TY - JOUR A1 - Scheunemann, Michael A1 - Brady, Siobhan M. A1 - Nikoloski, Zoran T1 - Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models JF - Scientific reports N2 - Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-26232-8 SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wuster, Wolfgang A1 - Chirio, Laurent A1 - Trape, Jean-Francois A1 - Ineich, Ivan A1 - Jackson, Kate A1 - Greenbaum, Eli A1 - Barron, Cesar A1 - Kusamba, Chifundera A1 - Nagy, Zoltan T. A1 - Storey, Richard A1 - Hall, Cara A1 - Wuster, Catharine E. A1 - Barlow, Axel A1 - Broadley, Donald G. T1 - Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich & Wuster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio & Wuster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively. KW - Integrative taxonomy KW - Africa KW - Naja melanoleuca KW - Naja guineensis sp nov. KW - Naja savannula sp nov. KW - Elapidae KW - systematics Y1 - 2018 U6 - https://doi.org/10.11646/zootaxa.4455.1.3 SN - 1175-5326 SN - 1175-5334 VL - 4455 IS - 1 SP - 68 EP - 98 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Crawford, Michael A1 - Jeltsch, Florian A1 - May, Felix A1 - Grimm, Volker A1 - Schlägel, Ulrike E. T1 - Intraspecific trait variation increases species diversity in a trait-based grassland model JF - Oikos N2 - Intraspecific trait variation (ITV) is thought to play a significant role in community assembly, but the magnitude and direction of its influence are not well understood. Although it may be critical to better explain population persistence, species interactions, and therefore biodiversity patterns, manipulating ITV in experiments is challenging. We therefore incorporated ITV into a trait‐ and individual‐based model of grassland community assembly by adding variation to the plants’ functional traits, which then drive life‐history tradeoffs. Varying the amount of ITV in the simulation, we examine its influence on pairwise‐coexistence and then on the species diversity in communities of different initial sizes. We find that ITV increases the ability of the weakest species to invade most, but that this effect does not scale to the community level, where the primary effect of ITV is to increase the persistence and abundance of the competitively‐average species. Diversity of the initial community is also of critical importance in determining ITV's efficacy; above a threshold of interspecific diversity, ITV does not increase diversity further. For communities below this threshold, ITV mainly helps to increase diversity in those communities that would otherwise be low‐diversity. These findings suggest that ITV actively maintains diversity by helping the species on the margins of persistence, but mostly in habitats of relatively low alpha and beta diversity. KW - community assembly KW - individual-based model KW - intraspecific trait variation Y1 - 2018 U6 - https://doi.org/10.1111/oik.05567 SN - 0030-1299 SN - 1600-0706 VL - 128 IS - 3 SP - 441 EP - 455 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Yan, Wan A1 - Fang, Liang A1 - Nöchel, Ulrich A1 - Gould, Oliver E. C. A1 - Behl, Marc A1 - Kratz, Karl A1 - Lendlein, Andreas T1 - Investigating the roles of crystallizable and glassy switching segments within multiblock copolymer shape-memory materials JF - MRS Advances N2 - The variation of the molecular architecture of multiblock copolymers has enabled the introduction of functional behaviour and the control of key mechanical properties. In the current study, we explore the synergistic relationship of two structural components in a shape-memory material formed of a multiblock copolymer with crystallizable poly(epsilon-caprolactone) and crystallizable polyfoligo(3S-iso-butylmorpholine-2,5-dione) segments (PCL-PIBMD). The thermal and structural properties of PCL-PIBMD films were compared with PCI.-PU and PMMD-PU investigated by means of DSC, SAXS and WARS measurements. The shape-memory properties were quantified by cyclic, thermomechanical tensile tests, where deformation strains up to 900% were applied for programming PCL-PIBMD films at 50 degrees C. Toluene vapor treatment experiments demonstrated that the temporary shape was fixed mainly by glassy PIBMD domains at strains lower than 600% with the PCL contribution to fixation increasing to 42 +/- 2% at programming strains of 900% This study into the shape-memory mechanism of PCL-PIBMD provides insight into the structure function relation in multiblock copolymers with both crystallizable and glassy switching segments. Y1 - 2018 U6 - https://doi.org/10.1557/adv.2018.590 SN - 2059-8521 VL - 3 IS - 63 SP - 3741 EP - 3749 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Burschel, Sabrina A1 - Decovic, Doris Kreuzer A1 - Nuber, Franziska A1 - Stiller, Marie A1 - Hofmann, Maud A1 - Zupok, Arkadiusz A1 - Siemiatkowska, Beata A1 - Gorka, Michal Jakub A1 - Leimkühler, Silke A1 - Friedrich, Thorsten T1 - Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli NADH BT - ubiquinone oxidoreductase (complex I) JF - Molecular microbiology N2 - The NADH:ubiquinone oxidoreductase (respiratory complex I) is the main entry point for electrons into the Escherichia coli aerobic respiratory chain. With its sophisticated setup of 13 different subunits and 10 cofactors, it is anticipated that various chaperones are needed for its proper maturation. However, very little is known about the assembly of E. coli complex I, especially concerning the incorporation of the iron-sulfur clusters. To identify iron-sulfur cluster carrier proteins possibly involved in the process, we generated knockout strains of NfuA, BolA, YajL, Mrp, GrxD and IbaG that have been reported either to be involved in the maturation of mitochondrial complex I or to exert influence on the clusters of bacterial complex. We determined the NADH and succinate oxidase activities of membranes from the mutant strains to monitor the specificity of the individual mutations for complex I. The deletion of NfuA, BolA and Mrp led to a decreased stability and partially disturbed assembly of the complex as determined by sucrose gradient centrifugation and native PAGE. EPR spectroscopy of cytoplasmic membranes revealed that the BolA deletion results in the loss of the binuclear Fe/S cluster N1b. Y1 - 2018 U6 - https://doi.org/10.1111/mmi.14137 SN - 0950-382X SN - 1365-2958 VL - 111 IS - 1 SP - 31 EP - 45 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Hochrein, Lena A1 - Mitchell, Leslie A. A1 - Schulz, Karina A1 - Messerschmidt, Katrin A1 - Müller-Röber, Bernd T1 - L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast JF - Nature Communications N2 - The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a lightcontrolled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light. The extent of recombination depends on induction time and concentration of the chromophore phycocyanobilin (PCB), which can be easily adjusted. The tool presented here provides improved recombination control over the previously reported estradiol-dependent SCRaMbLE induction system, mediating a larger variety of possible recombination events in SCRaMbLE-ing a reporter plasmid. Thereby, L-SCRaMbLE boosts the potential for further customization and provides a facile application for use in the S. cerevisiae genome reengineering project Sc2.0 or in other recombination-based systems. Y1 - 2018 U6 - https://doi.org/10.1038/s41467-017-02208-6 SN - 2041-1723 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Mittler, Udo A1 - Blasius, Bernd A1 - Gaedke, Ursula A1 - Ryabov, Alexey B. T1 - Length-volume relationship of lake phytoplankton JF - Limnology and Oceanography: Methods N2 - The shapes of phytoplankton units (unicellular organisms and colonies) are extremely diverse, and no unique relationship exists between their volume, V, and longest linear dimension, L. However, an approximate scaling between these parameters can be found because the shape variations within each size class are constrained by cell physiology, grazing pressure, and optimality of resource acquisition. To determine this scaling and to test for its seasonal and interannual variation under changing environmental conditions, we performed weighted regression analysis of time-dependent length-volume relations of the phytoplankton community in large deep Lake Constance from 1979 to 1999. We show that despite a large variability in species composition, the V(L) relationship can be approximated as a power law, V similar to L-alpha, with a scaling exponent alpha = 3 for small cells (L < 25 mu m) and alpha = 1.7 if the fitting is performed over the entire length range, including individual cells and colonies. The best description is provided by a transitional power function describing a regime change from a scaling exponent of 3 for small cells to an exponent of 0.4 in the range of large phytoplankton. Testing different weighted fitting approaches we show that remarkably the best prediction of the total community biovolume from measurements of L and cell density is obtained when the regression is weighted with the squares of species abundances. Our approach should also be applicable to other systems and allows converting phytoplankton length distributions (e.g., obtained with automatic monitoring such as flow cytometry) into distributions of biovolume and biovolume-related phytoplankton traits. Y1 - 2018 U6 - https://doi.org/10.1002/lom3.10296 SN - 1541-5856 VL - 17 IS - 1 SP - 58 EP - 68 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Fischer, Stefan A1 - Mayer-Scholl, Anne A1 - Imholt, Christian A1 - Spierling, Nastasja G. A1 - Heuser, Elisa A1 - Schmidt, Sabrina A1 - Reil, Daniela A1 - Rosenfeld, Ulrike A1 - Jacob, Jens A1 - Nöckler, Karsten A1 - Ulrich, Rainer G. T1 - Leptospira genomospecies and sequence type prevalence in small mammal populations in Germany JF - Vector-Borne and Zoonotic Diseases N2 - Leptospirosis is a worldwide emerging infectious disease caused by zoonotic bacteria of the genus Leptospira. Numerous mammals, including domestic and companion animals, can be infected by Leptospira spp., but rodents and other small mammals are considered the main reservoir. The annual number of recorded human leptospirosis cases in Germany (2001-2016) was 25-166. Field fever outbreaks in strawberry pickers, due to infection with Leptospira kirschneri serovar Grippotyphosa, were reported in 2007 and 2014. To identify the most commonly occurring Leptospira genomospecies, sequence types (STs), and their small mammal host specificity, a monitoring study was performed during 2010-2014 in four federal states of Germany. Initial screening of kidney tissues of 3,950 animals by PCR targeting the lipl32 gene revealed 435 rodents of 6 species and 89 shrews of three species positive for leptospiral DNA. PCR-based analyses resulted in the identification of the genomospecies L. kirschneri (62.7%), Leptospira interrogans (28.3%), and Leptospira borgpetersenii (9.0%), which are represented by four, one, and two STs, respectively. The average Leptospira prevalence was highest (approximate to 30%) in common voles (Microtus arvalis) and field voles (Microtus agrestis). Both species were exclusively infected with L. kirschneri. In contrast, in bank voles (Myodes glareolus) and yellow-necked mice (Apodemus flavicollis), DNA of all three genomospecies was detected, and in common shrews (Sorex araneus) DNA of L. kirschneri and L. borgpetersenii was identified. The association between individual infection status and demographic factors varied between species; infection status was always positively correlated to body weight. In conclusion, the study confirmed a broad geographical distribution of Leptospira in small mammals and suggested an important public health relevance of common and field voles as reservoirs of L. kirschneri. Furthermore, the investigations identified seasonal, habitat-related, as well as individual influences on Leptospira prevalence in small mammals that might impact public health. KW - demography KW - Germany KW - habitat KW - Leptospira spp KW - leptospirosis KW - MLST KW - rodent KW - shrew KW - SLST Y1 - 2018 U6 - https://doi.org/10.1089/vbz.2017.2140 SN - 1530-3667 SN - 1557-7759 VL - 18 IS - 4 SP - 188 EP - 199 PB - Liebert CY - New Rochelle ER - TY - JOUR A1 - Hoffmann, Julia A1 - Palme, Rupert A1 - Eccard, Jana T1 - Long-term dim light during nighttime changes activity patterns and space use in experimental small mammal populations JF - Environmental pollution N2 - Artificial light at night (ALAN) is spreading worldwide and thereby is increasingly interfering with natural dark-light cycles. Meanwhile, effects of very low intensities of light pollution on animals have rarely been investigated. We explored the effects of low intensity ALAN over seven months in eight experimental bank vole (Myodes glareolus) populations in large grassland enclosures over winter and early breeding season, using LED garden lamps. initial populations consisted of eight individuals (32 animals per hectare) in enclosures with or without ALAN. We found that bank voles under ALAN experienced changes in daily activity patterns and space use behavior, measured by automated radio telemetry. There were no differences in survival and body mass, measured with live trapping, and none in levels of fecal glucocorticoid metabolites. Voles in the ALAN treatment showed higher activity at night during half moon, and had larger day ranges during new moon. Thus, even low levels of light pollution as experienced in remote areas or by sky glow can lead to changes in animal behavior and could have consequences for species interactions. (C) 2018 Elsevier Ltd. All rights reserved. KW - Myodes glareolus KW - Light pollution KW - Chronic stress KW - Survival success KW - Artificial light KW - LED Y1 - 2018 U6 - https://doi.org/10.1016/j.envpol.2018.03.107 SN - 0269-7491 SN - 1873-6424 VL - 238 SP - 844 EP - 851 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Boch, Steffen A1 - Müller, Jörg A1 - Prati, Daniel A1 - Fischer, Markus T1 - Low-intensity management promotes bryophyte diversity in grasslands JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Bryophytes constitute an important and permanent component of the grassland flora and diversity in Europe. As most bryophyte species are sensitive to habitat change, their diversity is likely to decline following land-use intensification. Most previous studies on bryophyte diversity focused on specific habitats of high bryophyte diversity, such as bogs, montane grasslands, or calcareous dry grasslands. In contrast, mesic grasslands are rarely studied, although they are the most common grassland habitat in Europe. They are secondary vegetation, maintained by agricultural use and thus, are influenced by different forms of land use. We studied bryophyte species richness in three regions in Germany, in 707 plots of 16 m(2) representing different land-use types and environmental conditions. Our study is one of the few to inspect the relationships between bryophyte richness and land use across contrasting regions and using a high number of replicates. Among the managed grasslands, pastures harboured 2.5 times more bryophyte species than meadows and mown pastures. Similarly, bryophyte cover was about twice as high in fallows and pastures than in meadows and mown pastures. Among the pastures, bryophyte species richness was about three times higher in sheep grazed plots than in the ones grazed by cattle or horses. In general, bryophyte species richness and cover was more than 50% lower in fertilized than in unfertilized plots. Moreover, the amount of suitable substrates was linked to bryophyte diversity. Species richness of bryophytes growing on stones increased with stone cover, and the one of bryophytes growing on bark and deadwood increased with larger values of woody plant species and deadwood cover. Our findings highlight the importance of low-intensity land use and high structural heterogeneity for bryophyte conservation. They also caution against an intensification of traditionally managed pastures. In the light of our results, we recommend to maintain low-intensity sheep grazing on sites with low productivity, such as slopes on shallow soils. T2 - Extensive Landnutzung fördert die Moosdiversität im Grünland KW - biodiversity exploratories KW - competition KW - dry and mesic grasslands KW - grazing KW - fertilization KW - land use KW - liverwort KW - meadow KW - moss KW - pasture Y1 - 2018 U6 - https://doi.org/10.14471/2018.38.014 SN - 0722-494X IS - 38 SP - 311 EP - 328 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Scherer, Ulrike A1 - Tiedemann, Ralph A1 - Schlupp, Ingo T1 - Male size, not female preferences influence female reproductive success in a poeciliid fish (Poecilia latipinna) BT - a combined behavioural/genetic approach JF - BMC Research Notes N2 - Objective We investigated the potential role of indirect benefits for female mate preferences in a highly promiscuous species of live-bearing fishes, the sailfin molly Poecilia latipinna using an integrative approach that combines methods from animal behavior, life-history evolution, and genetics. Males of this species solely contribute sperm for reproduction, and consequently females do not receive any direct benefits. Despite this, females typically show clear mate preferences. It has been suggested that females can increase their reproductive success through indirect benefits from choosing males of higher quality. Results Although preferences for large body size have been recorded as an honest signal for genetic quality, this particular study resulted in female preference being unaffected by male body size. Nonetheless, larger males did sire more offspring, but with no effect on offspring quality. This study presents a methodical innovation by combining preference testing with life history measurements—such as the determination of the dry weight of fish embryos—and paternity analyses on single fish embryos. KW - Fitness KW - Life history KW - Mate choice KW - Microsatellite analysis KW - Offspring weight KW - Paternity analysis KW - Sailfin molly KW - Sexual selection Y1 - 2018 U6 - https://doi.org/10.1186/s13104-018-3487-2 SN - 1756-0500 VL - 11 IS - 364 SP - 1 EP - 5 PB - Biomed Central CY - London ER - TY - JOUR A1 - Chen, Pan A1 - Bornhorst, Julia A1 - Aschner, Michael T1 - Manganese metabolism in humans JF - Frontiers in Bioscience-Landmark N2 - Manganese (Mn) is an essential nutrient for intracellular activities; it functions as a cofactor for a variety of enzymes, including arginase, glutamine synthetase (GS), pyruvate carboxylase and Mn superoxide dismutase (Mn-SOD). Through these metalloproteins, Mn plays critically important roles in development, digestion, reproduction, antioxidant defense, energy production, immune response and regulation of neuronal activities. Mn deficiency is rare. In contrast Mn poisoning may be encountered upon overexposure to this metal. Excessive Mn tends to accumulate in the liver, pancreas, bone, kidney and brain, with the latter being the major target of Mn intoxication. Hepatic cirrhosis, polycythemia, hypermanganesemia, dystonia and Parkinsonism-like symptoms have been reported in patients with Mn poisoning. In recent years, Mn has come to the forefront of environmental concerns due to its neurotoxicity. Molecular mechanisms of Mn toxicity include oxidative stress, mitochondrial dysfunction, protein misfolding, endoplasmic reticulum (ER) stress, autophagy dysregulation, apoptosis, and disruption of other metal homeostasis. The mechanisms of Mn homeostasis are not fully understood. Here, we will address recent progress in Mn absorption, distribution and elimination across different tissues, as well as the intracellular regulation of Mn homeostasis in cells. We will conclude with recommendations for future research areas on Mn metabolism. KW - Manganese KW - Metal Metabolism KW - Homeostasis KW - Blood-Brain Barrier KW - Neurotoxicity KW - Transporters KW - Review Y1 - 2018 U6 - https://doi.org/10.2741/4665 SN - 1093-9946 SN - 1093-4715 VL - 23 IS - 9 SP - 1655 EP - 1679 PB - Frontiers in Bioscience INC CY - Irvine ER - TY - JOUR A1 - Koziel, Slawomir A1 - Scheffler, Christiane A1 - Tutkuviene, Janina A1 - Jakimaviciene, Egle Marija A1 - Mumm, Rebekka A1 - Barbieri, Davide A1 - Godina, Elena A1 - El-Shabrawi, Mortada A1 - Elhusseini, Mona A1 - Musalek, Martin A1 - Pruszkowska-Przybylska, Paulina A1 - El Dash, Hanaa H. A1 - Safar, Hebatalla Hassan A1 - Lehmann, Andreas A1 - Swanson, James A1 - Bogin, Barry A1 - Liu, Yuk-Chien A1 - Groth, Detlef A1 - Kirchengast, Sylvia A1 - Siniarska, Anna A1 - Nieczuja-Dwojacka, Joanna A1 - Kralik, Miroslav A1 - Satake, Takashi A1 - Harc, Tomasz A1 - Roelants, Mathieu A1 - Hermanussen, Michael T1 - Meeting Report: Growth and social environment BT - Proceedings of the 25th Aschauer Soiree, held at Krobielowice, Poland, November 18th 2017 JF - Pediatric Endocrinology Reviews N2 - Twenty-two scientists met at Krobielowice, Poland, to discuss the impact of the social environment, spatial proximity, migration, poverty, but also psychological factors such as body perception and satisfaction, and social stressors such as elite sports, and teenage pregnancies, on child and adolescent growth. The data analysis included linear mixed effects models with different random effects, Monte Carlo analyses, and network simulations. The work stressed the importance of the peer group, but also included historic material, some considerations about body proportions, and growth in chronic liver, and congenital heart disease. KW - Body height KW - Social environment KW - Strategic growth adjustment KW - Competitive growth KW - Community effects on growth Y1 - 2018 U6 - https://doi.org/10.17458/per.vol15.2018.ksh.mr.GrowthSocialEnvironment SN - 1565-4753 VL - 15 IS - 4 SP - 319 EP - 329 PB - Medical Media CY - Netanya ER - TY - JOUR A1 - Knoblauch, Christian A1 - Beer, Christian A1 - Liebner, Susanne A1 - Grigoriev, Mikhail N. A1 - Pfeiffer, Eva-Maria T1 - Methane production as key to the greenhouse gas budget of thawing permafrost JF - Nature climate change N2 - Permafrost thaw liberates frozen organic carbon, which is decomposed into carbon dioxide (CO2) and methane (CH4). The release of these greenhouse gases (GHGs) forms a positive feedback to atmospheric CO2 and CH4 concentrations and accelerates climate change(1,2). Current studies report a minor importance of CH4 production in water-saturated (anoxic) permafrost soils(3-6) and a stronger permafrost carbon-climate feedback from drained (oxic) soils(1,7). Here we show through seven-year laboratory incubations that equal amounts of CO2 and CH4 are formed in thawing permafrost under anoxic conditions after stable CH4-producing microbial communities have established. Less permafrost carbon was mineralized under anoxic conditions but more CO2-carbon equivalents (CO2Ce) were formed than under oxic conditions when the higher global warming potential (GWP) of CH4 is taken into account(8). A model of organic carbon decomposition, calibrated with the observed decomposition data, predicts a higher loss of permafrost carbon under oxic conditions (113 +/- 58 g CO2-C kgC(-1) (kgC, kilograms of carbon)) by 2100, but a twice as high production of CO2-Ce (241 +/- 138 g CO2-Ce kgC(-1)) under anoxic conditions. These findings challenge the view of a stronger permafrost carbon-climate feedback from drained soils1,7 and emphasize the importance of CH4 production in thawing permafrost on climate-relevant timescales. Y1 - 2018 U6 - https://doi.org/10.1038/s41558-018-0095-z SN - 1758-678X SN - 1758-6798 VL - 8 IS - 4 SP - 309 EP - 312 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Batista, A. M. M. A1 - Woodhouse, Jason Nicholas A1 - Grossart, Hans-Peter A1 - Giani, A. T1 - Methanogenic archaea associated to Microcystis sp. in field samples and in culture JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities. KW - Cyanobacteria KW - Methanogenic archaea KW - Bacterial community composition KW - Microcystis sp KW - Tropical reservoir Y1 - 2018 U6 - https://doi.org/10.1007/s10750-018-3655-3 SN - 0018-8158 SN - 1573-5117 VL - 831 IS - 1 SP - 163 EP - 172 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Schuurmans, Jasper Merijn A1 - Brinkmann, Bregje W. A1 - Makower, Katharina A1 - Dittmann, Elke A1 - Huisman, Jef A1 - Matthijs, Hans C. P. T1 - Microcystin interferes with defense against high oxidative stress in harmful cyanobacteria JF - Harmful algae N2 - Harmful cyanobacteria producing toxic microcystins are a major concern in water quality management. In recent years, hydrogen peroxide (H2O2) has been successfully applied to suppress cyanobacterial blooms in lakes. Physiological studies, however, indicate that microcystin protects cyanobacteria against oxidative stress, suggesting that H2O2 addition might provide a selective advantage for microcystin-producing (toxic) strains. This study compares the response of a toxic Microcystis strain, its non-toxic mutant, and a naturally non-toxic Microcystis strain to H2O2 addition representative of lake treatments. All three strains initially ceased growth upon H2O2 addition. Contrary to expectation, the non-toxic strain and non-toxic mutant rapidly degraded the added H2O2 and subsequently recovered, whereas the toxic strain did not degrade H2O2 and did not recover. Experimental catalase addition enabled recovery of the toxic strain, demonstrating that rapid H2O2 degradation is indeed essential for cyanobacterial survival. Interestingly, prior to H2O2 addition, gene expression of a thioredoxin and peroxiredoxin was much lower in the toxic strain than in its non-toxic mutant. Thioredoxin and peroxiredoxin are both involved in H2O2 degradation, and microcystin may potentially suppress their activity. These results show that microcystin-producing strains are less prepared for high levels of oxidative stress, and are therefore hit harder by H2O2 addition than non-toxic strains. KW - Cyanobacteria KW - Harmful algal blooms KW - Microcystins KW - Hydrogen peroxide KW - Microarrays KW - Microcystis aeruginosa Y1 - 2018 U6 - https://doi.org/10.1016/j.hal.2018.07.008 SN - 1568-9883 SN - 1878-1470 VL - 78 SP - 47 EP - 55 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Arias-Andres, Maria A1 - Kluemper, Uli A1 - Rojas-Jimenez, Keilor A1 - Grossart, Hans-Peter T1 - Microplastic pollution increases gene exchange in aquatic ecosystems JF - Environmental pollution N2 - Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJKS which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health. KW - Microplastics KW - Aquatic ecosystems KW - Biofilm KW - Horizontal gene transfer KW - Antibiotic resistance Y1 - 2018 U6 - https://doi.org/10.1016/j.envpol.2018.02.058 SN - 0269-7491 SN - 1873-6424 VL - 237 SP - 253 EP - 261 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Arias Andrés, María de Jesús A1 - Kettner, Marie Therese A1 - Miki, Takeshi A1 - Grossart, Hans-Peter T1 - Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog (R) EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities. (C) 2018 Elsevier B.V. All rights reserved. KW - Microplastics KW - Microorganisms KW - Biofilms KW - Total biomass KW - Heterotrophic activity KW - Functional diversity KW - Multi-functionality index Y1 - 2018 U6 - https://doi.org/10.1016/j.scitotenv.2018.04.199 SN - 0048-9697 SN - 1879-1026 VL - 635 SP - 1152 EP - 1159 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Heim, Wieland A1 - Eccard, Jana A1 - Bairlein, Franz T1 - Migration phenology determines niche use of East Asian buntings (Emberizidae) during stopover JF - Current zoology N2 - Stopover niche utilization of birds during migration has not gained much attention so far, since the majority of the studies focuses on breeding or wintering areas. However, stopover sites are crucial for migratory birds. They are often used by a multitude of species, which could lead to increased competition. In this work, we investigated niche use of 8 migratory and closely related Emberiza bunting species at a stopover site in Far East Russia, situated on the poorly studied East Asian fly-way. We used bird ringing data to evaluate morphological similarity as well as niche overlap on the trophic, spatial, and temporal dimension. Bill morphology was used as a proxy for their trophic niche. We were able to prove that a majority of the species occupies well-defined stopover niches on at least one of the dimensions. Niche breadth and niche overlap differ between spring and autumn season with higher overlap found during spring. Morphological differences are mostly related to overall size and wing pointedness. The temporal dimension is most important for segregation among the studied species. Furthermore, all species seem to exhibit a rather strict and consistent phenological pattern. Their occurrence at the study site is highly correlated with their geographic origin and the length of their migration route. We assume that buntings are able to use available resources opportunistically during stopover, while trying to follow a precise schedule in order to avoid competition and to ensure individual fitness. KW - bird migration KW - Emberiza KW - habitat use KW - non-breeding KW - phenology KW - stopover Y1 - 2018 U6 - https://doi.org/10.1093/cz/zoy016 SN - 1674-5507 SN - 2396-9814 VL - 64 IS - 6 SP - 681 EP - 692 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Garcia, Sarahi L. A1 - Buck, Moritz A1 - Hamilton, Joshua J. A1 - Wurzbacher, Christian A1 - Grossart, Hans-Peter A1 - McMahon, Katherine D. A1 - Eiler, Alexander T1 - Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria JF - mSphere N2 - Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members. KW - community KW - interactions KW - metagenomics KW - microbial ecology KW - mixed cultures KW - promiscuous Y1 - 2018 U6 - https://doi.org/10.1128/mSphere.00202-18 SN - 2379-5042 VL - 3 IS - 3 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Kaufmann, Hans Paul A1 - Duffus, Benjamin R. A1 - Mitrova, Biljana A1 - Iobbi-Nivol, Chantal A1 - Teutloff, Christian A1 - Nimtz, Manfred A1 - Jaensch, Lothar A1 - Wollenberger, Ulla A1 - Leimkühler, Silke T1 - Modulating the Molybdenum Coordination Sphere of Escherichia coli Trimethylamie N-Oxide Reductase JF - Biochemistry N2 - The well-studied enterobacterium Escherichia coli present in the human gut can reduce trimethylamine N-oxide (TMAO) to trimethylamine during anaerobic respiration. The TMAO reductase TorA is a monomeric, bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor-containing enzyme that belongs to the dimethyl sulfoxide reductase family of molybdoenzymes. We report on a system for the in vitro reconstitution of TorA with molybdenum cofactors (Moco) from different sources. Higher TMAO reductase activities for TorA were obtained when using Moco sources containing a sulfido ligand at the molybdenum atom. For the first time, we were able to isolate functional bis-MGD from Rhodobacter capsulatus formate dehydrogenase (FDH), which remained intact in its isolated state and after insertion into apo-TorA yielded a highly active enzyme. Combined characterizations of the reconstituted TorA enzymes by electron paramagnetic resonance spectroscopy and direct electrochemistry emphasize that TorA activity can be modified by changes in the Mo coordination sphere. The combination of these results together with studies of amino acid exchanges at the active site led us to propose a novel model for binding of the substrate to the molybdenum atom of TorA. Y1 - 2018 U6 - https://doi.org/10.1021/acs.biochem.7b01108 SN - 0006-2960 VL - 57 IS - 7 SP - 1130 EP - 1143 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Jetzschmann, Katharina J. A1 - Yarman, Aysu A1 - Rustam, L. A1 - Kielb, P. A1 - Urlacher, V. B. A1 - Fischer, A. A1 - Weidinger, I. M. A1 - Wollenberger, Ulla A1 - Scheller, Frieder W. T1 - Molecular LEGO by domain-imprinting of cytochrome P450 BM3 JF - Colloids and surfaces : an international journal devoted to fundamental and applied research on colloid and interfacial phenomena in relation to systems of biological origin ; B, Biointerfaces N2 - Hypothesis: Electrosynthesis of the MIP nano-film after binding of the separated domains or holocytochrome BM3 via an engineered anchor should result in domain-specific cavities in the polymer layer. Experiments: Both the two domains and the holo P450 BM3 have been bound prior polymer deposition via a N-terminal engineered his6-anchor to the electrode surface. Each step of MIP preparation was characterized by cyclic voltammetry of the redox-marker ferricyanide. Rebinding after template removal was evaluated by quantifying the suppression of the diffusive permeability of the signal for ferricyanide and by the NADH-dependent reduction of cytochrome c by the reductase domain (BMR). Findings: The working hypothesis is verified by the discrimination of the two domains by the respective MIPs: The holoenzyme P450 BM3 was ca. 5.5 times more effectively recognized by the film imprinted with the oxidase domain (BMO) as compared to the BMR-MIP or the non-imprinted polymer (NIP). Obviously, a cavity is formed during the imprinting process around the hiss-tag-anchored BMR which cannot accommodate the broader BMO or the P450 BM3. The affinity of the MIP towards P450 BM3 is comparable with that to the monomer in solution. The hiss-tagged P450 BM3 binds (30 percent) stronger which shows the additive effect of the interaction with the MIP and the binding to the electrode. KW - Molecularly imprinted polymers KW - Protein imprinting KW - Electropolymerization KW - Cytochrome P450 Y1 - 2018 U6 - https://doi.org/10.1016/j.colsurfb.2018.01.047 SN - 0927-7765 SN - 1873-4367 VL - 164 SP - 240 EP - 246 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Durgud, Meriem A1 - Gupta, Saurabh A1 - Ivanov, Ivan A1 - Omidbakhshfard, Mohammad Amin A1 - Benina, Maria A1 - Alseekh, Saleh A1 - Staykov, Nikola A1 - Hauenstein, Mareike A1 - Dijkwel, Paul P. A1 - Hortensteiner, Stefan A1 - Toneva, Valentina A1 - Brotman, Yariv A1 - Fernie, Alisdair A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness. Y1 - 2018 U6 - https://doi.org/10.1104/pp.18.00055 SN - 0032-0889 SN - 1532-2548 VL - 177 IS - 3 SP - 1319 EP - 1338 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Tucker, Marlee A. A1 - Boehning-Gaese, Katrin A1 - Fagan, William F. A1 - Fryxell, John M. A1 - Van Moorter, Bram A1 - Alberts, Susan C. A1 - Ali, Abdullahi H. A1 - Allen, Andrew M. A1 - Attias, Nina A1 - Avgar, Tal A1 - Bartlam-Brooks, Hattie A1 - Bayarbaatar, Buuveibaatar A1 - Belant, Jerrold L. A1 - Bertassoni, Alessandra A1 - Beyer, Dean A1 - Bidner, Laura A1 - van Beest, Floris M. A1 - Blake, Stephen A1 - Blaum, Niels A1 - Bracis, Chloe A1 - Brown, Danielle A1 - de Bruyn, P. J. Nico A1 - Cagnacci, Francesca A1 - Calabrese, Justin M. A1 - Camilo-Alves, Constanca A1 - Chamaille-Jammes, Simon A1 - Chiaradia, Andre A1 - Davidson, Sarah C. A1 - Dennis, Todd A1 - DeStefano, Stephen A1 - Diefenbach, Duane A1 - Douglas-Hamilton, Iain A1 - Fennessy, Julian A1 - Fichtel, Claudia A1 - Fiedler, Wolfgang A1 - Fischer, Christina A1 - Fischhoff, Ilya A1 - Fleming, Christen H. A1 - Ford, Adam T. A1 - Fritz, Susanne A. A1 - Gehr, Benedikt A1 - Goheen, Jacob R. A1 - Gurarie, Eliezer A1 - Hebblewhite, Mark A1 - Heurich, Marco A1 - Hewison, A. J. Mark A1 - Hof, Christian A1 - Hurme, Edward A1 - Isbell, Lynne A. A1 - Janssen, Rene A1 - Jeltsch, Florian A1 - Kaczensky, Petra A1 - Kane, Adam A1 - Kappeler, Peter M. A1 - Kauffman, Matthew A1 - Kays, Roland A1 - Kimuyu, Duncan A1 - Koch, Flavia A1 - Kranstauber, Bart A1 - LaPoint, Scott A1 - Leimgruber, Peter A1 - Linnell, John D. C. A1 - Lopez-Lopez, Pascual A1 - Markham, A. Catherine A1 - Mattisson, Jenny A1 - Medici, Emilia Patricia A1 - Mellone, Ugo A1 - Merrill, Evelyn A1 - Mourao, Guilherme de Miranda A1 - Morato, Ronaldo G. A1 - Morellet, Nicolas A1 - Morrison, Thomas A. A1 - Diaz-Munoz, Samuel L. A1 - Mysterud, Atle A1 - Nandintsetseg, Dejid A1 - Nathan, Ran A1 - Niamir, Aidin A1 - Odden, John A1 - Oliveira-Santos, Luiz Gustavo R. A1 - Olson, Kirk A. A1 - Patterson, Bruce D. A1 - de Paula, Rogerio Cunha A1 - Pedrotti, Luca A1 - Reineking, Bjorn A1 - Rimmler, Martin A1 - Rogers, Tracey L. A1 - Rolandsen, Christer Moe A1 - Rosenberry, Christopher S. A1 - Rubenstein, Daniel I. A1 - Safi, Kamran A1 - Said, Sonia A1 - Sapir, Nir A1 - Sawyer, Hall A1 - Schmidt, Niels Martin A1 - Selva, Nuria A1 - Sergiel, Agnieszka A1 - Shiilegdamba, Enkhtuvshin A1 - Silva, Joao Paulo A1 - Singh, Navinder A1 - Solberg, Erling J. A1 - Spiegel, Orr A1 - Strand, Olav A1 - Sundaresan, Siva A1 - Ullmann, Wiebke A1 - Voigt, Ulrich A1 - Wall, Jake A1 - Wattles, David A1 - Wikelski, Martin A1 - Wilmers, Christopher C. A1 - Wilson, John W. A1 - Wittemyer, George A1 - Zieba, Filip A1 - Zwijacz-Kozica, Tomasz A1 - Mueller, Thomas T1 - Moving in the Anthropocene BT - global reductions in terrestrial mammalian movements JF - Science N2 - Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission. Y1 - 2018 U6 - https://doi.org/10.1126/science.aam9712 SN - 0036-8075 SN - 1095-9203 VL - 359 IS - 6374 SP - 466 EP - 469 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Sustr, David A1 - Hlaváček, Antonín A1 - Duschl, Claus A1 - Volodkin, Dmitry T1 - Multi-fractional analysis of molecular diffusion in polymer multilayers by FRAP BT - a new simulation-based approach JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical N2 - Comprehensive analysis of the multifractional molecular diffusion provides a deeper understanding of the diffusion phenomenon in the fields of material science, molecular and cell biology, advanced biomaterials, etc. Fluorescence recovery after photobleaching (FRAP) is commonly employed to probe the molecular diffusion. Despite FRAP being a very popular method, it is not easy to assess multifractional molecular diffusion due to limited possibilities of approaches for analysis. Here we present a novel simulation-optimization-based approach (S-approach) that significantly broadens possibilities of the analysis. In the S-approach, possible fluorescence recovery scenarios are primarily simulated and afterward compared with a real measurement while optimizing parameters of a model until a sufficient match is achieved. This makes it possible to reveal multifractional molecular diffusion. Fluorescent latex particles of different size and fluorescein isothiocyanate in an aqueous medium were utilized as test systems. Finally, the S-approach has been used to evaluate diffusion of cytochrome c loaded into multilayers made of hyaluronan and polylysine. Software for evaluation of multifractional molecular diffusion by S-approach has been developed aiming to offer maximal versatility and user-friendly way for analysis. Y1 - 2017 U6 - https://doi.org/10.1021/acs.jpcb.7b11051 SN - 1520-6106 VL - 122 IS - 3 SP - 1323 EP - 1333 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Thorpe, Roger A1 - Barlow, Axel A1 - Surget-Groba, Yann A1 - Malhotra, Anita T1 - Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles JF - Molecular phylogenetics and evolution N2 - Lesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and comprehensive geographic sampling of most species. The multilocus phylogeny gives the first well-supported reconstruction of the interspecific relationships, and the densely sampled phylogeography reveals a highly dynamic system, driven by overseas dispersal, with several alternative post-dispersal colonisation trajectories. These radiations currently occupy both the outer-older (Eocene to Miocene), and the inner-younger (< 8mybp), Lesser Antillean arcs. The origin of these radiations corresponds with the age of the ancient outer arc. However, the ages of extant species (compatible with the age of other small terrestrial amniotes) are much younger, about the age of the emergence of the younger arc, or less. The difference between the age of the radiation and the age of the extant species suggests substantial species turnover on older arc islands, most likely through competitive replacement. Although extant anoles are extremely speciose, this may represent only a fraction of their biodiversity over time. While paraphyly enables us to infer several recent colonization events, the absence of the younger arc islands and extant species at the earlier and middle stages of the radiation, does not allow the earlier inter-island colonization to be reliably inferred. Reproductive isolation in allopatry takes a very considerable time (in excess of 8my) and sympatry appears to occur only late in the radiation. The resolved multilocus phylogeny, and relative species age, raise difficulties for some earlier hypotheses regarding size evolution, and provide no evidence for within-island speciation. KW - Anolis KW - Multilocus phylogeny KW - Lesser antilles KW - Species age KW - Species turnover KW - Island colonization Y1 - 2018 U6 - https://doi.org/10.1016/j.ympev.2018.06.014 SN - 1055-7903 SN - 1095-9513 VL - 127 SP - 682 EP - 695 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Dey, Pradip A1 - Bergmann, Tobias A1 - Cuellar-Camacho, Jose Luis A1 - Ehrmann, Svenja A1 - Chowdhury, Mohammad Suman A1 - Zhang, Minze A1 - Dahmani, Ismail A1 - Haag, Rainer A1 - Azad, Walid T1 - Multivalent flexible nanogels exhibit broad-spectrum antiviral activity by blocking virus entry JF - ACS nano N2 - The entry process of viruses into host cells is complex and involves stable but transient multivalent interactions with different cell surface receptors. The initial contact of several viruses begins with attachment to heparan sulfate (HS) proteoglycans on the cell surface, which results in a cascade of events that end up with virus entry. The development of antiviral agents based on multivalent interactions to shield virus particles and block initial interactions with cellular receptors has attracted attention in antiviral research. Here, we designed nanogels with different degrees of flexibility based on dendritic polyglycerol sulfate to mimic cellular HS. The designed nanogels are nontoxic and broad-spectrum, can multivalently interact with viral glycoproteins, shield virus surfaces, and efficiently block infection. We also visualized virus-nanogel interactions as well as the uptake of nanogels by the cells through clathrin-mediated endocytosis using confocal microscopy. As many human viruses attach to the cells through HS moieties, we introduce our flexible nanogels as robust inhibitors for these viruses. KW - multivalent KW - herpes simplex virus KW - heparan sulfate KW - nanoparticles KW - click chemistry KW - polyglycerol Y1 - 2018 U6 - https://doi.org/10.1021/acsnano.8b01616 SN - 1936-0851 SN - 1936-086X VL - 12 IS - 7 SP - 6429 EP - 6442 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hu, Chenlin A1 - Ludsin, Stuart A. A1 - Martin, Jay F. A1 - Dittmann, Elke A1 - Lee, Jiyoung T1 - Mycosporine-like amino acids (MAAs)-producing Microcystis in Lake Erie BT - Development of a qPCR assay and insight into its ecology JF - Harmful algae N2 - Mycosporine-like amino acids (MAAs) are UV-absorbing metabolites found in cyanobacteria. While their protective role from UV in Microcystis has been studied in a laboratory setting, a full understanding of the ecology of MAA-producing versus non-MAA-producing Microcystis in natural environments is lacking. This study presents a new tool for quantifying MAA-producing Microcystis and applies it to obtain insight into the dynamics of MAA-producing and non-MAA-producing Microcystis in Lake Erie. This study first developed a sensitive, specific TaqMan real-time PCR assay that targets MAA synthetase gene C (mysC) of Microcystis (quantitative range: 1.7 × 101 to 1.7 × 107 copies/assay). Using this assay, Microcystis was quantified with a MAA-producing genotype (mysC+) in water samples (n = 96) collected during March-November 2013 from 21 Lake Erie sites (undetectable − 8.4 × 106 copies/ml). The mysC+ genotype comprised 0.3–37.8% of the Microcystis population in Lake Erie during the study period. The proportion of the mysC+ genotype during high solar UV irradiation periods (mean = 18.8%) was significantly higher than that during lower UV periods (mean = 9.7%). Among the MAAs, shinorine (major) and porphyra (minor) were detected with HPLC-PDA-MS/MS from the Microcystis isolates and water samples. However, no significant difference in the MAA concentrations existed between higher and lower solar UV periods when the MAA concentrations were normalized with Microcystis mysC abundance. Collectively, this study’s findings suggest that the MAA-producing Microcystis are present in Lake Erie, and they may be ecologically advantageous under high UV conditions, but not to the point that they exclusively predominate over the non-MAA-producers. KW - Shinorine KW - Porphyra KW - UV irradiation KW - Sunscreen KW - Eutrophication KW - Harmful algal bloom Y1 - 2018 U6 - https://doi.org/10.1016/j.hal.2018.05.010 SN - 1568-9883 SN - 1878-1470 VL - 77 SP - 1 EP - 10 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kurze, Susanne A1 - Heinken, Thilo A1 - Fartmann, Thomas T1 - Nitrogen enrichment in host plants increases the mortality of common Lepidoptera species JF - Oecologia N2 - The recent decline of Lepidoptera species strongly correlates with the increasing intensification of agriculture in Western and Central Europe. However, the effects of changed host-plant quality through agricultural fertilization on this insect group remain largely unexplored. For this reason, we tested the response of six common butterfly and moth species to host-plant fertilization using fertilizer quantities usually applied in agriculture. The larvae of the study species Coenonympha pamphilus, Lycaena phlaeas, Lycaena tityrus, Pararge aegeria, Rivula sericealis and Timandra comae were distributed according to a split-brood design to three host-plant treatments comprising one control treatment without fertilization and two fertilization treatments with an input of 150 and 300kgNha(-1)year(-1), respectively. In L.tityrus, we used two additional fertilization treatments with an input of 30 and 90kgNha(-1)year(-1), respectively. Fertilization increased the nitrogen concentration of both host-plant species, Rumex acetosella and Poa pratensis, and decreased the survival of larvae in all six Lepidoptera species by at least one-third, without clear differences between sorrel- and grass-feeding species. The declining survival rate in all species contradicts the well-accepted nitrogen-limitation hypothesis, which predicts a positive response in species performance to dietary nitrogen content. In contrast, this study presents the first evidence that current fertilization quantities in agriculture exceed the physiological tolerance of common Lepidoptera species. Our results suggest that (1) the negative effect of plant fertilization on Lepidoptera has previously been underestimated and (2) that it contributes to the range-wide decline of Lepidoptera. KW - Agricultural fertilization KW - Global change KW - Host-plant quality KW - Nitrogen-limitation hypothesis KW - Rearing experiment Y1 - 2018 U6 - https://doi.org/10.1007/s00442-018-4266-4 SN - 0029-8549 SN - 1432-1939 VL - 188 IS - 4 SP - 1227 EP - 1237 PB - Springer CY - New York ER - TY - JOUR A1 - Scheffler, Christiane A1 - Kruetzfeldt, Louisa-Marie A1 - Dasgupta, Parasmani A1 - Hermanussen, Michael T1 - No association between fat tissue and height in 5019 children and adolescents, measured between 1982 and 2011 in Kolkata/India JF - Journal of biological and clinical anthropology JF - Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Body height has traditionally been looked upon as a mirror of the condition of society, short height being an indicator of poor nutritional status, poor education, and low social status and income. This view has recently been questioned. We aimed to quantify the effects of nutrition, education, sibship size, and household income, factors that are conventionally considered to be related to child growth, on body height of children and adolescents raised under urban Indian conditions. Sample and methods: We re-analyzed several anthropometric measurements and questionnaires with questions on sibship size, fathers’ and mother’s education, and monthly family expenditure, from two cross-sectional growth studies performed in Kolkata, India. The first Kolkata Growth Study (KG1) took place in 1982-1983, with data on 825 Bengali boys aged 7 to 16 years; and the second Kolkata Growth Study (KG2) between 1999 and 2011 with data of 1999 boys aged 7 to 21 years from Bengali Hindu families, and data of 2195 girls obtained between 2005 and 2011. Results: Indian children showed positive insignificant secular trends in height and a significant secular trend in weight and BMI between between 1982 and 2011. Yet, multiple regression analysis failed to detect an association between nutritional status (expressed in terms of skinfold thickness), monthly family expenditure and sibship size with body height of these children. The analysis only revealed an influence of parental education on female, but not on male height. Conclusion: We failed to detect influences of nutrition, sibship size, and monthly family expenditure on body height in a large sample of children and adolescents raised in Kolkata, India, between 1982 and 2011. We found a mild positive association between parental education and girls’ height. The data question current concepts regarding the impact of nutrition, and household and economic factors on growth, but instead underscore the effect of parental education. KW - body height KW - nutrition KW - social growth adjustment Y1 - 2018 U6 - https://doi.org/10.1127/anthranz/2018/0827 SN - 0003-5548 VL - 74 IS - 5 SP - 403 EP - 411 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Ehrlich, Elias A1 - Gaedke, Ursula T1 - Not attackable or not crackable BT - How pre-and post-attack defenses with different competition costs affect prey coexistence and population dynamics JF - Ecology and Evolution N2 - It is well-known that prey species often face trade-offs between defense against predation and competitiveness, enabling predator-mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre-attack (e.g., camouflage)and post-attack defenses (e.g., weaponry) that act at different phases of the predator—prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre-or post-attack defended paying costs either by a higher half-saturation constant for resource uptake or a lower maximum growth rate. We show that post-attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre-attack defenses by interfering with the predator’s functional response: Because the predator spends time handling “noncrackable” prey, the undefended prey is indirectly facilitated. A high half-saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator-induced resource peaks preventing the extinction of the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom-up and top-down control of the prey community. KW - coexistence KW - competition–defense trade‐off KW - defense against predation KW - functional response KW - indirect facilitation KW - predator–prey cycles Y1 - 2018 U6 - https://doi.org/10.1002/ece3.4145 SN - 2045-7758 VL - 8 IS - 13 SP - 6625 EP - 6637 PB - Wiley ER - TY - JOUR A1 - Hilgers, Leon A1 - Hartmann, Stefanie A1 - Hofreiter, Michael A1 - von Rintelen, Thomas T1 - Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation JF - Molecular biology and evolution N2 - The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations. KW - chitin synthase KW - novelty KW - radula KW - RNAseq KW - shell KW - Tylomelania sarasinorum Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy052 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 7 SP - 1638 EP - 1652 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schibalski, Anett A1 - Körner, Katrin A1 - Maier, Martin A1 - Jeltsch, Florian A1 - Schröder, Boris T1 - Novel model coupling approach for resilience analysis of coastal plant communities JF - Ecological applications : a publication of the Ecological Society of America N2 - Resilience is a major research focus covering a wide range of topics from biodiversity conservation to ecosystem (service) management. Model simulations can assess the resilience of, for example, plant species, measured as the return time to conditions prior to a disturbance. This requires process-based models (PBM) that implement relevant processes such as regeneration and reproduction and thus successfully reproduce transient dynamics after disturbances. Such models are often complex and thus limited to either short-term or small-scale applications, whereas many research questions require species predictions across larger spatial and temporal scales. We suggest a framework to couple a PBM and a statistical species distribution model (SDM), which transfers the results of a resilience analysis by the PBM to SDM predictions. The resulting hybrid model combines the advantages of both approaches: the convenient applicability of SDMs and the relevant process detail of PBMs in abrupt environmental change situations. First, we simulate dynamic responses of species communities to a disturbance event with a PBM. We aggregate the response behavior in two resilience metrics: return time and amplitude of the response peak. These metrics are then used to complement long-term SDM projections with dynamic short-term responses to disturbance. To illustrate our framework, we investigate the effect of abrupt short-term groundwater level and salinity changes on coastal vegetation at the German Baltic Sea. We found two example species to be largely resilient, and, consequently, modifications of SDM predictions consisted mostly of smoothing out peaks in the occurrence probability that were not confirmed by the PBM. Discrepancies between SDM- and PBM-predicted species responses were caused by community dynamics simulated in the PBM and absent from the SDM. Although demonstrated with boosted regression trees (SDM) and an existing individual-based model, IBC-grass (PBM), our flexible framework can easily be applied to other PBM and SDM types, as well as other definitions of short-term disturbances or long-term trends of environmental change. Thus, our framework allows accounting for biological feedbacks in the response to short- and long-term environmental changes as a major advancement in predictive vegetation modeling. KW - Baltic Sea KW - hybrid model KW - Lolium perenne KW - model coupling KW - Scirpus maritimus KW - transient dynamics Y1 - 2018 U6 - https://doi.org/10.1002/eap.1758 SN - 1051-0761 SN - 1939-5582 VL - 28 IS - 6 SP - 1640 EP - 1654 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Eccard, Jana A1 - Scheffler, Ingo A1 - Franke, Steffen A1 - Hoffmann, Julia T1 - Off-grid BT - solar powered LED illumination impacts epigeal arthropods JF - Insect conservation and diversity N2 - 1. Advances in LED technology combined with solar, storable energy bring light to places remote from electricity grids. Worldwide more than 1.3 billion of people are living off-grid, often in developing regions of high insect biodiversity. In developed countries, dark refuges for wildlife are threatened by ornamental garden lights. Solar powered LEDs (SPLEDs) are cheaply available, dim, and often used to illuminate foot paths, but little is known on their effects on ground living (epigeal) arthropods. 2. We used off-the-shelf garden lamps with a single ‘white’ LED (colour temperature 7250 K) to experimentally investigate effects on attraction and nocturnal activity of ground beetles (Carabidae). 3. We found two disparate and species-specific effects of SPLEDs. (i) Some nocturnal, phototactic species were not reducing activity under illumination and were strongly attracted to lamps (>20-fold increase in captures compared to dark controls). Such species aggregate in lit areas and SPLEDs may become ecological traps, while the species is drawn from nearby, unlit assemblages. (ii) Other nocturnal species were reducing mobility and activity under illumination without being attracted to light, which may cause fitness reduction in lit areas. 4. Both reactions offer mechanistic explanations on how outdoor illumination can change population densities of specific predatory arthropods, which may have cascading effects on epigeal arthropod assemblages. The technology may thus increase the area of artificial light at night (ALAN) impacting insect biodiversity. 5. Measures are needed to mitigate effects, such as adjustment of light colour temperature and automated switch-offs. KW - Artificial light at night (ALAN) KW - Carabidae KW - illuminance KW - light pollution KW - light spectrum KW - nocturnal epigeal insect KW - phototaxis KW - solar powered light-emitting diode KW - spectral irradiance KW - white light Y1 - 2018 U6 - https://doi.org/10.1111/icad.12303 SN - 1752-458X SN - 1752-4598 VL - 11 IS - 6 SP - 600 EP - 607 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Dunsing, Valentin A1 - Luckner, Madlen A1 - Zuehlke, Boris A1 - Petazzi, Roberto Arturo A1 - Herrmann, Andreas A1 - Chiantia, Salvatore T1 - Optimal fluorescent protein tags for quantifying protein oligomerization in living cells JF - Scientific reports N2 - Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-28858-0 SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Alberti, Federica A1 - Gonzalez, Javier A1 - Paijmans, Johanna L. A. A1 - Basler, Nikolas A1 - Preick, Michaela A1 - Henneberger, Kirstin A1 - Trinks, Alexandra A1 - Rabeder, Gernot A1 - Conard, Nicholas J. A1 - Muenzel, Susanne C. A1 - Joger, Ulrich A1 - Fritsch, Guido A1 - Hildebrandt, Thomas A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Optimized DNA sampling of ancient bones using Computed Tomography scans JF - Molecular ecology resources N2 - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era. KW - ancient DNA KW - computer tomography KW - palaeogenomics KW - paleogenetics KW - petrous bone Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12911 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1196 EP - 1208 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Bizic-Ionescu, Mina A1 - Ionescu, Danny A1 - Grossart, Hans-Peter T1 - Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems JF - Frontiers in microbiology N2 - The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems. KW - particle-associated bacteria KW - microbial communities KW - inter- and intra-species interactions KW - antagonism KW - phage KW - transcriptome Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.02569 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Malinova, Irina A1 - Qasim, Hadeel M. A1 - Brust, Henrike A1 - Fettke, Jörg T1 - Parameters of Starch Granule Genesis in Chloroplasts of Arabidopsis thaliana JF - Frontiers in Plant Science N2 - Starch is the primary storage carbohydrate in most photosynthetic organisms and allows the accumulation of carbon and energy in form of an insoluble and semi-crystalline particle. In the last decades large progress, especially in the model plant Arabidopsis thaliana, was made in understanding the structure and metabolism of starch and its conjunction. The process underlying the initiation of starch granules remains obscure, although this is a fundamental process and seems to be strongly regulated, as in Arabidopsis leaves the starch granule number per chloroplast is fixed with 5-7. Several single, double, and triple mutants were reported in the last years that showed massively alterations in the starch granule number per chloroplast and allowed further insights in this important process. This mini review provides an overview of the current knowledge of processes involved in the initiation and formation of starch granules. We discuss the central role of starch synthase 4 and further proteins for starch genesis and affecting metabolic factors. KW - starch biosynthesis KW - starch granule biogenesis KW - starch synthase KW - plastidial phosphorylase KW - maltooligosaccharides Y1 - 2018 U6 - https://doi.org/10.3389/fpls.2018.00761 SN - 1664-462X VL - 9 SP - 1 EP - 7 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Barlow, Axel A1 - Cahill, James A. A1 - Hartmann, Stefanie A1 - Theunert, Christoph A1 - Xenikoudakis, Georgios A1 - Gonzalez-Fortes, Gloria M. A1 - Paijmans, Johanna L. A. A1 - Rabeder, Gernot A1 - Frischauf, Christine A1 - Garcia-Vazquez, Ana A1 - Murtskhvaladze, Marine A1 - Saarma, Urmas A1 - Anijalg, Peeter A1 - Skrbinsek, Tomaz A1 - Bertorelle, Giorgio A1 - Gasparian, Boris A1 - Bar-Oz, Guy A1 - Pinhasi, Ron A1 - Slatkin, Montgomery A1 - Dalen, Love A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Partial genomic survival of cave bears in living brown bears JF - Nature Ecology & Evolution N2 - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species. Y1 - 2018 U6 - https://doi.org/10.1038/s41559-018-0654-8 SN - 2397-334X VL - 2 IS - 10 SP - 1563 EP - 1570 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Tejos, Ricardo A1 - Rodriguez-Furlan, Cecilia A1 - Adamowski, Maciej A1 - Sauer, Michael A1 - Norambuena, Lorena A1 - Friml, Jiri T1 - PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana JF - Journal of cell science N2 - Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis. KW - PATELLIN KW - Auxin KW - Arabidopsis thaliana KW - Auxin transport KW - Canalization Y1 - 2018 U6 - https://doi.org/10.1242/jcs.204198 SN - 0021-9533 SN - 1477-9137 VL - 131 IS - 2 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Beckmann, Nadine A1 - Kadow, Stephanie A1 - Schumacher, Fabian A1 - Goethert, Joachim R. A1 - Kesper, Stefanie A1 - Draeger, Annette A1 - Schulz-Schaeffer, Walter J. A1 - Wang, Jiang A1 - Becker, Jan U. A1 - Kramer, Melanie A1 - Kuehn, Claudine A1 - Kleuser, Burkhard A1 - Becker, Katrin Anne A1 - Gulbins, Erich A1 - Carpinteiro, Alexander T1 - Pathological manifestations of Farber disease in a new mouse model JF - Biological chemistry N2 - Farber disease (FD) is a rare lysosomal storage disorder resulting from acid ceramidase deficiency and subsequent ceramide accumulation. No treatments are clinically available and affected patients have a severely shortened lifespan. Due to the low incidence, the pathogenesis of FD is still poorly understood. Here, we report a novel acid ceramidase mutant mouse model that enables the study of pathogenic mechanisms of FD and ceramide accumulation. Asah1(tmEx1) mice were generated by deletion of the acid ceramidase signal peptide sequence. The effects on lysosomal targeting and activity of the enzyme were assessed. Ceramide and sphingomyelin levels were quantified by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and disease manifestations in several organ systems were analyzed by histology and biochemistry. We show that deletion of the signal peptide sequence disrupts lysosomal targeting and enzyme activity, resulting in ceramide and sphingomyelin accumulation. The affected mice fail to thrive and die early. Histiocytic infiltrations were observed in many tissues, as well as lung inflammation, liver fibrosis, muscular disease manifestations and mild kidney injury. Our new mouse model mirrors human FD and thus offers further insights into the pathogenesis of this disease. In the future, it may also facilitate the development of urgently needed therapies. KW - acid ceramidase KW - ceramide KW - Farber disease KW - lysosomal storage disorders Y1 - 2018 U6 - https://doi.org/10.1515/hsz-2018-0170 SN - 1431-6730 SN - 1437-4315 VL - 399 IS - 10 SP - 1183 EP - 1202 PB - De Gruyter CY - Berlin ER - TY - JOUR A1 - Wang, Ming A1 - White, Neil A1 - Grimm, Volker A1 - Hofman, Helen A1 - Doley, David A1 - Thorp, Grant A1 - Cribb, Bronwen A1 - Wherritt, Ella A1 - Han, Liqi A1 - Wilkie, John A1 - Hanan, Jim T1 - Pattern-oriented modelling as a novel way to verify and validate functional-structural plant models BT - a demonstration with the annual growth module of avocado JF - Annals of botany N2 - Background and Aims Functional-structural plant (FSP) models have been widely used to understand the complex interactions between plant architecture and underlying developmental mechanisms. However, to obtain evidence that a model captures these mechanisms correctly, a clear distinction must be made between model outputs used for calibration and thus verification, and outputs used for validation. In pattern-oriented modelling (POM), multiple verification patterns are used as filters for rejecting unrealistic model structures and parameter combinations, while a second, independent set of patterns is used for validation. Key Results After calibration, our model simultaneously reproduced multiple observed architectural patterns. The model then successfully predicted, without further calibration, the validation patterns. The model supports the hypothesis that carbon allocation can be modelled as being dependent on current organ biomass and sink strength of each organ type, and also predicted the observed developmental timing of the leaf sink-source transition stage. KW - Pattern-oriented modelling KW - agent-based model KW - individual-based model KW - functional-structural plant model KW - model analysis KW - model verification KW - model validation KW - ODD (Overview, Design concepts, Details) protocol KW - Persea americana KW - plant architecture KW - carbon allocation KW - L-systems Y1 - 2018 U6 - https://doi.org/10.1093/aob/mcx187 SN - 0305-7364 SN - 1095-8290 VL - 121 IS - 5 SP - 941 EP - 959 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Tischew, Sabine A1 - Dierschke, Hartmut A1 - Schwabe, Angelika A1 - Garve, Eckhard A1 - Heinken, Thilo A1 - Holzel, Norbert A1 - Bergmeier, Erwin A1 - Remy, Dominique A1 - Haerdtle, Werner T1 - Pflanzengesellschaft des Jahres 2019: Die Glatthaferwiese T1 - Plant Community of the Year 2019: Oatgras Meadow JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Um Themen des Schutzes von Pflanzengemeinschaften wirksamer in der breiten Öffentlichkeit zu kommunizieren wird der Vorstand der „Floristisch-Soziologischen Arbeitsgemeinschaft (FlorSoz)“ ab 2019 eine „Pflanzengesellschaft des Jahres“ ausrufen. Damit sollen politische und administrative Entscheidungs- und Umsetzungsprozesse zur Erhaltung der Vielfalt von Ökosystemen und Pflanzengesellschaften in Deutschlands gezielt unterstützt werden. Für das Jahr 2019 wurde die Glatthaferwiese ausgewählt. Sie zählt aktuell zu den durch Artenverarmung und Flächenrückgang besonders bedrohten Pflanzengesellschaften Deutschlands. Es sind deshalb dringend Maßnahmen zum Schutz und zur Wiederherstellung notwendig. Dieser Artikel gibt einen kurzen Überblick zur naturschutzfachlichen Bedeutung von Glatthaferwiesen und deren Ökosystemleistungen sowie zur floristisch-soziologischen Erforschung, zu Ursachen ihres Rückgangs und zu geeigneten Gegenmaßnahmen. N2 - Aiming at a better promotion of topics related to the conservation of ecosystems and plant communities, the board of the Floristisch-Soziologische Arbeitsgemeinschaft (FlorSoz)" has launched the initiative to announce a "Plant Community of the Year". Therewith we hope to raise awareness and stimulate civil society and politics in promoting more efficient conservation strategies. For the forthcoming year, we choose the oatgras meadow as Plant Community of the Year 2019. These lowland hay meadows belong to the most threatened plant communities in Germany. Concepts and schemes aiming at the conservation and restoration of lowland hay meadows are urgently needed. This article provides a short overview of the high nature-conservation value of lowland hay meadows and their ecosystem services as well as of the floristic-phytosociological research, reasons for their sharp decline and appropriate countermeasures. Y1 - 2018 U6 - https://doi.org/10.14471/2018.38.011 SN - 0722-494X IS - 38 SP - 287 EP - 295 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - Zhao, Liming A1 - Xia, Yan A1 - Wu, Xiao-Yuan A1 - Schippers, Jos H. M. A1 - Jing, Hai-Chun T1 - Phenotypic analysis and molecular markers of leaf senescence JF - Plant Senescence: Methods and Protocols N2 - The process of leaf senescence consists of the final stage of leaf development. It has evolved as a mechanism to degrade macromolecules and micronutrients and remobilize them to other developing parts of the plant; hence it plays a central role for the survival of plants and crop production. During senescence, a range of physiological, morphological, cellular, and molecular events occur, which are generally referred to as the senescence syndrome that includes several hallmarks such as visible yellowing, loss of chlorophyll and water content, increase of ion leakage and cell death, deformation of chloroplast and cell structure, as well as the upregulation of thousands of so-called senescence-associated genes (SAGs) and downregulation of photosynthesis-associated genes (PAGs). This chapter is devoted to methods characterizing the onset and progression of leaf senescence at the morphological, physiological, cellular, and molecular levels. Leaf senescence normally progresses in an age-dependent manner but is also induced prematurely by a variety of environmental stresses in plants. Focused on the hallmarks of the senescence syndrome, a series of protocols is described to asses quantitatively the senescence process caused by developmental cues or environmental perturbations. We first briefly describe the senescence process, the events associated with the senescence syndrome, and the theories and methods to phenotype senescence. Detailed protocols for monitoring senescence in planta and in vitro, using the whole plant and the detached leaf, respectively, are presented. For convenience, most of the protocols use the model plant species Arabidopsis and rice, but they can be easily extended to other plants. KW - Leaf senescence KW - Visible yellowing KW - Chlorophyll KW - Ion leakage KW - Cell death KW - Senescence-associated genes (SAGs) KW - Arabidopsis KW - Rice Y1 - 2018 SN - 978-1-4939-7672-0 SN - 978-1-4939-7670-6 U6 - https://doi.org/10.1007/978-1-4939-7672-0_3 SN - 1064-3745 SN - 1940-6029 VL - 1744 SP - 35 EP - 48 PB - Humana Press Inc. CY - Totowa ER - TY - JOUR A1 - Horreo, Jose L. A1 - Pelaez, Maria L. A1 - Suarez, Teresa A1 - Breedveld, Merel Cathelijne A1 - Heulin, Benoit A1 - Surget-Groba, Yann A1 - Oksanen, Tuula A. A1 - Fitze, Patrick S. T1 - Phylogeography, evolutionary history and effects of glaciations in a species (Zootoca vivipara) inhabiting multiple biogeographic regions JF - Journal of biogeography N2 - Location Eurasia. Methods We generated the largest molecular dataset to date of Z. vivipara, ran phylogenetic analyses, reconstructed its evolutionary history, determined the location of glacial refuges and reconstructed ancestral biogeographic regions. Results The phylogenetic analyses revealed a complex evolutionary history, driven by expansions and contractions of the distribution due to glacials and interglacials, and the colonization of new biogeographic regions by all lineages of Z. vivipara. Many glacial refugia were detected, most were located close to the southern limit of the Last Glacial Maximum. Two subclades recolonized large areas covered by permafrost during the last glaciation: namely, Western and Northern Europe and North-Eastern Europe and Asia. KW - ancestral area reconstruction KW - ancestral biogeographic region reconstruction KW - biogeography KW - glacial refuges KW - last glacial maxima KW - molecular diversity KW - phylogeny KW - post-glacial recolonization Y1 - 2018 U6 - https://doi.org/10.1111/jbi.13349 SN - 0305-0270 SN - 1365-2699 VL - 45 IS - 7 SP - 1616 EP - 1627 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Lämke, Jörn. S. A1 - Unsicker, Sybille Barbara T1 - Phytochemical variation in treetops BT - causes and consequences for tree-insect herbivore interactions JF - Oecologia N2 - The interaction of plants and their herbivorous opponents has shaped the evolution of an intricate network of defences and counter-defences for millions of years. The result is an astounding diversity of phytochemicals and plant strategies to fight and survive. Trees are specifically challenged to resist the plethora of abiotic and biotic stresses due to their dimension and longevity. Here, we review the recent literature on the consequences of phytochemical variation in trees on insect-tree-herbivore interactions. We discuss the importance of genotypic and phenotypic variation in tree defence against insects and suggest some molecular mechanisms that might bring about phytochemical diversity in crowns of individual trees. KW - Chromatin-based mechanisms KW - Genotypic variation KW - Insect herbivore KW - Phenotypic plasticity KW - Tree defence Y1 - 2018 U6 - https://doi.org/10.1007/s00442-018-4087-5 SN - 0029-8549 SN - 1432-1939 VL - 187 IS - 2 SP - 377 EP - 388 PB - Springer CY - New York ER - TY - JOUR A1 - Möser, Christin A1 - Lorenz, Jessica S. A1 - Sajfutdinow, Martin A1 - Smith, David M. T1 - Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence JF - International journal of molecular sciences N2 - DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways. KW - DNA nanostructure KW - ephrin KW - EphA2 KW - SWL KW - PC-3 cells KW - multivalence Y1 - 2018 U6 - https://doi.org/10.3390/ijms19113482 SN - 1422-0067 VL - 19 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Lukan, Tjaša A1 - Machens, Fabian A1 - Coll, Anna A1 - Baebler, Špela A1 - Messerschmidt, Katrin A1 - Gruden, Kristina T1 - Plant X-tender BT - an extension of the AssemblX system for the assembly and expression of multigene constructs in plants JF - PLOS ONE N2 - Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0190526 SN - 1932-6203 VL - 13 IS - 1 PB - Public Library of Science CY - San Fransisco ER - TY - JOUR A1 - Wen, Xi A1 - Unger, Viktoria A1 - Jurasinski, Gerald A1 - Koebsch, Franziska A1 - Horn, Fabian A1 - Rehder, Gregor A1 - Sachs, Torsten A1 - Zak, Dominik A1 - Lischeid, Gunnar A1 - Knorr, Klaus-Holger A1 - Boettcher, Michael E. A1 - Winkel, Matthias A1 - Bodelier, Paul L. E. A1 - Liebner, Susanne T1 - Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions JF - Biogeosciences N2 - The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm(-1), respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re) establishment of methanogens and slow (re) establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-6519-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 21 SP - 6519 EP - 6536 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Stoessel, Daniel A1 - Schulte, Claudia A1 - dos Santos, Marcia C. Teixeira A1 - Scheller, Dieter A1 - Rebollo-Mesa, Irene A1 - Deuschle, Christian A1 - Walther, Dirk A1 - Schauer, Nicolas A1 - Berg, Daniela A1 - da Costa, Andre Nogueira A1 - Maetzler, Walter T1 - Promising Metabolite Profiles in the Plasma and CSF of Early Clinical JF - Frontiers in Aging Neuroscience N2 - Parkinson's disease (PD) shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF). Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (<= 1.5 kDa) in the plasma and CSF from early PD patients (disease duration 0-4 years; n = 80 and 40, respectively), and sex-and age-matched controls (n = 76 and 38, respectively). We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. The semetabolites differentiated the test set with an AUC of 0.8 (plasma) and 0.9 (CSF). Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD KW - biomarker KW - untargeted metabolomics KW - neurodegeneration KW - plasma KW - CSF KW - machinelearning Y1 - 2018 U6 - https://doi.org/10.3389/fnagi.2018.00051 SN - 1663-4365 VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER -