@article{ReadKegelKluteetal.2013, author = {Read, Betsy A. and Kegel, Jessica and Klute, Mary J. and Kuo, Alan and Lefebvre, Stephane C. and Maumus, Florian and Mayer, Christoph and Miller, John and Monier, Adam and Salamov, Asaf and Young, Jeremy and Aguilar, Maria and Claverie, Jean-Michel and Frickenhaus, Stephan and Gonzalez, Karina and Herman, Emily K. and Lin, Yao-Cheng and Napier, Johnathan and Ogata, Hiroyuki and Sarno, Analissa F. and Shmutz, Jeremy and Schroeder, Declan and de Vargas, Colomban and Verret, Frederic and von Dassow, Peter and Valentin, Klaus and Van de Peer, Yves and Wheeler, Glen and Dacks, Joel B. and Delwiche, Charles F. and Dyhrman, Sonya T. and Gl{\"o}ckner, Gernot and John, Uwe and Richards, Thomas and Worden, Alexandra Z. and Zhang, Xiaoyu and Grigoriev, Igor V. and Allen, Andrew E. and Bidle, Kay and Borodovsky, M. and Bowler, C. and Brownlee, Colin and Cock, J. Mark and Elias, Marek and Gladyshev, Vadim N. and Groth, Marco and Guda, Chittibabu and Hadaegh, Ahmad and Iglesias-Rodriguez, Maria Debora and Jenkins, J. and Jones, Bethan M. and Lawson, Tracy and Leese, Florian and Lindquist, Erika and Lobanov, Alexei and Lomsadze, Alexandre and Malik, Shehre-Banoo and Marsh, Mary E. and Mackinder, Luke and Mock, Thomas and M{\"u}ller-R{\"o}ber, Bernd and Pagarete, Antonio and Parker, Micaela and Probert, Ian and Quesneville, Hadi and Raines, Christine and Rensing, Stefan A. and Riano-Pachon, Diego Mauricio and Richier, Sophie and Rokitta, Sebastian and Shiraiwa, Yoshihiro and Soanes, Darren M. and van der Giezen, Mark and Wahlund, Thomas M. and Williams, Bryony and Wilson, Willie and Wolfe, Gordon and Wurch, Louie L.}, title = {Pan genome of the phytoplankton Emiliania underpins its global distribution}, series = {Nature : the international weekly journal of science}, volume = {499}, journal = {Nature : the international weekly journal of science}, number = {7457}, publisher = {Nature Publ. Group}, address = {London}, organization = {Emiliania Huxleyi Annotation}, issn = {0028-0836}, doi = {10.1038/nature12221}, pages = {209 -- 213}, year = {2013}, abstract = {Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.}, language = {en} } @article{GliwickaNowakBalazadehetal.2013, author = {Gliwicka, Marta and Nowak, Katarzyna and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Gaj, Malgorzata D.}, title = {Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0069261}, pages = {20}, year = {2013}, abstract = {Molecular mechanisms controlling plant totipotency are largely unknown and studies on somatic embryogenesis (SE), the process through which already differentiated cells reverse their developmental program and become embryogenic, provide a unique means for deciphering molecular mechanisms controlling developmental plasticity of somatic cells. Among various factors essential for embryogenic transition of somatic cells transcription factors (TFs), crucial regulators of genetic programs, are believed to play a central role. Herein, we used quantitative real-time polymerase chain reaction (qRT-PCR) to identify TF genes affected during SE induced by in vitro culture in Arabidopsis thaliana. Expression profiles of 1,880 TFs were evaluated in the highly embryogenic Col-0 accession and the non-embryogenic tanmei/emb2757 mutant. Our study revealed 729 TFs whose expression changes during the 10-days incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. The embryo-induction stage of SE occurring during the first 5 days of culture was associated with a robust and dramatic change of the TF transcriptome characterized by the drastic up-regulation of the expression of a great majority (over 80\%) of the TFs active during embryogenic culture. In contrast to SE induction, the advanced stage of embryo formation showed attenuation and stabilization of transcript levels of many TFs. In total, 519 of the SE-modulated TFs were functionally annotated and transcripts related with plant development, phytohormones and stress responses were found to be most abundant. The involvement of selected TFs in SE was verified using T-DNA insertion lines and a significantly reduced embryogenic response was found for the majority of them. This study provides comprehensive data focused on the expression of TF genes during SE and suggests directions for further research on functional genomics of SE.}, language = {en} } @article{RietschGodinaScheffler2013, author = {Rietsch, Katrin and Godina, Elena and Scheffler, Christiane}, title = {Decreased External Skeletal Robustness in Schoolchildren - a Global Trend? ; Ten Year Comparison of Russian and German Data}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0068195}, pages = {7}, year = {2013}, abstract = {Objectives: Obesity and a reduced physical activity are global developments. Physical activity affects the external skeletal robustness which decreased in German children. It was assumed that the negative trend of decreased external skeletal robustness can be found in other countries. Therefore anthropometric data of Russian and German children from the years 2000 and 2010 were compared. Methods: Russian (2000/2010 n = 1023/268) and German (2000/2010 n = 2103/1750) children aged 6-10 years were investigated. Height, BMI and external skeletal robustness (Frame-Index) were examined and compared for the years and the countries. Statistical analysis was performed by Mann-Whitney-Test. Results: Comparison 2010 and 2000: In Russian children BMI was significantly higher; boys were significantly taller and exhibited a decreased Frame-Index (p = .002) in 2010. German boys showed significantly higher BMI in 2010. In both sexes Frame-Index (p = .001) was reduced in 2010. Comparison Russian and German children in 2000: BMI, height and Frame-Index were different between Russian and German children. German children were significantly taller but exhibited a lower Frame-Index (p<.001). Even German girls showed a significantly higher BMI. Comparison Russian and German children in 2010: BMI and Frame-Index were different. Russian children displayed a higher Frame-Index (p<.001) compared with Germans. Conclusions: In Russian children BMI has increased in recent years. Frame-Index is still higher in Russian children compared with Germans however in Russian boys Frame-Index is reduced. This trend and the physical activity should be observed in the future.}, language = {en} } @article{ZarattiniMuraKetmaier2013, author = {Zarattini, Paola and Mura, Graziella and Ketmaier, Valerio}, title = {Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {713}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-013-1487-8}, pages = {19 -- 34}, year = {2013}, abstract = {Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70\%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.}, language = {en} } @article{BosserdtGajovicEichelmanScheller2013, author = {Bosserdt, Maria and Gajovic-Eichelman, Nenad and Scheller, Frieder W.}, title = {Modulation of direct electron transfer of cytochrome c by use of a molecularly imprinted thin film}, series = {Analytical \& bioanalytical chemistry}, volume = {405}, journal = {Analytical \& bioanalytical chemistry}, number = {20}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-013-7009-8}, pages = {6437 -- 6444}, year = {2013}, abstract = {We describe the preparation of a molecularly imprinted polymer film (MIP) on top of a self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) on gold, where the template cytochrome c (cyt c) participates in direct electron transfer (DET) with the underlying electrode. To enable DET, a non-conductive polymer film is electrodeposited from an aqueous solution of scopoletin and cyt c on to the surface of a gold electrode previously modified with MUA. The electroactive surface concentration of cyt c was 0.5 pmol cm(-2). In the absence of the MUA layer, no cyt c DET was observed and the pseudo-peroxidatic activity of the scopoletin-entrapped protein, assessed via oxidation of Ampliflu red in the presence of hydrogen peroxide, was only 30 \% of that for the MIP on MUA. This result indicates that electrostatic adsorption of cyt c by the MUA-SAM substantially increases the surface concentration of cyt c during the electrodeposition step, and is a prerequisite for the productive orientation required for DET. After template removal by treatment with sulfuric acid, rebinding of cyt c to the MUA-MIP-modified electrode occurred with an affinity constant of 100,000 mol(-1) L, a value three times higher than that determined by use of fluorescence titration for the interaction between scopoletin and cyt c in solution. The DET of cyt c in the presence of myoglobin, lysozyme, and bovine serum albumin (BSA) reveals that the MIP layer suppresses the effect of competing proteins.}, language = {en} } @article{BailleulGrimmChionetal.2013, author = {Bailleul, Frederic and Grimm, Volker and Chion, Clement and Hammill, Mike}, title = {Modeling implications of food resource aggregation on animal migration phenology}, series = {Ecology and evolution}, volume = {3}, journal = {Ecology and evolution}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.656}, pages = {2535 -- 2546}, year = {2013}, abstract = {The distribution of poikilotherms is determined by the thermal structure of the marine environment that they are exposed to. Recent research has indicated that changes in migration phenology of beluga whales in the Arctic are triggered by changes in the thermal structure of the marine environment in their summering area. If sea temperatures reflect the spatial distribution of food resources, then changes in the thermal regime will affect how homogeneous or clumped food is distributed. We explore, by individual-based modelling, the hypothesis that changes in migration phenology are not necessarily or exclusively triggered by changes in food abundance, but also by changes in the spatial aggregation of food. We found that the level of food aggregation can significantly affect the relationship between the timing of the start of migration to the winter grounds and the total prey capture of individuals. Our approach strongly indicates that changes in the spatial distribution of food resources should be considered for understanding and quantitatively predicting changes in the phenology of animal migration.}, language = {en} } @article{RuelensdeMaagdProostetal.2013, author = {Ruelens, Philip and de Maagd, Ruud A. and Proost, Sebastian and Theissen, G{\"u}nther and Geuten, Koen and Kaufmann, Kerstin}, title = {FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {8}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3280}, pages = {8}, year = {2013}, abstract = {MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC- like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described.}, language = {en} } @article{CzechWendeMoerletal.2013, author = {Czech, Andreas and Wende, Sandra and Moerl, Mario and Pan, Tao and Ignatova, Zoya}, title = {Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress}, series = {PLoS Genetics : a peer-reviewed, open-access journal}, volume = {9}, journal = {PLoS Genetics : a peer-reviewed, open-access journal}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003767}, pages = {9}, year = {2013}, abstract = {Stress-induced changes of gene expression are crucial for survival of eukaryotic cells. Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels. In this study, we demonstrate that exposure to oxidative stress results in a quick repression of translation by deactivation of the aminoacylends of all transfer-RNA (tRNA). An oxidative-stress activated nuclease, angiogenin, cleaves first within the conserved single-stranded 3'-CCA termini of all tRNAs, thereby blocking their use in translation. This CCA deactivation is reversible and quickly repairable by the CCA-adding enzyme [ATP(CTP): tRNA nucleotidyltransferase]. Through this mechanism the eukaryotic cell dynamically represses and reactivates translation at low metabolic costs.}, language = {en} } @article{ChengvandenBerghZengetal.2013, author = {Cheng, Shifeng and van den Bergh, Erik and Zeng, Peng and Zhong, Xiao and Xu, Jiajia and Liu, Xin and Hofberger, Johannes and de Bruijn, Suzanne and Bhide, Amey S. and Kuelahoglu, Canan and Bian, Chao and Chen, Jing and Fan, Guangyi and Kaufmann, Kerstin and Hall, Jocelyn C. and Becker, Annette and Br{\"a}utigam, Andrea and Weber, Andreas P. M. and Shi, Chengcheng and Zheng, Zhijun and Li, Wujiao and Lv, Mingju and Tao, Yimin and Wang, Junyi and Zou, Hongfeng and Quan, Zhiwu and Hibberd, Julian M. and Zhang, Gengyun and Zhu, Xin-Guang and Xu, Xun and Schranz, M. Eric}, title = {The Tarenaya hassleriana Genome Provides insight Into Reproductive Trait and Genome Evolution of Crucifers}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {8}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.113.113480}, pages = {2813 -- 2830}, year = {2013}, abstract = {The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.}, language = {en} } @article{LiangHeinrichSimardetal.2013, author = {Liang, Wei and Heinrich, Ingo and Simard, Sonia and Helle, Gerhard and Linan, Isabel Dorado and Heinken, Thilo}, title = {Climate signals derived from cell anatomy of Scots pine in NE Germany}, series = {Tree physiology}, volume = {33}, journal = {Tree physiology}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0829-318X}, doi = {10.1093/treephys/tpt059}, pages = {833 -- 844}, year = {2013}, abstract = {Tree-ring chronologies of Pinus sylvestris L. from latitudinal and altitudinal limits of the species distribution have been widely used for climate reconstructions, but there are many sites within the temperate climate zone, as is the case in northeastern Germany, at which there is little evidence of a clear climate signal in the chronologies. In this study, we developed long chronologies of several cell structure variables (e. g., average lumen area and cell wall thickness) from P. sylvestris growing in northeastern Germany and investigated the influence of climate on ring widths and cell structure variables. We found significant correlations between cell structure variables and temperature, and between tree-ring width and relative humidity and vapor pressure, respectively, enabling the development of robust reconstructions from temperate sites that have not yet been realized. Moreover, it has been shown that it may not be necessary to detrend chronologies of cell structure variables and thus low-frequency climate signals may be retrieved from longer cell structure chronologies. The relatively extensive resource of archaeological material of P. sylvestris covering approximately the last millennium may now be useful for climate reconstructions in northeastern Germany and other sites in the temperate climate zone.}, language = {en} } @article{FabianGastLaueetal.2013, author = {Fabian, Heinz and Gast, Klaus and Laue, Michael and Jetzschmann, Katharina J. and Naumann, Dieter and Ziegler, Andreas and Uchanska-Ziegler, Barbara}, title = {IR spectroscopic analyses of amyloid fibril formation of beta(2)-microglobulin using a simplified procedure for its in vitro generation at neutral pH}, series = {Biophysical chemistry : an international journal devoted to the physical chemistry of biological phenomena}, volume = {179}, journal = {Biophysical chemistry : an international journal devoted to the physical chemistry of biological phenomena}, number = {5}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0301-4622}, doi = {10.1016/j.bpc.2013.05.001}, pages = {35 -- 46}, year = {2013}, abstract = {beta(2)-microglobulin (beta(2)m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant beta(2)m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the beta-strands in the fully formed amyloid structure of beta(2)m. This study highlights the power of an approach to investigate the formation of beta(2)m fibrils by a combination of biophysical techniques including IR spectroscopy.}, language = {en} } @article{MalinovaSteupFettke2013, author = {Malinova, Irina and Steup, Martin and Fettke, J{\"o}rg}, title = {Carbon transitions from either Calvin cycle or transitory starch to heteroglycans as revealed by 14-C-labeling experiments using protoplasts from Arabidopsis}, series = {Physiologia plantarum}, volume = {149}, journal = {Physiologia plantarum}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0031-9317}, doi = {10.1111/ppl.12033}, pages = {25 -- 44}, year = {2013}, abstract = {Plants metabolize transitory starch by precisely coordinated plastidial and cytosolic processes. The latter appear to include the action of water-soluble heteroglycans (SHG(in)) whose monosaccharide pattern is similar to that of apoplastic glycans (SHG(ex)) but, unlike SHG(ex), SHG(in) strongly interacts with glucosyl transferases. In this study, we analyzed starch metabolism using mesophyll protoplasts from wild-type plants and two knock-out mutants [deficient in the cytosolic transglucosidase, disproportionating isoenzyme 2 (DPE2) or the plastidial phosphoglucomutase (PGM1)] from Arabidopsis thaliana. Protoplasts prelabeled by photosynthetic (CO2)-C-14 fixation were transferred to an unlabeled medium and were darkened or illuminated. Carbon transitions from the Calvin cycle or from starch to both SHG(in) and SHG(ex) were analyzed. In illuminated protoplasts, starch turn-over was undetectable but darkened protoplasts continuously degraded starch. During illumination, neither the total C-14 content nor the labeling patterns of the sugar residues of SHG(in) were significantly altered but both the total amount and the labeling of the constituents of SHG(ex) increased with time. In darkened protoplasts, the C-14-content of most of the sugar residues of SHG(in) transiently and strongly increased and then declined. This effect was not observed in any SHG(ex) constituent. In darkened DPE2-deficient protoplasts, none of the SHG(in) constituents exhibited an essential transient increase in labeling. In contrast, some residues of SHG(in) from the PGM1 mutant exhibited a transient increase in label but this effect significantly differed from that of the wild type. Two conclusions are reached: first, SHG(in) and SHG(ex) exert different metabolic functions and second, SHG(in) is directly involved in starch degradation.}, language = {en} } @article{AllanWeisserFischeretal.2013, author = {Allan, Eric and Weisser, Wolfgang W. and Fischer, Markus and Schulze, Ernst-Detlef and Weigelt, Alexandra and Roscher, Christiane and Baade, Jussi and Barnard, Romain L. and Bessler, Holger and Buchmann, Nina and Ebeling, Anne and Eisenhauer, Nico and Engels, Christof and Fergus, Alexander J. F. and Gleixner, Gerd and Gubsch, Marlen and Halle, Stefan and Klein, Alexandra-Maria and Kertscher, Ilona and Kuu, Annely and Lange, Markus and Le Roux, Xavier and Meyer, Sebastian T. and Migunova, Varvara D. and Milcu, Alexandru and Niklaus, Pascal A. and Oelmann, Yvonne and Pasalic, Esther and Petermann, Jana S. and Poly, Franck and Rottstock, Tanja and Sabais, Alexander C. W. and Scherber, Christoph and Scherer-Lorenzen, Michael and Scheu, Stefan and Steinbeiss, Sibylle and Schwichtenberg, Guido and Temperton, Vicky and Tscharntke, Teja and Voigt, Winfried and Wilcke, Wolfgang and Wirth, Christian and Schmid, Bernhard}, title = {A comparison of the strength of biodiversity effects across multiple functions}, series = {Oecologia}, volume = {173}, journal = {Oecologia}, number = {1}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-012-2589-0}, pages = {223 -- 237}, year = {2013}, abstract = {In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 \% of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.}, language = {en} } @article{SchaldachWimmerKochetal.2013, author = {Schaldach, R{\"u}diger and Wimmer, Florian and Koch, Jennifer and Volland, Jan and Geissler, Katja and K{\"o}chy, Martin}, title = {Model-based analysis of the environmental impacts of grazing management on Eastern Mediterranean ecosystems in Jordan}, series = {Journal of environmental management}, volume = {127}, journal = {Journal of environmental management}, number = {9}, publisher = {Elsevier}, address = {London}, issn = {0301-4797}, doi = {10.1016/j.jenvman.2012.11.024}, pages = {S84 -- S95}, year = {2013}, abstract = {Eastern Mediterranean ecosystems are prone to desertification when under grazing pressure. Therefore, management of grazing intensity plays a crucial role to avoid or to diminish land degradation and to sustain both livelihoods and ecosystem functioning. The dynamic land-use model LandSHIFT was applied to a case study on the country level for Jordan. The impacts of different stocking densities on the environment were assessed through a set of simulation experiments for various combinations of climate input and assumptions about the development of livestock numbers. Indicators used for the analysis include a set of landscape metrics to account for habitat fragmentation and the "Human Appropriation of Net Primary Production" (HANPP), i.e., the difference between the amount of net primary production (NPP) that would be available in a natural ecosystem and the amount of NPP that remains under human management. Additionally, the potential of the economic valuation of ecosystem services, including landscape and grazing services, as an analysis concept was explored. We found that lower management intensities had a positive effect on HANPP but at the same time resulted in a strong increase of grazing area. This effect was even more pronounced under climate change due to a predominantly negative effect on the biomass productivity of grazing land. Also Landscape metrics tend to indicate decreasing habitat fragmentation as a consequence of lower grazing pressure. The valuation of ecosystem services revealed that low grazing intensity can lead to a comparatively higher economic value on the country level average. The results from our study underline the importance of considering grazing management as an important factor to manage dry-land ecosystems in a sustainable manner.}, language = {en} } @article{PlathPfenningerLerpetal.2013, author = {Plath, Martin and Pfenninger, Markus and Lerp, Hannes and Riesch, R{\"u}diger and Eschenbrenner, Christoph and Slattery, Patrick A. and Bierbach, David and Herrmann, Nina and Schulte, Matthias and Arias-Rodriguez, Lenin and Rimber Indy, Jeane and Passow, Courtney and Tobler, Michael}, title = {Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments}, series = {Evolution}, volume = {67}, journal = {Evolution}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0014-3820}, doi = {10.1111/evo.12133}, pages = {2647 -- 2661}, year = {2013}, abstract = {We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RIs) was negatively correlated with the strength of natural selection (RIm), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.}, language = {en} } @article{BochPratiMuelleretal.2013, author = {Boch, Steffen and Prati, Daniel and M{\"u}ller, J{\"o}rg and Socher, Stephanie and Baumbach, Henryk and Buscot, Francois and Gockel, Sonja and Hemp, Andreas and Hessenm{\"o}ller, Dominik and Kalko, Elisabeth K. V. and Linsenmair, K. Eduard and Pfeiffer, Simone and Pommer, Ulf and Sch{\"o}ning, Ingo and Schulze, Ernst-Detlef and Seilwinder, Claudia and Weisser, Wolfgang W. and Wells, Konstans and Fischer, Markus}, title = {High plant species richness indicates management-related disturbances rather than the conservation status of forests}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {14}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {6}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2013.06.001}, pages = {496 -- 505}, year = {2013}, abstract = {There is a wealth of smaller-scale studies on the effects of forest management on plant diversity. However, studies comparing plant species diversity in forests with different management types and intensity, extending over different regions and forest stages, and including detailed information on site conditions are missing. We studied vascular plants on 1500 20 m x 20 m forest plots in three regions of Germany (Schwabische Alb, Hainich-Dun, Schorfheide-Chorin). In all regions, our study plots comprised different management types (unmanaged, selection cutting, deciduous and coniferous age-class forests, which resulted from clear cutting or shelterwood logging), various stand ages, site conditions, and levels of management-related disturbances. We analyzed how overall richness and richness of different plant functional groups (trees, shrubs, herbs, herbaceous species typically growing in forests and herbaceous light-demanding species) responded to the different management types. On average, plant species richness was 13\% higher in age-class than in unmanaged forests, and did not differ between deciduous age-class and selection forests. In age-class forests of the Schwabische Alb and Hainich-Dun, coniferous stands had higher species richness than deciduous stands. Among age-class forests, older stands with large quantities of standing biomass were slightly poorer in shrub and light-demanding herb species than younger stands. Among deciduous forests, the richness of herbaceous forest species was generally lower in unmanaged than in managed forests, and it was even 20\% lower in unmanaged than in selection forests in Hainich-Dun. Overall, these findings show that disturbances by management generally increase plant species richness. This suggests that total plant species richness is not suited as an indicator for the conservation status of forests, but rather indicates disturbances.}, language = {en} } @article{MatallanaRamirezRaufFarageBarhometal.2013, author = {Matallana-Ramirez, Lilian P. and Rauf, Mamoona and Farage-Barhom, Sarit and Dortay, Hakan and Xue, Gang-Ping and Droege-Laser, Wolfgang and Lers, Amnon and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis}, series = {Molecular plant}, volume = {6}, journal = {Molecular plant}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-2052}, doi = {10.1093/mp/sst012}, pages = {1438 -- 1452}, year = {2013}, abstract = {The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence.}, language = {en} } @article{KlausKleinebeckerPratietal.2013, author = {Klaus, Valentin H. and Kleinebecker, Till and Prati, Daniel and Gossner, Martin M. and Alt, Fabian and Boch, Steffen and Gockel, Sonja and Hemp, Andreas and Lange, Markus and M{\"u}ller, J{\"o}rg and Oelmann, Yvonne and Pasalic, Esther and Renner, Swen C. and Socher, Stephanie A. and T{\"u}rke, Manfred and Weisser, Wolfgang W. and Fischer, Markus and H{\"o}lzel, Norbert}, title = {Does organic grassland farming benefit plant and arthropod diversity at the expense of yield and soil fertility?}, series = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, volume = {177}, journal = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-8809}, doi = {10.1016/j.agee.2013.05.019}, pages = {1 -- 9}, year = {2013}, abstract = {Organic management is one of the most popular strategies to reduce negative environmental impacts of intensive agriculture. However, little is known about benefits for biodiversity and potential worsening of yield under organic grasslands management across different grassland types, i.e. meadow, pasture and mown pasture. Therefore, we studied the diversity of vascular plants and foliage-living arthropods (Coleoptera, Araneae, Heteroptera, Auchenorrhyncha), yield, fodder quality, soil phosphorus concentrations and land-use intensity of organic and conventional grasslands across three study regions in Germany. Furthermore, all variables were related to the time since conversion to organic management in order to assess temporal developments reaching up to 18 years. Arthropod diversity was significantly higher under organic than conventional management, although this was not the case for Araneae, Heteroptera and Auchenorrhyncha when analyzed separately. On the contrary, arthropod abundance, vascular plant diversity and also yield and fodder quality did not considerably differ between organic and conventional grasslands. Analyses did not reveal differences in the effect of organic management among grassland types. None of the recorded abiotic and biotic parameters showed a significant trend with time since transition to organic management, except soil organic phosphorus concentrations which decreased with time. This implies that permanent grasslands respond slower and probably weaker to organic management than crop fields do. However, as land-use intensity and inorganic soil phosphorus concentrations were significantly lower in organic grasslands, overcoming seed and dispersal limitation by re-introducing plant species might be needed to exploit the full ecological potential of organic grassland management. We conclude that although organic management did not automatically increase the diversity of all studied taxa, it is a reasonable and useful way to support agro-biodiversity.}, language = {en} } @article{LiesenjohannLiesenjohannPalmeetal.2013, author = {Liesenjohann, Monique and Liesenjohann, Thilo and Palme, Rupert and Eccard, Jana}, title = {Differential behavioural and endocrine responses of common voles (Microtus arvalis) to nest predators and resource competitors}, series = {BMC ecology}, volume = {13}, journal = {BMC ecology}, number = {17}, publisher = {BioMed Central}, address = {London}, issn = {1472-6785}, doi = {10.1186/1472-6785-13-33}, pages = {10}, year = {2013}, abstract = {Background: Adaptive behavioural strategies promoting co-occurrence of competing species are known to result from a sympatric evolutionary past. Strategies should be different for indirect resource competition (exploitation, e.g., foraging and avoidance behaviour) than for direct interspecific interference (e.g., aggression, vigilance, and nest guarding). We studied the effects of resource competition and nest predation in sympatric small mammal species using semi-fossorial voles and shrews, which prey on vole offspring during their sensitive nestling phase. Experiments were conducted in caged outdoor enclosures. Focus common vole mothers (Microtus arvalis) were either caged with a greater white-toothed shrew (Crocidura russula) as a potential nest predator, with an herbivorous field vole (Microtus agrestis) as a heterospecific resource competitor, or with a conspecific resource competitor. Results: We studied behavioural adaptations of vole mothers during pregnancy, parturition, and early lactation, specifically modifications of the burrow architecture and activity at burrow entrances. Further, we measured pre- and postpartum faecal corticosterone metabolites (FCMs) of mothers to test for elevated stress hormone levels. Only in the presence of the nest predator were prepartum FCMs elevated, but we found no loss of vole nestlings and no differences in nestling body weight in the presence of the nest predator or the heterospecific resource competitor. Although the presence of both the shrew and the field vole induced prepartum modifications to the burrow architecture, only nest predators caused an increase in vigilance time at burrow entrances during the sensitive nestling phase. Conclusion: Voles displayed an adequate behavioural response for both resource competitors and nest predators. They modified burrow architecture to improve nest guarding and increased their vigilance at burrow entrances to enhance offspring survival chances. Our study revealed differential behavioural adaptations to resource competitors and nest predators.}, language = {en} } @article{KierzkowskiLenhardSmithetal.2013, author = {Kierzkowski, Daniel and Lenhard, Michael and Smith, Richard and Kuhlemeier, Cris}, title = {Interaction between meristem tissue layers controls phyllotaxis}, series = {Developmental cell}, volume = {26}, journal = {Developmental cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {1534-5807}, doi = {10.1016/j.devcel.2013.08.017}, pages = {616 -- 628}, year = {2013}, abstract = {Phyllotaxis and vein formation are among the most conspicuous patterning processes in plants. The expression and polarization of the auxin efflux carrier PIN1 is the earliest marker for both processes, with mathematical models indicating that PIN1 can respond to auxin gradients and/or auxin flux. Here, we use cell-layer-specific PIN1 knockouts and partial complementation of auxin transport mutants to examine the interaction between phyllotactic patterning, which occurs primarily in the L1 surface layer of the meristem, and midvein specification in the inner tissues. We show that PIN1 expression in the L1 is sufficient for correct organ positioning, as long as the L1-specific influx carriers are present. Thus, differentiation of inner tissues can proceed without PIN1 or any of the known polar transporters. On theoretical grounds, we suggest that canalization of auxin flux between an auxin source and an auxin sink may involve facilitated diffusion rather than polar transport.}, language = {en} } @article{SchmiederNitschkeSteupetal.2013, author = {Schmieder, Peter and Nitschke, Felix and Steup, Martin and Mallow, Keven and Specker, Edgar}, title = {Determination of glucan phosphorylation using heteronuclear H-1,C-13 double and H-1,C-13,P-31 triple-resonance NMR spectra}, series = {Magnetic resonance in chemistry}, volume = {51}, journal = {Magnetic resonance in chemistry}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0749-1581}, doi = {10.1002/mrc.3996}, pages = {655 -- 661}, year = {2013}, abstract = {Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear H-1,C-13 and H-1,C-13,P-31 techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples.}, language = {en} } @article{WasofLenoirGalletMoronetal.2013, author = {Wasof, Safaa and Lenoir, Jonathan and Gallet-Moron, Emilie and Jamoneau, Aurelien and Brunet, J{\"o}rg and Cousins, Sara A. O. and De Frenne, Pieter and Diekmann, Martin and Hermy, Martin and Kolb, Annette and Liira, Jaan and Verheyen, Kris and Wulf, Monika and Decocq, Guillaume}, title = {Ecological niche shifts of understorey plants along a latitudinal gradient of temperate forests in north-western Europe}, series = {Global ecology and biogeography : a journal of macroecology}, volume = {22}, journal = {Global ecology and biogeography : a journal of macroecology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1466-822X}, doi = {10.1111/geb.12073}, pages = {1130 -- 1140}, year = {2013}, abstract = {Aim In response to environmental changes and to avoid extinction, species may either track suitable environmental conditions or adapt to the modified environment. However, whether and how species adapt to environmental changes remains unclear. By focusing on the realized niche (i.e. the actual space that a species inhabits and the resources it can access as a result of limiting biotic factors present in its habitat), we here examine shifts in the realized-niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) of 26 common and widespread forest understorey plants across their distributional ranges. Location Temperate forests along a ca. 1800-km-long latitudinal gradient from northern France to central Sweden and Estonia. Methods We derived species' realized-niche width from a -diversity metric, which increases if the focal species co-occurs with more species. Based on the concept that species' scores in a detrended correspondence analysis (DCA) represent the locations of their realized-niche positions, we developed a novel approach to run species-specific DCAs allowing the focal species to shift its realized-niche position along the studied latitudinal gradient while the realized-niche positions of other species were held constant. Results None of the 26 species maintained both their realized-niche width and position along the latitudinal gradient. Few species (9 of 26: 35\%) shifted their realized-niche width, but all shifted their realized-niche position. With increasing latitude, most species (22 of 26: 85\%) shifted their realized-niche position for soil nutrients and pH towards nutrient-poorer and more acidic soils. Main conclusions Forest understorey plants shifted their realized niche along the latitudinal gradient, suggesting local adaptation and/or plasticity. This macroecological pattern casts doubt on the idea that the realized niche is stable in space and time, which is a key assumption of species distribution models used to predict the future of biodiversity, hence raising concern about predicted extinction rates.}, language = {en} } @article{PlueDeFrenneAcharyaetal.2013, author = {Plue, Jan and De Frenne, Pieter and Acharya, Kamal P. and Brunet, Jorg and Chabrerie, Olivier and Decocq, Guillaume and Diekmann, Martin and Graae, Bente J. and Heinken, Thilo and Hermy, Martin and Kolb, Annette and Lemke, Isgard and Liira, Jaan and Naaf, Tobias and Shevtsova, Anna and Verheyen, Kris and Wulf, Monika and Cousins, Sara A. O.}, title = {Climatic control of forest herb seed banks along a latitudinal gradient}, series = {Global ecology and biogeography : a journal of macroecology}, volume = {22}, journal = {Global ecology and biogeography : a journal of macroecology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1466-822X}, doi = {10.1111/geb.12068}, pages = {1106 -- 1117}, year = {2013}, abstract = {Aim Seed banks are central to the regeneration strategy of many plant species. Any factor altering seed bank density thus affects plant regeneration and population dynamics. Although seed banks are dynamic entities controlled by multiple environmental drivers, climatic factors are the most comprehensive, but still poorly understood. This study investigates how climatic variation structures seed production and resulting seed bank patterns. Location Temperate forests along a 1900km latitudinal gradient in north-western (NW) Europe. Methods Seed production and seed bank density were quantified in 153 plots along the gradient for four forest herbs with different seed longevity: Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica. We tested the importance of climatic and local environmental factors in shaping seed production and seed bank density. Results Seed production was determined by population size, and not by climatic factors. G.urbanum and M.effusum seed bank density declined with decreasing temperature (growing degree days) and/or increasing temperature range (maximum-minimum temperature). P.nemoralis and S.sylvatica seed bank density were limited by population size and not by climatic variables. Seed bank density was also influenced by other, local environmental factors such as soil pH or light availability. Different seed bank patterns emerged due to differential seed longevities. Species with long-lived seeds maintained constant seed bank densities by counteracting the reduced chance of regular years with high seed production at colder northern latitudes. Main conclusions Seed bank patterns show clear interspecific variation in response to climate across the distribution range. Not all seed banking species may be as well equipped to buffer climate change via their seed bank, notably in short-term persistent species. Since the buffering capacity of seed banks is key to species persistence, these results provide crucial information to advance climatic change predictions on range shifts, community and biodiversity responses.}, language = {en} } @article{DrygalaZoller2013, author = {Drygala, Frank and Zoller, Hinrich}, title = {Spatial use and interaction of the invasive raccoon dog and the native red fox in Central Europe - competition or coexistence?}, series = {European journal of wildlife research}, volume = {59}, journal = {European journal of wildlife research}, number = {5}, publisher = {Springer}, address = {New York}, issn = {1612-4642}, doi = {10.1007/s10344-013-0722-y}, pages = {683 -- 691}, year = {2013}, abstract = {The main objective was to discover extent of interference and/or exploitative competition between the native red fox (Vulpes vulpes) and the introduced, invasive raccoon dog (Nyctereues proconoides) in the intensively used, agricultural landscape of northeast Germany (Mecklenburg-Western Pomerania) using very high frequency (VHF) radio telemetry. We recorded location data for 12 foxes and 16 raccoon dogs between July 2004 and December 2006. Species had similar average home range sizes estimated in each season (K95). Home ranges of adjacent raccoon dogs and foxes overlapped from 0.5 to 74.5 \% with a mean of 26.4 \%. We found a significantly different home range overlap index between the species showing that raccoon dog ranges shifted between seasons to a greater extent than red fox ranges. The raccoon dog differed significantly from the red fox in its use of habitat types, preferring dense vegetation cover and avoiding open areas. The red fox displayed less preference for or avoidance of specific habitat types. Moreover, an almost neutral inter-specific interaction index ranging from -0.12 to 0.12 indicates that raccoon dogs and red foxes ignored each other. It is concluded that widespread and available resources and differences in spatial use patterns prevent competition between red foxes and raccoon dogs in the agricultural landscape of northeast Germany.}, language = {en} } @article{SagollaLoehmannsroebenHille2013, author = {Sagolla, Kristina and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Hille, Carsten}, title = {Time-resolved fluorescence microscopy for quantitative Ca2+ imaging in living cells}, series = {Analytical \& bioanalytical chemistry}, volume = {405}, journal = {Analytical \& bioanalytical chemistry}, number = {26}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-013-7290-6}, pages = {8525 -- 8537}, year = {2013}, abstract = {Calcium (Ca2+) is a ubiquitous intracellular second messenger and involved in a plethora of cellular processes. Thus, quantification of the intracellular Ca2+ concentration ([Ca2+](i)) and of its dynamics is required for a comprehensive understanding of physiological processes and potential dysfunctions. A powerful approach for studying [Ca2+](i) is the use of fluorescent Ca2+ indicators. In addition to the fluorescence intensity as a common recording parameter, the fluorescence lifetime imaging microscopy (FLIM) technique provides access to the fluorescence decay time of the indicator dye. The nanosecond lifetime is mostly independent of variations in dye concentration, allowing more reliable quantification of ion concentrations in biological preparations. In this study, the feasibility of the fluorescent Ca2+ indicator Oregon Green Bapta-1 (OGB-1) for two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was evaluated. In aqueous solution, OGB-1 displayed a Ca2+-dependent biexponential fluorescence decay behaviour, indicating the presence of a Ca2+-free and Ca2+-bound dye form. After sufficient dye loading into living cells, an in situ calibration procedure has also unravelled the Ca2+-free and Ca2+-bound dye forms from a global biexponential fluorescence decay analysis, although the dye's Ca2+ sensitivity is reduced. Nevertheless, quantitative [Ca2+](i) recordings and its stimulus-induced changes in salivary gland cells could be performed successfully. These results suggest that OGB-1 is suitable for 2P-FLIM measurements, which can gain access to cellular physiology.}, language = {en} } @article{SchmidtSchippersMieuletetal.2013, author = {Schmidt, Romy and Schippers, Jos H. M. and Mieulet, Delphine and Obata, Toshihiro and Fernie, Alisdair R. and Guiderdoni, Emmanuel and M{\"u}ller-R{\"o}ber, Bernd}, title = {Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways}, series = {The plant journal}, volume = {76}, journal = {The plant journal}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12286}, pages = {258 -- 273}, year = {2013}, abstract = {Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.}, language = {en} } @article{MuellerWindhofMaximovetal.2013, author = {M{\"u}ller, Sara and Windhof, Indra M. and Maximov, Vladimir and Jurkowski, Tomasz and Jeltsch, Albert and F{\"o}rstner, Konrad U. and Sharma, Cynthia M. and Gr{\"a}f, Ralph and Nellen, Wolfgang}, title = {Target recognition, RNA methylation activity and transcriptional regulation of the dictyostelium discoideum Dnmt2-homologue (DnmA)}, series = {Nucleic acids research}, volume = {41}, journal = {Nucleic acids research}, number = {18}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkt634}, pages = {8615 -- 8627}, year = {2013}, abstract = {Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNA(Asp(GUC)) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNA(Glu(CUC/UUC)) and tRNA(Gly(GCC)) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation.}, language = {en} } @article{HechavarriaMaciasVateretal.2013, author = {Hechavarria, Julio C. and Macias, Silvio and Vater, Marianne and Voss, Cornelia and Mora, Emanuel C. and Kossl, Manfred}, title = {Blurry topography for precise target-distance computations in the auditory cortex of echolocating bats}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {10}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3587}, pages = {11}, year = {2013}, abstract = {Echolocating bats use the time from biosonar pulse emission to the arrival of echo (defined as echo delay) to calculate the space depth of targets. In the dorsal auditory cortex of several species, neurons that encode increasing echo delays are organized rostrocaudally in a topographic arrangement defined as chronotopy. Precise chronotopy could be important for precise target-distance computations. Here we show that in the cortex of three echolocating bat species (Pteronotus quadridens, Pteronotus parnellii and Carollia perspicillata), chronotopy is not precise but blurry. In all three species, neurons throughout the chronotopic map are driven by short echo delays that indicate the presence of close targets and the robustness of map organization depends on the parameter of the receptive field used to characterize neuronal tuning. The timing of cortical responses (latency and duration) provides a binding code that could be important for assembling acoustic scenes using echo delay information from objects with different space depths.}, language = {en} } @article{BreitkopfSchlueterXuetal.2013, author = {Breitkopf, Hendrik and Schl{\"u}ter, P. M. and Xu, S. and Schiestl, Florian P. and Cozzolino, S. and Scopece, G.}, title = {Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?}, series = {Journal of evolutionary biology}, volume = {26}, journal = {Journal of evolutionary biology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1010-061X}, doi = {10.1111/jeb.12216}, pages = {2197 -- 2208}, year = {2013}, abstract = {Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic distance among populations with contrasting predominant pollinators. We analysed floral hydrocarbons as a proxy for floral divergence between populations. Floral adoption of pollinators and their fidelity was tested using pollinator choice experiments. Interpopulation gene flow and population differentiation levels were estimated using AFLP markers. The Tyrrhenian O.sphegodes population preferentially attracted the pollinator bee Andrena bimaculata, whereas the Adriatic O.sphegodes population exclusively attracted A.nigroaenea. Significant differences in scent component proportions were identified in O.sphegodes populations that attracted different preferred pollinators. High interpopulation gene flow was detected, but populations were genetically structured at species level. The high interpopulation gene flow levels independent of preferred pollinators suggest that local adaptation to different pollinators has not (yet) generated detectable genome-wide separation. Alternatively, despite extensive gene flow, few genes underlying floral isolation remain differentiated as a consequence of divergent selection. Different pollination ecotypes in O.sphegodes might represent a local selective response imposed by temporal variation in a geographical mosaic of pollinators as a consequence of the frequent disturbance regimes typical of Ophrys habitats.}, language = {en} } @article{BaumannArndtMueller2013, author = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V}, series = {BMC biotechnology}, volume = {13}, journal = {BMC biotechnology}, number = {10}, publisher = {BioMed Central}, address = {London}, issn = {1472-6750}, doi = {10.1186/1472-6750-13-81}, pages = {11}, year = {2013}, abstract = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.}, language = {en} } @article{RuzanskiSmirnovaRejzeketal.2013, author = {Ruzanski, Christian and Smirnova, Julia and Rejzek, Martin and Cockburn, Darrell and Pedersen, Henriette L. and Pike, Marilyn and Willats, William G. T. and Svensson, Birte and Steup, Martin and Ebenh{\"o}h, Oliver and Smith, Alison M. and Field, Robert A.}, title = {A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night}, series = {The journal of biological chemistry}, volume = {288}, journal = {The journal of biological chemistry}, number = {40}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M113.497867}, pages = {28581 -- 28598}, year = {2013}, abstract = {Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway.}, language = {en} } @article{HenzeRailaScholzeetal.2013, author = {Henze, Andrea and Raila, Jens and Scholze, Alexandra and Zidek, Walter and Tepel, Martin and Schweigert, Florian J.}, title = {Does N-Acetylcysteine modulate post-translational modifications of transthyretin in hemodialysis patients?}, series = {Antioxidants \& redox signaling}, volume = {19}, journal = {Antioxidants \& redox signaling}, number = {11}, publisher = {Liebert}, address = {New Rochelle}, issn = {1523-0864}, doi = {10.1089/ars.2012.5125}, pages = {1166 -- 1172}, year = {2013}, abstract = {It is assumed that effects of the thiol antioxidant N-acetylcysteine (NAC) are mediated by interaction with protein-associated cysteine residues, however, information on protein level in vivo are missing. Therefore, we analyzed NAC-induced modifications of the protein transthyretin (TTR) in plasma of hemodialysis patients in a randomized, placebo-controlled study. TTR was selected due to its low molecular weight and the free cysteine residue in the polypeptide chain, which is known to be extensively modified by formation of mixed disulfides. The intravenous application of NAC during a hemodialysis session resulted in a substantial increase of native TTR from median 15\% (range 8.8\%-30\%) to median 40\% (37-50) and reduction of S-cysteinylated TTR [51\% (44-60) vs. 6.6\% (2.4-10)]. Additionally the pronounced formation of a TTR-NAC adduct was detected. However, all these modifications seemed to be reversible. Additionally, in vitro incubation of plasma with NAC confirmed the in vivo results and indicated that changes in post-translational modification pattern of TTR were a function of NAC concentration. Based on these observations and the essential metabolic and biochemical role of protein-associated cysteine residues we hypothesize that the interaction of NAC with proteins may explain altered protein functions due to modification of cysteine residues. Antioxid. Redox Signal. 19, 1166-1172.}, language = {en} } @article{ReschkeSigfridssonKaufmannetal.2013, author = {Reschke, Stefan and Sigfridsson, Kajsa G. V. and Kaufmann, Paul and Leidel, Nils and Horn, Sebastian and Gast, Klaus and Schulzke, Carola and Haumann, Michael and Leimk{\"u}hler, Silke}, title = {Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in escherichia coli}, series = {The journal of biological chemistry}, volume = {288}, journal = {The journal of biological chemistry}, number = {41}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M113.497453}, pages = {29736 -- 29745}, year = {2013}, abstract = {The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.}, language = {en} } @article{YarmanScheller2013, author = {Yarman, Aysu and Scheller, Frieder W.}, title = {Coupling biocatalysis with molecular imprinting in a biomimetic sensor}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {52}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {44}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201305368}, pages = {11521 -- 11525}, year = {2013}, language = {en} } @article{LukasFrostWacker2013, author = {Lukas, Marcus and Frost, Paul C. and Wacker, Alexander}, title = {The neonate nutrition hypothesis - early feeding affects the body stoichiometry of Daphnia offspring}, series = {Freshwater biology}, volume = {58}, journal = {Freshwater biology}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/fwb.12213}, pages = {2333 -- 2344}, year = {2013}, abstract = {Aquatic herbivores consume variable quantities and qualities of food. In freshwater systems, where phosphorus (P) is often a primary limiting element, inadequate dietary P can slow maternal growth and reduce body P content. There remains uncertainty about whether and how dietary effects on mothers are transferred to offspring by way of egg provisioning. Using the keystone herbivore Daphnia, we tested a novel explanation (the neonate nutrition hypothesis') to determine whether the early nutrition of newborns affects their elemental composition and whether the indications of differences in maternal P nutrition found previously might be overestimated. We thus examined the P content of mothers and their eggs from deposition through development to the birth of neonates. We examined further whether very short periods of ingestion (3h) by the offspring alter the overall P content of juvenile Daphnia. We showed that strong dietary P effects on mothers were not directly transferred to their eggs. Irrespective of the supply of P in the maternal diet, the P content of eggs in different developmental stages and in (unfed) neonates did not differ. This indicates that Daphnia mothers do not reduce the quality (in terms of P) of newly produced offspring after intermittent periods (i.e. several days) of poor nutrition. In contrast, the P content of neonates reflected that of their food after brief periods of feeding, indicating that even temporary exposure to nutrient poor food immediately after birth may strongly affect the elemental composition of neonates. Our results thus support the neonate nutrition hypothesis, which, like differential maternal provisioning, is a possible explanation for the variable elemental quality of young Daphnia.}, language = {en} } @article{BrothersHiltMeyeretal.2013, author = {Brothers, Soren M. and Hilt, Sabine and Meyer, Stephanie and K{\"o}hler, Jan}, title = {Plant community structure determines primary productivity in shallow, eutrophic lakes}, series = {Freshwater biology}, volume = {58}, journal = {Freshwater biology}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/fwb.12207}, pages = {2264 -- 2276}, year = {2013}, abstract = {Regime shifts are commonly associated with the loss of submerged macrophytes in shallow lakes; yet, the effects of this on whole-lake primary productivity remain poorly understood. This study compares the annual gross primary production (GPP) of two shallow, eutrophic lakes with different plant community structures but similar nutrient concentrations. Daily GPP rates were substantially higher in the lake containing submerged macrophytes (58623gCm(-2)year(-1)) than in the lake featuring only phytoplankton and periphyton (40823gCm(-2)year(-1); P<0.0001). Comparing lake-centre diel oxygen curves to compartmental estimates of GPP confirmed that single-site oxygen curves may provide unreliable estimates of whole-lake GPP. The discrepancy between approaches was greatest in the macrophyte-dominated lake during the summer, with a high proportion of GPP occurring in the littoral zone. Our empirical results were used to construct a simple conceptual model relating GPP to nutrient availability for these alternative ecological regimes. This model predicted that lakes featuring submerged macrophytes may commonly support higher rates of GPP than phytoplankton-dominated lakes, but only within a moderate range of nutrient availability (total phosphorus ranging from 30 to 100gL(-1)) and with mean lake depths shallower than 3 or 4m. We conclude that shallow lakes with a submerged macrophyte-epiphyton complex may frequently support a higher annual primary production than comparable lakes that contain only phytoplankton and periphyton. We thus suggest that a regime shift involving the loss of submerged macrophytes may decrease the primary productivity of many lakes, with potential consequences for the entire food webs of these ecosystems.}, language = {en} } @article{SchwarzerHeinkenLuthardtetal.2013, author = {Schwarzer, Christian and Heinken, Thilo and Luthardt, Vera and Joshi, Jasmin Radha}, title = {Latitudinal shifts in species interactions interfere with resistance of southern but not of northern bog-plant communities to experimental climate change}, series = {The journal of ecology}, volume = {101}, journal = {The journal of ecology}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0022-0477}, doi = {10.1111/1365-2745.12158}, pages = {1484 -- 1497}, year = {2013}, abstract = {The persistence of species under changed climatic conditions depends on adaptations and plastic responses to these conditions and on interactions with their local plant community resulting in direct and indirect effects of changed climatic conditions. Populations at species' range margins may be especially crucial in containing a gene pool comprising adaptations to extreme climatic conditions. Many species of northern European bog ecosystems reach their southern lowland range limit in central Europe. In a common-garden experiment, we experimentally assessed the impact of projected climatic changes on five bog-plant species (including peat moss Sphagnum magellanicum) sampled along a latitudinal gradient of 1400km from Scandinavia to the marginal lowland populations in Germany. Populations were cultivated in monocultures and in experimental communities composed of all five species from their local community, and exposed to five combinations of three climate treatments (warming, fluctuating water-tables, fertilization) in a southern common garden. Whereas most monocultures showed a decreasing biomass production from southern to northern origins under southern environmental conditions, in the experimental mixed-species communities, an increasing biomass production towards northern communities was observed together with a shift in interspecific interactions along the latitudinal gradient. While negative dominance effects prevailed in southern communities, higher net biodiversity effects were observed in northern subarctic communities. The combined effects of climate treatments increased biomass production in monocultures of most origins. In communities, however, overall the treatments did not result in significantly changed biomass production. Among individual treatments, water-table fluctuations caused a significant decrease in biomass production, but only in southern communities, indicating higher vulnerability to changed climatic conditions. Here, negative effects of climate treatments on graminoids were not compensated by the slightly increased growth of peat moss that benefited from interspecific interactions only in northern communities.Synthesis. We conclude that shifting interactions within multispecies communities caused pronounced responses to changed climatic conditions in wetland communities of temperate southern marginal, but not of northern subarctic origin. Therefore, future models investigating the impacts of climate change on plant communities should consider geographical variation in species interactions an important factor influencing community responses to changed climatic conditions.}, language = {en} } @article{MartinsHejaziFettkeetal.2013, author = {Martins, Marina Camara Mattos and Hejazi, Mahdi and Fettke, J{\"o}rg and Steup, Martin and Feil, Regina and Krause, Ursula and Arrivault, Stephanie and Vosloh, Daniel and Figueroa, Carlos Maria and Ivakov, Alexander and Yadav, Umesh Prasad and Piques, Maria and Metzner, Daniela and Stitt, Mark and Lunn, John Edward}, title = {Feedback inhibition of starch degradation in arabidopsis leaves mediated by trehalose 6-phosphate}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {163}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.113.226787}, pages = {1142 -- 1163}, year = {2013}, abstract = {Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by beta-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 mu M in the cytosol, 0.2 to 0.5 mu M in the chloroplasts, and 0.05 mu M in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night.}, language = {en} } @article{WinckArvidssonMauricioRianoPachonetal.2013, author = {Winck, Flavia Vischi and Arvidsson, Samuel Janne and Mauricio Riano-Pachon, Diego and Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Urbina Gomez, David Alejandro and Rupprecht, Jens and M{\"u}ller-R{\"o}ber, Bernd}, title = {Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0079909}, pages = {16}, year = {2013}, abstract = {The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.}, language = {en} } @article{TanentzapLeeSchulz2013, author = {Tanentzap, Andrew J. and Lee, William G. and Schulz, Katharina A. C.}, title = {Niches drive peaked and positive relationships between diversity and disturbance in natural ecosystems}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {4}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {11}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES13-00102.1}, pages = {28}, year = {2013}, abstract = {A unified understanding of the relationship between disturbance and biodiversity is needed to predict biotic responses to global change. Recent advances have identified the need to deconstruct traditional models of disturbance into intensity and frequency to reconcile empirical studies that appear to generate contradictory associations between species diversity and disturbance. We integrate results from theoretical simulation modelling, field-based surveys of 5176 vegetation plots from 48 transects across 6 sites, and experimental pot-based manipulations of flooding to identify how disturbance drives species diversity within ephemeral wetlands in South Island, New Zealand. We find empirical, hump-shaped and positive relationships between species diversity and both disturbance intensity and frequency, mirroring patterns from a simulation model in which species differed in their demographic responses to disturbance. More generally, our simulations show that the relationships between diversity and disturbance shift from positive to hump-shaped to negative as species that are favored at low disturbance because of their resistance strategies, defined by low mortality and recruitment, decline within communities relative to resilient species. Resilient species with higher mortality and recruitment rates are instead favored as disturbance intensity and frequency intensify. Our theoretical findings suggest that sites must also have a third group of unique species with intermediate resilience and resistance. Analyses of community composition along our disturbance gradients support this prediction, emphasizing that shifts in community-level resistance and resilience drive empirical associations between diversity and disturbance. Overall, terrestrial plants may be unable to resist intense and frequent flooding, even with specialized traits. Only fast-growing species with high regeneration from seed may respond once flooding subsides and dominate community composition in these situations, especially on nutrient-rich soils. However, different strategies can co-occur at intermediate disturbance, ultimately increasing species richness. As disturbances become more pervasive globally, our results suggest that differences in the niches of species, rather than demographic stochasticity, drive biodiversity patterns. These niche-based processes may especially prevail, without accompanying losses in species richness, where sites are initially dominated by resistant taxa or life history strategies that balance resistance and resilience.}, language = {en} } @article{BrothersHiltAttermeyeretal.2013, author = {Brothers, Soren M. and Hilt, Sabine and Attermeyer, Katrin and Grossart, Hans-Peter and Kosten, Sarian and Lischke, Betty and Mehner, Thomas and Meyer, Nils and Scharnweber, Inga Kristin and K{\"o}hler, Jan}, title = {A regime shift from macrophyte to phytoplankton dominance enhances carbon burial in a shallow, eutrophic lake}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {4}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {11}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES13-00247.1}, pages = {17}, year = {2013}, abstract = {Ecological regime shifts and carbon cycling in aquatic systems have both been subject to increasing attention in recent years, yet the direct connection between these topics has remained poorly understood. A four-fold increase in sedimentation rates was observed within the past 50 years in a shallow eutrophic lake with no surface in-or outflows. This change coincided with an ecological regime shift involving the complete loss of submerged macrophytes, leading to a more turbid, phytoplankton-dominated state. To determine whether the increase in carbon (C) burial resulted from a comprehensive transformation of C cycling pathways in parallel to this regime shift, we compared the annual C balances (mass balance and ecosystem budget) of this turbid lake to a similar nearby lake with submerged macrophytes, a higher transparency, and similar nutrient concentrations. C balances indicated that roughly 80\% of the C input was permanently buried in the turbid lake sediments, compared to 40\% in the clearer macrophyte-dominated lake. This was due to a higher measured C burial efficiency in the turbid lake, which could be explained by lower benthic C mineralization rates. These lower mineralization rates were associated with a decrease in benthic oxygen availability coinciding with the loss of submerged macrophytes. In contrast to previous assumptions that a regime shift to phytoplankton dominance decreases lake heterotrophy by boosting whole-lake primary production, our results suggest that an equivalent net metabolic shift may also result from lower C mineralization rates in a shallow, turbid lake. The widespread occurrence of such shifts may thus fundamentally alter the role of shallow lakes in the global C cycle, away from channeling terrestrial C to the atmosphere and towards burying an increasing amount of C.}, language = {en} } @article{ZhangPaijmansChangetal.2013, author = {Zhang, Hucai and Paijmans, Johanna L. A. and Chang, Fengqin and Wu, Xiaohong and Chen, Guangjie and Lei, Chuzhao and Yang, Xiujuan and Wei, Zhenyi and Bradley, Daniel G. and Orlando, Ludovic and O'Connor, Terry and Hofreiter, Michael}, title = {Morphological and genetic evidence for early Holocene cattle management in northeastern China}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {6}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3755}, pages = {7}, year = {2013}, abstract = {The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.}, language = {en} } @article{DeFrenneRodriguezSanchezCoomesetal.2013, author = {De Frenne, Pieter and Rodriguez-Sanchez, Francisco and Coomes, David Anthony and B{\"a}ten, Lander and Verstr{\"a}ten, Gorik and Vellend, Mark and Bernhardt-R{\"o}mermann, Markus and Brown, Carissa D. and Brunet, J{\"o}rg and Cornelis, Johnny and Decocq, Guillaume M. and Dierschke, Hartmut and Eriksson, Ove and Gilliam, Frank S. and Hedl, Radim and Heinken, Thilo and Hermy, Martin and Hommel, Patrick and Jenkins, Michael A. and Kelly, Daniel L. and Kirby, Keith J. and Mitchell, Fraser J. G. and Naaf, Tobias and Newman, Miles and Peterken, George and Petrik, Petr and Schultz, Jan and Sonnier, Gregory and Van Calster, Hans and Waller, Donald M. and Walther, Gian-Reto and White, Peter S. and Woods, Kerry D. and Wulf, Monika and Graae, Bente Jessen and Verheyen, Kris}, title = {Microclimate moderates plant responses to macroclimate warming}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {46}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1311190110}, pages = {18561 -- 18565}, year = {2013}, abstract = {Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., "thermophilization" of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that "climatic lags" may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of 12-67 y, we document significant thermophilization of ground-layer plant communities. These changes reflect concurrent declines in species adapted to cooler conditions and increases in species adapted to warmer conditions. However, thermophilization, particularly the increase of warm-adapted species, is attenuated in forests whose canopies have become denser, probably reflecting cooler growing-season ground temperatures via increased shading. As standing stocks of trees have increased in many temperate forests in recent decades, local microclimatic effects may commonly be moderating the impacts of macroclimate warming on forest understories. Conversely, increases in harvesting woody biomass-e.g., for bioenergy-may open forest canopies and accelerate thermophilization of temperate forest biodiversity.}, language = {en} } @article{LimFriemelMarumetal.2013, author = {Lim, Sze Chern and Friemel, Martin and Marum, Justine E. and Tucker, Elena J. and Bruno, Damien L. and Riley, Lisa G. and Christodoulou, John and Kirk, Edwin P. and Boneh, Avihu and DeGennaro, Christine M. and Springer, Michael and Mootha, Vamsi K. and Rouault, Tracey A. and Leimk{\"u}hler, Silke and Thorburn, David R. and Compton, Alison G.}, title = {Mutations in LYRM4, encoding ironsulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes}, series = {Human molecular genetics}, volume = {22}, journal = {Human molecular genetics}, number = {22}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0964-6906}, doi = {10.1093/hmg/ddt295}, pages = {4460 -- 4473}, year = {2013}, abstract = {Ironsulfur clusters (ISCs) are important prosthetic groups that define the functions of many proteins. Proteins with ISCs (called ironsulfur or FeS proteins) are present in mitochondria, the cytosol, the endoplasmic reticulum and the nucleus. They participate in various biological pathways including oxidative phosphorylation (OXPHOS), the citric acid cycle, iron homeostasis, heme biosynthesis and DNA repair. Here, we report a homozygous mutation in LYRM4 in two patients with combined OXPHOS deficiency. LYRM4 encodes the ISD11 protein, which forms a complex with, and stabilizes, the sulfur donor NFS1. The homozygous mutation (c.203GT, p.R68L) was identified via massively parallel sequencing of 1000 mitochondrial genes (MitoExome sequencing) in a patient with deficiency of complexes I, II and III in muscle and liver. These three complexes contain ISCs. Sanger sequencing identified the same mutation in his similarly affected cousin, who had a more severe phenotype and died while a neonate. Complex IV was also deficient in her skeletal muscle. Several other FeS proteins were also affected in both patients, including the aconitases and ferrochelatase. Mutant ISD11 only partially complemented for an ISD11 deletion in yeast. Our in vitro studies showed that the l-cysteine desulfurase activity of NFS1 was barely present when co-expressed with mutant ISD11. Our findings are consistent with a defect in the early step of ISC assembly affecting a broad variety of FeS proteins. The differences in biochemical and clinical features between the two patients may relate to limited availability of cysteine in the newborn period and suggest a potential approach to therapy.}, language = {en} } @article{LukoszekMuellerRoeberIgnatova2013, author = {Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya}, title = {Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {587}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {22}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2013.09.033}, pages = {3692 -- 3695}, year = {2013}, abstract = {Up to 15\% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.}, language = {en} } @article{JedrusikBodeStudenckaSmolkaetal.2013, author = {Jedrusik-Bode, Monika and Studencka, Maja and Smolka, Christian and Baumann, Tobias and Schmidt, Henning and Kampf, Jan and Paap, Franziska and Martin, Sophie and Tazi, Jamal and M{\"u}ller, Kristian M. and Kr{\"u}ger, Marcus and Braun, Thomas and Bober, Eva}, title = {The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals}, series = {Journal of cell science}, volume = {126}, journal = {Journal of cell science}, number = {22}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0021-9533}, doi = {10.1242/jcs.130708}, pages = {5166 -- +}, year = {2013}, abstract = {SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress.}, language = {en} } @article{ReschkeNiksWilsonetal.2013, author = {Reschke, Stefan and Niks, Dimitri and Wilson, Heather and Sigfridsson, Kajsa G. V. and Haumann, Michael and Rajagopalan, K. V. and Hine, Russ and Leimk{\"u}hler, Silke}, title = {Effect of exchange of the cysteine molybdenum ligand with selenocysteine on the structure and function of the active site in human sulfite oxidase}, series = {Biochemistry}, volume = {52}, journal = {Biochemistry}, number = {46}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/bi4008512}, pages = {8295 -- 8303}, year = {2013}, abstract = {Sulfite oxidase (SO) is an essential molybdoenzyme for humans, catalyzing the final step in the degradation of sulfur-containing amino acids and lipids, which is the oxidation of sulfite to sulfate. The catalytic site of SO consists of a molybdenum ion bound to the dithiolene sulfurs of one molybdopterin (MPT) molecule, carrying two oxygen ligands, and is further coordinated by the thiol sulfur of a conserved cysteine residue. We have exchanged four non-active site cysteines in the molybdenum cofactor (Moco) binding domain of human SO (SOMD) with serine using site-directed mutagenesis. This facilitated the specific replacement of the active site Cys207 with selenocysteine during protein expression in Escherichia coli. The sulfite oxidizing activity (k(cat)/K-M) of SeSOMD4Ser was increased at least 1.5-fold, and the pH optimum was shifted to a more acidic value compared to those of SOMD4Ser and SOMD4Cys(wt) X-ray absorption spectroscopy revealed a Mow Se bond length of 2.51 A, likely caused by the specific binding of Sec207 to the molybdenum, and otherwise rather similar square-pyramidal S/Se(Cys)(O2MoS2)-S-VI(MPT) site structures in the three constructs. The low-pH form of the Mo(V) electron paramagnetic resonance (EPR) signal of SeSOM4Ser was altered compared to those of SOMD4Ser and SOMD4cy,(,), with g, in particular shifted to a lower magnetic field, due to the Se ligation at the molybdenum. In contrast, the Mo(V) EPR signal of the high-pH form was unchanged. The substantially stronger effect of substituting selenocysteine for cysteine at low pH as compared to high pH is most likely due to the decreased covalency of the Mo Se bond.}, language = {en} } @article{XuWollenbergerQianetal.2013, author = {Xu, Xuan and Wollenberger, Ursula and Qian, Jing and Lettau, Katrin and Jung, Christiane and Liu, Songqin}, title = {Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite}, series = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, volume = {94}, journal = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, number = {47}, publisher = {Elsevier}, address = {Lausanne}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2013.04.005}, pages = {7 -- 12}, year = {2013}, abstract = {Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @article{VanderMeerScottWaightetal.2013, author = {Van der Meer, Q. H. A. and Scott, James M. and Waight, T. E. and Sudo, Masafumi and Schersten, A. and Cooper, Alan F. and Spell, Terry L.}, title = {Magmatism during Gondwana break-up: new geochronological data from Westland, New Zealand}, series = {New Zealand journal of geology and geophysics : an international journal of pacific rim geosciences}, volume = {56}, journal = {New Zealand journal of geology and geophysics : an international journal of pacific rim geosciences}, number = {4}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {0028-8306}, doi = {10.1080/00288306.2013.826699}, pages = {229 -- 242}, year = {2013}, abstract = {Newly determined Late Cretaceous Ar-40/Ar-39 ages on megacrystic kaersutite from four lamprophyre dikes, and a U-Pb zircon age on a trachyte, from central and north Westland (New Zealand) are presented. These ages suggest that the intrusion of mafic dikes (88-86 and 69 Ma) was not necessarily restricted to the previously established narrow age range of 80-92 Ma. The younger lamprophyre and trachyte dikes (c. 68-70 Ma) imply that tensional stresses in the Western Province were either renewed at this time, or that extension and related magmatism continued during opening of the Tasman Sea. Extension-related magmatism in the region not only preceded Tasman seafloor spreading initiation (starting at c. 83 Ma, lasting to c. 53 Ma), but may have sporadically continued for up to 15 Ma after continental break-up.}, language = {en} } @article{NahavandiKetmaierPlathetal.2013, author = {Nahavandi, Nahid and Ketmaier, Valerio and Plath, Martin and Tiedemann, Ralph}, title = {Diversification of Ponto-Caspian aquatic fauna - morphology and molecules retrieve congruent evolutionary relationships in Pontogammarus maeoticus (Amphipoda: Pontogammaridae)}, series = {Molecular phylogenetics and evolution}, volume = {69}, journal = {Molecular phylogenetics and evolution}, number = {3}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2013.05.021}, pages = {1063 -- 1076}, year = {2013}, abstract = {The geological history of the Ponto-Caspian region, with alternating cycles of isolation and reconnection among the three main basins (Black and Azov Seas, and the more distant Caspian Sea) as well as between them and the Mediterranean Sea, profoundly affected the diversification of its aquatic fauna, leading to a high degree of endemism. Two alternative hypotheses on the origin of this amazing biodiversity have been proposed, corresponding to phases of allopatric separation of aquatic fauna among sea basins: a Late Miocene origin (10-6 MYA) vs. a more recent Pleistocene ancestry (<2 MYA). Both hypotheses support a vicariant origin of (1) Black + Azov Sea lineages on the one hand, and (2) Caspian Sea lineages on the other. Here, we present a study on the Ponto-Caspian endemic amphipod Pontogammarus maeoticus. We assessed patterns of divergence based on (a) two mitochondrial and one nuclear gene, and (b) a morphometric analysis of 23 morphological traits in 16 populations from South and West Caspian Sea, South Azov Sea and North-West Black Sea. Genetic data indicate a long and independent evolutionary history, dating back from the late Miocene to early Pleistocene (6.6-1.6 MYA), for an unexpected, major split between (i) a Black Sea clade and (ii) a well-supported clade grouping individuals from the Caspian and Azov Seas. Absence of shared haplotypes argues against either recent or human-mediated exchanges between Caspian and Azov Seas. A mismatch distribution analysis supports more stable population demography in the Caspian than in the Black Sea populations. Morphological divergence largely followed patterns of genetic divergence: our analyses grouped samples according to the basin of origin and corroborated the close phylogenetic affinity between Caspian and Azov Sea lineages. Altogether, our results highlight the necessity of careful (group-specific) evaluation of evolutionary trajectories in marine taxa that should certainly not be inferred from the current geographical proximity of sea basins alone. (C) 2013 Elsevier Inc. All rights reserved.}, language = {en} }