TY - JOUR A1 - Peng, Lei A1 - Utesch, Tillmann A1 - Yarman, Aysu A1 - Jeoung, Jae-Hun A1 - Steinborn, Silke A1 - Dobbek, Holger A1 - Mroginski, Maria Andrea A1 - Tanne, Johannes A1 - Wollenberger, Ursula A1 - Scheller, Frieder W. T1 - Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein JF - Chemistry - a European journal N2 - Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant k(s) values between 0.93 and 2.86 s(-1) and apparent formal potentials E-app(0)' between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH. KW - electrochemistry KW - electron transfer KW - heme proteins KW - molecular modeling KW - monolayers Y1 - 2015 U6 - https://doi.org/10.1002/chem.201405932 SN - 0947-6539 SN - 1521-3765 VL - 21 IS - 20 SP - 7596 EP - 7602 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yokoyama, Kenichi A1 - Leimkühler, Silke T1 - The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria JF - Biochimica et biophysica acta : Molecular cell research N2 - The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. (C) 2014 Elsevier B.V. All rights reserved. KW - Molybdenum-iron-iron-sulfur cluster KW - Molybdenum cofactor KW - tRNA KW - Sulfur transfer KW - L-Cysteine desulfurase Y1 - 2015 U6 - https://doi.org/10.1016/j.bbamcr.2014.09.021 SN - 0167-4889 SN - 0006-3002 VL - 1853 IS - 6 SP - 1335 EP - 1349 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kanzleiter, Timo A1 - Jaehnert, Markus A1 - Schulze, Gunnar A1 - Selbig, Joachim A1 - Hallahan, Nicole A1 - Schwenk, Robert Wolfgang A1 - Schürmann, Annette T1 - Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice JF - American journal of physiology : Endocrinology and metabolism N2 - The adaptive response of skeletal muscle to exercise training is tightly controlled and therefore requires transcriptional regulation. DNA methylation is an epigenetic mechanism known to modulate gene expression, but its contribution to exercise-induced adaptations in skeletal muscle is not well studied. Here, we describe a genome-wide analysis of DNA methylation in muscle of trained mice (n = 3). Compared with sedentary controls, 2,762 genes exhibited differentially methylated CpGs (P < 0.05, meth diff >5%, coverage > 10) in their putative promoter regions. Alignment with gene expression data (n = 6) revealed 200 genes with a negative correlation between methylation and expression changes in response to exercise training. The majority of these genes were related to muscle growth and differentiation, and a minor fraction involved in metabolic regulation. Among the candidates were genes that regulate the expression of myogenic regulatory factors (Plexin A2) as well as genes that participate in muscle hypertrophy (Igfbp4) and motor neuron innervation (Dok7). Interestingly, a transcription factor binding site enrichment study discovered significantly enriched occurrence of CpG methylation in the binding sites of the myogenic regulatory factors MyoD and myogenin. These findings suggest that DNA methylation is involved in the regulation of muscle adaptation to regular exercise training. KW - DNA methylation KW - regular exercise training KW - muscle development Y1 - 2015 U6 - https://doi.org/10.1152/ajpendo.00289.2014 SN - 0193-1849 SN - 1522-1555 VL - 308 IS - 10 SP - E912 EP - E920 PB - American Chemical Society CY - Bethesda ER - TY - JOUR A1 - Jetzschmann, Katharina J. A1 - Jagerszki, Gyula A1 - Dechtrirat, Decha A1 - Yarman, Aysu A1 - Gajovic-Eichelmann, Nenad A1 - Gilsing, Hans-Detlev A1 - Schulz, Burkhard A1 - Gyurcsanyi, Robert E. A1 - Scheller, Frieder W. T1 - Vectorially Imprinted Hybrid Nanofilm for Acetylcholinesterase Recognition JF - Advanced functional materials N2 - Effective recognition of enzymatically active tetrameric acetylcholinesterase (AChE) is accomplished by a hybrid nanofilm composed of a propidium-terminated self-assembled monolayer (Prop-SAM) which binds AChE via its peripheral anionic site (PAS) and an ultrathin electrosynthesized molecularly imprinted polymer (MIP) cover layer of a novel carboxylate-modified derivative of 3,4-propylenedioxythiophene. The rebinding of the AChE to the MIP/Prop-SAM nanofilm covered electrode is detected by measuring in situ the enzymatic activity. The oxidative current of the released thiocholine is dependent on the AChE concentration from approximate to 0.04 x 10(-6) to 0.4 x 10(-6)m. An imprinting factor of 9.9 is obtained for the hybrid MIP, which is among the best values reported for protein imprinting. The dissociation constant characterizing the strength of the MIP-AChE binding is 4.2 x 10(-7)m indicating the dominant role of the PAS-Prop-SAM interaction, while the benefit of the MIP nanofilm covering the Prop-SAM layer is the effective suppression of the cross-reactivity toward competing proteins as compared with the Prop-SAM. The threefold selectivity gain provided by i) the shape-specific MIP filter, ii) the propidium-SAM, iii) signal generation only by the AChE bound to the nanofilm shows promise for assessing AChE activity levels in cerebrospinal fluid. KW - acetylcholinesterase KW - biomimetic sensors KW - molecularly imprinted electropolymers KW - peripheral anionic site KW - propidium Y1 - 2015 U6 - https://doi.org/10.1002/adfm.201501900 SN - 1616-301X SN - 1616-3028 VL - 25 IS - 32 SP - 5178 EP - 5183 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hartmann, Tobias A1 - Schwanhold, Nadine A1 - Leimkühler, Silke T1 - Assembly and catalysis of molybdenum or tungsten-containing formate dehydrogenases from bacteria JF - Biochimica et biophysica acta : Proteins and proteomics N2 - The global carbon cycle depends on the biological transformations of C-1 compounds, which include the reductive incorporation of CO2 into organic molecules (e.g. in photosynthesis and other autotrophic pathways), in addition to the production of CO2 from formate, a reaction that is catalyzed by formate dehydrogenases (FDHs). FDHs catalyze, in general, the oxidation of formate to CO2 and H+. However, selected enzymes were identified to act as CO2 reductases, which are able to reduce CO2 to formate under physiological conditions. This reaction is of interest for the generation of formate as a convenient storage form of H-2 for future applications. Cofactor-containing FDHs are found in anaerobic bacteria and archaea, in addition to facultative anaerobic or aerobic bacteria. These enzymes are highly diverse and employ different cofactors such as the molybdenum cofactor (Moco), FeS clusters and flavins, or cytochromes. Some enzymes include tungsten (W) in place of molybdenum (Mo) at the active site. For catalytic activity, a selenocysteine (SeCys) or cysteine (Cys) ligand at the Mo atom in the active site is essential for the reaction. This review will focus on the characterization of Mo- and W-containing FDHs from bacteria, their active site structure, subunit compositions and its proposed catalytic mechanism. We will give an overview on the different mechanisms of substrate conversion available so far, in addition to providing an outlook on bio-applications of FDHs. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. (C) 2014 Elsevier B.V. All rights reserved. KW - Molybdenum cofactor KW - L-Cysteine desulfurase KW - Formate dehydrogenase KW - Chaperone KW - Bis-MGD Y1 - 2015 U6 - https://doi.org/10.1016/j.bbapap.2014.12.006 SN - 1570-9639 SN - 0006-3002 VL - 1854 IS - 9 SP - 1090 EP - 1100 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Cornetti, Luca A1 - Valente, Luis M. A1 - Dunning, Luke T. A1 - Quan, Xueping A1 - Black, Richard A. A1 - Hebert, Olivier A1 - Savolainen, Vincent T1 - The Genome of the "Great Speciator" Provides Insights into Bird Diversification JF - Genome biology and evolution N2 - Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. KW - genome evolution KW - positive selection KW - gene duplication KW - phylogenomics KW - demography KW - morphological divergence Y1 - 2015 U6 - https://doi.org/10.1093/gbe/evv168 SN - 1759-6653 VL - 7 IS - 9 SP - 2680 EP - 2691 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Zeng, Ting A1 - Leimkühler, Silke A1 - Koetz, Joachim A1 - Wollenberger, Ursula T1 - Effective Electrochemistry of Human Sulfite Oxidase Immobilized on Quantum-Dots-Modified Indium Tin Oxide Electrode JF - ACS applied materials & interfaces N2 - The bioelectrocatalytic sulfite oxidation by human sulfite oxidase (hSO) on indium tin oxide (ITO) is reported, which is facilitated by functionalizing of the electrode surface with polyethylenimine (PEI)-entrapped CdS nanoparticles and enzyme. hSO was assembled onto the electrode with a high surface loading of electroactive enzyme. In the presence of sulfite but without additional mediators, a high bioelectrocatalytic current was generated. Reference experiments with only PEI showed direct electron transfer and catalytic activity of hSO, but these were less pronounced. The application of the polyelectrolyte-entrapped quantum dots (QDs) on ITO electrodes provides a compatible surface for enzyme binding with promotion of electron transfer. Variations of the buffer solution conditions, e.g., ionic strength, pH, viscosity, and the effect of oxygen, were studied in order to understand intramolecular and heterogeneous electron transfer from hSO to the electrode. The results are consistent with a model derived for the enzyme by using flash photolysis in solution and spectroelectrochemistry and molecular dynamic simulations of hSO on monolayer-modified gold electrodes. Moreover, for the first time a photoelectrochemical electrode involving immobilized hSO is demonstrated where photoexcitation of the CdS/hSO-modified electrode lead to an enhanced generation of bioelectrocatalytic currents upon sulfite addition. Oxidation starts already at the redox potential of the electron transfer domain of hSO and is greatly increased by application of a small overpotential to the CdS/hSO-modified ITO. KW - human sulfite oxidase KW - direct electrochemistry KW - bioelectrocatalysis KW - photocurrent KW - CdS quantum dots Y1 - 2015 U6 - https://doi.org/10.1021/acsami.5b06665 SN - 1944-8244 VL - 7 IS - 38 SP - 21487 EP - 21494 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hahn, Aaron A1 - Engelhard, Christopher A1 - Reschke, Stefan A1 - Teutloff, Christian A1 - Bittl, Robert A1 - Leimkühler, Silke A1 - Risse, Thomas T1 - Structural Insights into the Incorporation of the Mo Cofactor into Sulfite Oxidase from Site-Directed Spin Labeling JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - Mononuclear molybdoenzymes catalyze a broad range of redox reactions and are highly conserved in all kingdoms of life. This study addresses the question of how the Mo cofactor (Moco) is incorporated into the apo form of human sulfite oxidase (hSO) by using site-directed spin labeling to determine intramolecular distances in the nanometer range. Comparative measurements of the holo and apo forms of hSO enabled the localization of the corresponding structural changes, which are localized to a short loop (residues 263-273) of the Moco-containing domain. A flap-like movement of the loop provides access to the Moco binding-pocket in the apo form of the protein and explains the earlier studies on the in vitro reconstitution of apo-hSO with Moco. Remarkably, the loop motif can be found in a variety of structurally similar molybdoenzymes among various organisms, thus suggesting a common mechanism of Moco incorporation. KW - biocatalysis KW - cofactors KW - enzymes KW - EPR spectroscopy KW - protein structures Y1 - 2015 U6 - https://doi.org/10.1002/anie.201504772 SN - 1433-7851 SN - 1521-3773 VL - 54 IS - 40 SP - 11865 EP - 11869 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Riedelsberger, Janin A1 - Dreyer, Ingo A1 - Gonzalez, Wendy T1 - Outward Rectification of Voltage-Gated K+ Channels Evolved at Least Twice in Life History JF - PLoS one N2 - Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories-hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0137600 SN - 1932-6203 VL - 10 IS - 9 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Mazumder, Mostafizur A1 - Brechun, Katherine E. A1 - Kim, Yongjoo B. A1 - Hoffmann, Stefan A. A1 - Chen, Yih Yang A1 - Keiski, Carrie-Lynn A1 - Arndt, Katja Maren A1 - McMillen, David R. A1 - Woolley, G. Andrew T1 - An Escherichia coli system for evolving improved light-controlled DNA-binding proteins JF - Protein engineering design & selection N2 - Light-switchable proteins offer numerous opportunities as tools for manipulating biological systems with exceptional degrees of spatiotemporal control. Most designed light-switchable proteins currently in use have not been optimised using the randomisation and selection/screening approaches that are widely used in other areas of protein engineering. Here we report an approach for screening light-switchable DNA-binding proteins that relies on light-dependent repression of the transcription of a fluorescent reporter. We demonstrate that the method can be used to recover a known light-switchable DNA-binding protein from a random library. KW - directed evolution KW - fluorescent reporter KW - optogenetics Y1 - 2015 U6 - https://doi.org/10.1093/protein/gzv033 SN - 1741-0126 SN - 1741-0134 VL - 28 IS - 9 SP - 293 EP - 302 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Campbell, Kevin L. A1 - Hofreiter, Michael T1 - Resurrecting phenotypes from ancient DNA sequences: promises and perspectives JF - Canadian journal of zoology = Revue canadienne de zoologie N2 - Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller's sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these "living" processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology. KW - paleophysiology KW - ancient DNA KW - extinct species KW - adaptation KW - protein structure Y1 - 2015 U6 - https://doi.org/10.1139/cjz-2014-0337 SN - 0008-4301 SN - 1480-3283 VL - 93 IS - 9 SP - 701 EP - 710 PB - NRC Research Press CY - Ottawa ER - TY - JOUR A1 - Albert, Aurelie A1 - Auffret, Alistair G. A1 - Cosyns, Eric A1 - Cousins, Sara A. O. A1 - Eichberg, Carsten A1 - Eycott, Amy E. A1 - Heinken, Thilo A1 - Hoffmann, Maurice A1 - Jaroszewicz, Bogdan A1 - Malo, Juan E. A1 - Marell, Anders A1 - Mouissie, Maarten A1 - Pakeman, Robin J. A1 - Picard, Melanie A1 - Plue, Jan A1 - Poschlod, Peter A1 - Provoost, Sam A1 - Schulze, Kiowa Alraune A1 - Baltzinger, Christophe T1 - Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis JF - Oikos N2 - Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter - which differentially affects individuals according to their characteristics and shapes species assemblages - and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal by ungulates in fragmented landscapes, comparing eight plant traits and two habitat indicators between dispersed and non-dispersed plants. We found that ungulates dispersed at least 44% of the available plant species. Moreover, some plant traits and habitat indicators increased the likelihood for plant of being dispersed. Persistent or nitrophilous plant species from open habitats or bearing dry or elongated diaspores were more likely to be dispersed by ungulates, whatever the dispersal mechanism. In addition, endozoochory was more likely for diaspores bearing elongated appendages whereas epizoochory was more likely for diaspores released relatively high in vegetation. Hoof-epizoochory was more likely for light diaspores without hooked appendages. Fur-epizoochory was more likely for diaspores with appendages, particularly elongated or hooked ones. We thus observed a gradient of filtering effect among the three dispersal mechanisms. Endozoochory had an effect of rather weak intensity (impacting six plant characteristics with variations between ungulate-dispersed and non-dispersed plant species mostly below 25%), whereas hoof-epizoochory had a stronger effect (eight characteristics included five ones with above 75% variation), and fur-epizoochory an even stronger one (nine characteristics included six ones with above 75% variation). Our results demonstrate that seed dispersal by ungulates is an ecological filter whose intensity varies according to the dispersal mechanism considered. Ungulates can thus play a key role in plant community dynamics and have implications for plant spatial distribution patterns at multiple scales. Y1 - 2015 U6 - https://doi.org/10.1111/oik.02512 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 9 SP - 1109 EP - 1120 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Heinze, Johannes A1 - Werner, Tony A1 - Weber, Ewald A1 - Rillig, Matthias C. A1 - Joshi, Jasmin Radha T1 - Soil biota effects on local abundances of three grass species along a land-use gradient JF - Oecologia N2 - Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands. KW - Biodiversity KW - Grassland KW - Land-use intensity KW - Community composition KW - Plant-soil feedback Y1 - 2015 U6 - https://doi.org/10.1007/s00442-015-3336-0 SN - 0029-8549 SN - 1432-1939 VL - 179 IS - 1 SP - 249 EP - 259 PB - Springer CY - New York ER - TY - JOUR A1 - Bernhardt-Römermann, Markus A1 - Baeten, Lander A1 - Craven, Dylan A1 - De Frenne, Pieter A1 - Hedl, Radim A1 - Lenoir, Jonathan A1 - Bert, Didier A1 - Brunet, Jorg A1 - Chudomelova, Marketa A1 - Decocq, Guillaume A1 - Dierschke, Hartmut A1 - Dirnboeck, Thomas A1 - Dörfler, Inken A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Hommel, Patrick A1 - Jaroszewicz, Bogdan A1 - Keczynski, Andrzej A1 - Kelly, Daniel L. A1 - Kirby, Keith J. A1 - Kopecky, Martin A1 - Macek, Martin A1 - Malis, Frantisek A1 - Mirtl, Michael A1 - Mitchell, Fraser J. G. A1 - Naaf, Tobias A1 - Newman, Miles A1 - Peterken, George A1 - Petrik, Petr A1 - Schmidt, Wolfgang A1 - Standovar, Tibor A1 - Toth, Zoltan A1 - Van Calster, Hans A1 - Verstraeten, Gorik A1 - Vladovic, Jozef A1 - Vild, Ondrej A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Drivers of temporal changes in temperate forest plant diversity vary across spatial scales JF - Global change biology N2 - Global biodiversity is affected by numerous environmental drivers. Yet, the extent to which global environmental changes contribute to changes in local diversity is poorly understood. We investigated biodiversity changes in a meta-analysis of 39 resurvey studies in European temperate forests (3988 vegetation records in total, 17-75years between the two surveys) by assessing the importance of (i) coarse-resolution (i.e., among sites) vs. fine-resolution (i.e., within sites) environmental differences and (ii) changing environmental conditions between surveys. Our results clarify the mechanisms underlying the direction and magnitude of local-scale biodiversity changes. While not detecting any net local diversity loss, we observed considerable among-site variation, partly explained by temporal changes in light availability (a local driver) and density of large herbivores (a regional driver). Furthermore, strong evidence was found that presurvey levels of nitrogen deposition determined subsequent diversity changes. We conclude that models forecasting future biodiversity changes should consider coarse-resolution environmental changes, account for differences in baseline environmental conditions and for local changes in fine-resolution environmental conditions. KW - atmospheric nitrogen deposition KW - evenness KW - forestREplot KW - forest management KW - game browsing KW - Shannon diversity KW - spatiotemporal resurvey data KW - species richness Y1 - 2015 U6 - https://doi.org/10.1111/gcb.12993 SN - 1354-1013 SN - 1365-2486 VL - 21 IS - 10 SP - 3726 EP - 3737 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Dittmann-Thünemann, Elke A1 - Gugger, Muriel A1 - Sivonen, Kaarina A1 - Fewer, David P. T1 - Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria JF - Trends in microbiology N2 - Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms. Y1 - 2015 U6 - https://doi.org/10.1016/j.tim.2015.07.008 SN - 0966-842X SN - 1878-4380 VL - 23 IS - 10 SP - 642 EP - 652 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Sonnemann, Ilja A1 - Pfestorf, Hans A1 - Jeltsch, Florian A1 - Wurst, Susanne T1 - Community-Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance JF - PLoS one N2 - Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive-and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root herbivores with large, fast growing plants may counteract dominance of those species, thus promoting plant diversity. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0141148 SN - 1932-6203 VL - 10 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Li, Chenhong A1 - Corrigan, Shannon A1 - Yang, Lei A1 - Straube, Nicolas A1 - Harris, Mark A1 - Hofreiter, Michael A1 - White, William T. A1 - Naylor, Gavin J. P. T1 - DNA capture reveals transoceanic gene flow in endangered river sharks JF - Proceedings of the National Academy of Sciences of the United States of America N2 - For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks. KW - freshwater sharks KW - DNA KW - museum specimens Y1 - 2015 U6 - https://doi.org/10.1073/pnas.1508735112 SN - 0027-8424 VL - 112 IS - 43 SP - 13302 EP - 13307 PB - National Acad. of Sciences CY - Washington ER - TY - INPR A1 - Kehr, Jan-Christoph A1 - Dittmann-Thünemann, Elke T1 - Protective tunicate endosymbiont with extreme genome reduction T2 - Environmental microbiology Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12941 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 10 SP - 3430 EP - 3432 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Prokopovic, Vladimir Z. A1 - Duschl, Claus A1 - Volodkin, Dmitry T1 - Hyaluronic Acid/Poly-l-Lysine Multilayers as Reservoirs for Storage and Release of Small Charged Molecules JF - Macromolecular bioscience N2 - Polyelectrolyte multilayer films are nowadays very attractive for bioapplications due to their tunable properties and ability to control cellular response. Here we demonstrate that multilayers made of hyaluronic acid and poly-l-lysine act as high-capacity reservoirs for small charged molecules. Strong accumulation within the film is explained by electrostatically driven binding to free charges of polyelectrolytes. Binding and release mechanisms are discussed based on charge balance and polymer dynamics in the film. Our results show that transport of molecules through the film-solution interface limits the release rate. The multilayers might serve as an effective platform for drug delivery and tissue engineering due to high potential for drug loading and controlled release. KW - diffusion KW - drug delivery KW - dye KW - release mechanism Y1 - 2015 U6 - https://doi.org/10.1002/mabi.201500093 SN - 1616-5187 SN - 1616-5195 VL - 15 IS - 10 SP - 1357 EP - 1363 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Le Duc, Diana A1 - Renaud, Gabriel A1 - Krishnan, Arunkumar A1 - Almen, Markus Sallman A1 - Huynen, Leon A1 - Prohaska, Sonja J. A1 - Ongyerth, Matthias A1 - Bitarello, Barbara D. A1 - Schioth, Helgi B. A1 - Hofreiter, Michael A1 - Stadler, Peter F. A1 - Prüfer, Kay A1 - Lambert, David A1 - Kelso, Janet A1 - Schöneberg, Torsten T1 - Kiwi genome provides insights into evolution of a nocturnal lifestyle JF - Genome biology : biology for the post-genomic era N2 - Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites. Y1 - 2015 U6 - https://doi.org/10.1186/s13059-015-0711-4 SN - 1465-6906 SN - 1474-760X VL - 16 PB - BioMed Central CY - London ER -