - Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus) JF - Pest management science N2 - BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry KW - climate change KW - population dynamics KW - bank vole KW - regression tree KW - outbreak Y1 - 2015 U6 - https://doi.org/10.1002/ps.3838 SN - 1526-498X SN - 1526-4998 VL - 71 IS - 2 SP - 166 EP - 172 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hüttl, Christine A1 - Hettrich, Cornelia A1 - Riedel, Melanie A1 - Henklein, Petra A1 - Rawel, Harshadrai Manilal A1 - Bier, Frank Fabian T1 - Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition JF - Chemical biology & drug design N2 - A straightforward synthesis strategy to multimerize a peptide mimotopes for antibody B13-DE1 recognition is described based on lysine dendrons as multivalent scaffolds. Lysine dendrons that possess N-terminal alkyne residues at the periphery were quantitative functionalized with azido peptides using click chemistry. The solid-phase peptide synthesis (SPPS) allows preparing the peptide dendron in high purity and establishing the possibility of automation. The presented peptide dendron is a promising candidate as multivalent ligand and was used for antibody B13-DE1 recognition. The binding affinity increases with higher dendron generation without loss of specificity. The analysis of biospecific interaction between the synthesized peptide dendron and the antibody was done via surface plasmon resonance (SPR) technique. The presented results show a promising tool for investigations of antigen-antibody reactions. KW - click chemistry KW - lysine dendron KW - peptide mimotopes KW - solid-phase peptide synthesis KW - surface plasmon resonance Y1 - 2015 U6 - https://doi.org/10.1111/cbdd.12444 SN - 1747-0277 SN - 1747-0285 VL - 85 IS - 5 SP - 565 EP - 573 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hönicke, Christiane A1 - Bliss, Peter A1 - Moritz, Robin F. A. T1 - Effect of density on traffic and velocity on trunk trails of Formica pratensis JF - The science of nature N2 - The allocation of large numbers of workers facilitates the swift intake of locally available resources which is essential for ant colony survival. To organise the traffic between nest and food source, the black-meadow ant Formica pratensis establishes permanent trunk trails, which are maintained by the ants. To unravel the ant organisation and potential traffic rules on these trails, we analysed velocity and lane segregation under various densities by experimentally changing feeding regimes. Even under the highest ant densities achieved, we never observed any traffic jams. On the contrary, velocity increased after supplementary feeding despite an enhanced density. Furthermore, inbound ants returning to the nest had a higher velocity than those leaving the colony. Whilst at low and medium density the ants used the centre of the trail, they used the full width of the trail at high density. Outbound ants also showed some degree of lane segregation which contributes to traffic organisation. KW - Density KW - Trunk trail KW - Traffic KW - Lateralization KW - Formica pratensis Y1 - 2015 U6 - https://doi.org/10.1007/s00114-015-1267-6 SN - 0028-1042 SN - 1432-1904 VL - 102 IS - 3-4 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Hu, Chenlin A1 - Völler, Ginka A1 - Sussmuth, Roderich A1 - Dittmann-Thünemann, Elke A1 - Kehr, Jan-Christoph T1 - Functional assessment of mycosporine-like amino acids in Microcystis aeruginosa strain PCC 7806 JF - Environmental microbiology N2 - The biological role of the widespread mycosporine-like amino acids (MAAs) in cyanobacteria is under debate. Here, we have constructed and characterized two mutants impaired in MAA biosynthesis in the bloom-forming cyanobacterium Microcystis aeruginosaPCC 7806. We could identify shinorine as the sole MAA type of the strain, which is exclusively located in the extracellular matrix. Bioinformatic studies as wells as polymerase chain reaction screening revealed that the ability to produce MAAs is sporadically distributed within the genus. Growth experiments and reactive oxygen species quantification with wild-type and mutant strains did not support a role of shinorine in protection against UV or other stress conditions in M.aeruginosaPCC 7806. The shinorine content per dry weight of cells as well as transcription of the mys gene cluster was not significantly elevated in response to UV-A, UV-B or any other stress condition tested. Remarkably, both mutants exhibited pronounced morphological changes compared with the wild type. We observed an increased accumulation and an enhanced hydrophobicity of the extracellular matrix. Our study suggests that MAAs in Microcystis play a negligible role in protection against UV radiation but might be a strain-specific trait involved in extracellular matrix formation and cell-cell interaction. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12577 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 5 SP - 1548 EP - 1559 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Horn, Sebastian A1 - Hempel, Stefan A1 - Ristow, Michael A1 - Rillig, Matthias C. A1 - Kowarik, Ingo A1 - Caruso, Tancredi T1 - Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland JF - Acta oecologica : international journal of ecology N2 - Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved. KW - Assembly pattern KW - Dispersal limitation KW - Festuca brevipila KW - Niche partitioning KW - Null model KW - Plant community ecology KW - Variance partitioning Y1 - 2015 U6 - https://doi.org/10.1016/j.actao.2015.01.004 SN - 1146-609X SN - 1873-6238 VL - 63 SP - 56 EP - 62 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. A1 - Goodchild, Helen A1 - Speller, Camilla F. A1 - Barlow, Axel A1 - González-Fortes, Gloria M. A1 - Thomas, Jessica A. A1 - Ludwig, Arne A1 - Collins, Matthew J. T1 - The future of ancient DNA: Technical advances and conceptual shifts JF - Bioessays : ideas that push the boundaries N2 - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. KW - ancient DNA KW - hybridisation capture KW - multi-locus data KW - next generation sequencing (NGS) KW - palaeogenomics KW - population genomics Y1 - 2015 U6 - https://doi.org/10.1002/bies.201400160 SN - 0265-9247 SN - 1521-1878 VL - 37 IS - 3 SP - 284 EP - 293 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hess, Anne-Katrin A1 - Saffert, Paul A1 - Liebeton, Klaus A1 - Ignatova, Zoya T1 - Optimization of Translation Profiles Enhances Protein Expression and Solubility JF - PLoS one N2 - mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0127039 SN - 1932-6203 VL - 10 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Herter, Susanne A1 - McKenna, Shane M. A1 - Frazer, Andrew R. A1 - Leimkühler, Silke A1 - Carnell, Andrew J. A1 - Turner, Nicholas J. T1 - Galactose Oxidase Variants for the Oxidation of Amino Alcohols in Enzyme Cascade Synthesis JF - ChemCatChem : heterogeneous & homogeneous & bio- & nano-catalysis ; a journal of ChemPubSoc Europe N2 - The use of selected engineered galactose oxidase (GOase) variants for the oxidation of amino alcohols to aldehydes under mild conditions in aqueous systems is reported. GOase variant F-2 catalyses the regioselective oxidation of N-carbobenzyloxy (Cbz)-protected 3-amino-1,2-propanediol to the corresponding -hydroxyaldehyde which was then used in an aldolase reaction. Another variant, M3-5, was found to exhibit activity towards free and N-Cbz-protected aliphatic and aromatic amino alcohols allowing the synthesis of lactams such as 3,4-dihydronaphthalen-1(2H)-one, 2-pyrrolidone and valerolactam in one-pot tandem reactions with xanthine dehydrogenase (XDH) or aldehyde oxidase (PaoABC). KW - aldehyde oxidase KW - amino alcohols KW - cascade reactions KW - enzyme catalysis KW - lactams Y1 - 2015 U6 - https://doi.org/10.1002/cctc.201500218 SN - 1867-3880 SN - 1867-3899 VL - 7 IS - 15 SP - 2313 EP - 2317 PB - Wiley-VCH CY - Weinheim ER -