TY - THES A1 - Adamla, Frauke T1 - Polyglutamine- and aging-dependent aberrancies in transcription and translation Y1 - 2015 ER - TY - JOUR A1 - Adamla, Frauke A1 - Ignatova, Zoya T1 - Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans JF - Scientific reports N2 - Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process. Y1 - 2015 U6 - https://doi.org/10.1038/srep10692 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London 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 - Allan, Eric A1 - Manning, Pete A1 - Alt, Fabian A1 - Binkenstein, Julia A1 - Blaser, Stefan A1 - Blüthgen, Nico A1 - Böhm, Stefan A1 - Grassein, Fabrice A1 - Hölzel, Norbert A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Morris, E. Kathryn A1 - Oelmann, Yvonne A1 - Prati, Daniel A1 - Renner, Swen C. A1 - Rillig, Matthias C. A1 - Schaefer, Martin A1 - Schloter, Michael A1 - Schmitt, Barbara A1 - Schöning, Ingo A1 - Schrumpf, Marion A1 - Solly, Emily A1 - Sorkau, Elisabeth A1 - Steckel, Juliane A1 - Steffen-Dewenter, Ingolf A1 - Stempfhuber, Barbara A1 - Tschapka, Marco A1 - Weiner, Christiane N. A1 - Weisser, Wolfgang W. A1 - Werner, Michael A1 - Westphal, Catrin A1 - Wilcke, Wolfgang A1 - Fischer, Markus T1 - Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition JF - Ecology letters N2 - Global change, especially land-use intensification, affects human well-being by impacting the delivery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is a major component of global change effects on multifunctionality in real-world ecosystems, as in experimental ones, remains unclear. Therefore, we assessed biodiversity, functional composition and 14 ecosystem services on 150 agricultural grasslands differing in land-use intensity. We also introduce five multifunctionality measures in which ecosystem services were weighted according to realistic land-use objectives. We found that indirect land-use effects, i.e. those mediated by biodiversity loss and by changes to functional composition, were as strong as direct effects on average. Their strength varied with land-use objectives and regional context. Biodiversity loss explained indirect effects in a region of intermediate productivity and was most damaging when land-use objectives favoured supporting and cultural services. In contrast, functional composition shifts, towards fast-growing plant species, strongly increased provisioning services in more inherently unproductive grasslands. KW - Biodiversity-ecosystem functioning KW - ecosystem services KW - global change KW - land use KW - multifunctionality Y1 - 2015 U6 - https://doi.org/10.1111/ele.12469 SN - 1461-023X SN - 1461-0248 VL - 18 IS - 8 SP - 834 EP - 843 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Allhoff, Korinna Theresa A1 - Ritterskamp, Daniel A1 - Rall, Björn C. A1 - Drossel, Barbara A1 - Guill, Christian T1 - Evolutionary food web model based on body masses gives realistic networks with permanent species turnover JF - Scientific reports N2 - The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50% of the network are not observed. Y1 - 2015 U6 - https://doi.org/10.1038/srep10955 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Alseekh, Saleh T1 - Identification and mode of inheritance of quantitative trait loci (QTL) for metabolite abundance in tomato Y1 - 2015 ER - TY - JOUR A1 - Alseekh, Saleh A1 - Tohge, Takayuki A1 - Wendenberg, Regina A1 - Scossa, Federico A1 - Omranian, Nooshin A1 - Li, Jie A1 - Kleessen, Sabrina A1 - Giavalisco, Patrick A1 - Pleban, Tzili A1 - Müller-Röber, Bernd A1 - Zamir, Dani A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. T1 - Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato JF - The plant cell N2 - A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism. Y1 - 2015 U6 - https://doi.org/10.1105/tpc.114.132266 SN - 1040-4651 SN - 1532-298X VL - 27 IS - 3 SP - 485 EP - 512 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Alter, S. Elizabeth A1 - Meyer, Matthias A1 - Post, Klaas A1 - Czechowski, Paul A1 - Gravlund, Peter A1 - Gaines, Cork A1 - Rosenbaum, Howard C. A1 - Kaschner, Kristin A1 - Turvey, Samuel T. A1 - van der Plicht, Johannes A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100 JF - Molecular ecology N2 - Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range. KW - ancient DNA KW - climate change KW - last glacial maximum KW - marine mammal Y1 - 2015 U6 - https://doi.org/10.1111/mec.13121 SN - 0962-1083 SN - 1365-294X VL - 24 IS - 7 SP - 1510 EP - 1522 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Apelt, Federico T1 - Implementation of an imaging-based approach using a 3D light-field camera to analyse plant growth behaviour Y1 - 2015 ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Nikoloski, Zoran A1 - Stitt, Mark A1 - Kragler, Friedrich T1 - Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth JF - The plant journal N2 - Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge. KW - plant growth KW - hyponasty KW - 3D imaging KW - light-field camera KW - Arabidopsis thaliana KW - pgm KW - technical advance Y1 - 2015 U6 - https://doi.org/10.1111/tpj.12833 SN - 0960-7412 SN - 1365-313X VL - 82 IS - 4 SP - 693 EP - 706 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Arabi, Fayezeh T1 - Functional characterization of Sulfur Deficiency Induced genes, SDI1 and SDI2, in Arabidopsis thaliana Y1 - 2015 ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Tittel, Joerg A1 - Allgaier, Martin A1 - Frindte, Katharina A1 - Wurzbacher, Christian A1 - Hilt, Sabine A1 - Kamjunke, Norbert A1 - Grossart, Hans-Peter T1 - Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition JF - Microbial ecology N2 - The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties. KW - Bacterial growth efficiency KW - Continuous cultures KW - Carbon decomposition KW - Leaf litter KW - Photolysis Y1 - 2015 U6 - https://doi.org/10.1007/s00248-014-0549-4 SN - 0095-3628 SN - 1432-184X VL - 69 IS - 2 SP - 361 EP - 371 PB - Springer CY - New York ER - TY - THES A1 - Balazadeh, Salma T1 - New insights into the molecular mechanisms of leaf senescence Y1 - 2015 ER - TY - THES A1 - Balk, Maria T1 - 3D structured shape-memory hydrogels with enzymatically-induced shape shifting Y1 - 2015 ER - TY - JOUR A1 - Benina, Maria A1 - Ribeiro, Dimas Mendes A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. T1 - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels. KW - Arabidopsis KW - gene regulation KW - oxidative stress KW - tissue-specific KW - translation Y1 - 2015 U6 - https://doi.org/10.1111/pce.12355 SN - 0140-7791 SN - 1365-3040 VL - 38 IS - 2 SP - 349 EP - 363 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bergholz, Kolja A1 - Jeltsch, Florian A1 - Weiß, Lina A1 - Pottek, Janine A1 - Geißler, Katja A1 - Ristow, Michael T1 - Fertilization affects the establishment ability of species differing in seed mass via direct nutrient addition and indirect competition effects JF - Oikos N2 - Fertilization causes species loss and species dominance changes in plant communities worldwide. However, it still remains unclear how fertilization acts upon species functional traits, e.g. seed mass. Seed mass is a key trait of the regeneration strategy of plants, which influences a range of processes during the seedling establishment phase. Fertilization may select upon seed mass, either directly by increased nutrient availability or indirectly by increased competition. Since previous research has mainly analyzed the indirect effects of fertilization, we disentangled the direct and indirect effects to examine how nutrient availability and competition influence the seed mass relationships on four key components during seedling establishment: seedling emergence, time of seedling emergence, seedling survival and seedling growth. We conducted a common garden experiment with 22 dry grassland species with a two-way full factorial design that simulated additional nutrient supply and increased competition. While we found no evidence that fertilization either directly by additional nutrient supply or indirectly by increased competition alters the relationship between seed mass and (time of) seedling emergence, we revealed that large seed mass is beneficial under nutrient-poor conditions (seedlings have greater chances of survival, particularly in nutrient-poor soils) as well as under competition (large-seeded species produced larger seedlings, which suffered less from competition than small-seeded species). Based on these findings, we argue that both factors, i.e. nutrient availability and competition intensity, ought to be considered to understand how fertilization influences seedling establishment and species composition with respect to seed mass in natural communities. We propose a simple conceptual model, in which seed mass in natural communities is determined by competition intensity and nutrient availability. Here, we hypothesize that seed mass shows a U-shaped pattern along gradients of soil fertility, which may explain the contrasting soil fertility-seed mass relationships found in the recent literature. Y1 - 2015 U6 - https://doi.org/10.1111/oik.02193 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 11 SP - 1547 EP - 1554 PB - Wiley-Blackwell CY - Hoboken 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 - Bhaskar, Thanga Bhuvanesh Vijaya A1 - Ma, Nan A1 - Lendlein, Andreas A1 - Roch, Toralf T1 - The interaction of human macrophage subsets with silicone as a biomaterial JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Silicones are widely used as biomaterials for medical devices such as extracorporeal equipments. However, there is often conflicting evidence about their supposed cell-and histocompatibility. Macrophages could mediate silicone-induced adverse responses such as foreign body reaction and fibrous encapsulation. The polarization behaviour of macrophages could determine the clinical outcome after implantation of biomaterials. Induction of classically activated macrophages (CAM) may induce and support uncontrolled inflammatory responses and undesired material degradation. In contrast, polarization into alternatively activated macrophages (AAM) is assumed to support healing processes and implant integration. This study compared the interaction of non-polarized macrophages (M0), CAM, and AAM with commercially available tissue culture polystyrene (TCP) and a medical grade silicone-based biomaterial, regarding the secretion of inflammatory mediators such as cytokines and chemokines. Firstly, by using the Limulus amoebocyte lysate (LAL) test the silicone films were shown to be free of soluble endotoxins, which is the prerequisite to investigate their interaction with primary immune cells. Primary human monocyte-derived macrophages (M0) were polarized into CAM and AAM by addition of suitable differentiation factors. These macrophage subsets were incubated on the materials for 24 hours and their viability and cytokine secretion was assessed. In comparison to TCP, cell adhesion was lower on silicone after 24 hours for all three macrophage subsets. However, compared to TCP, silicone induced higher levels of certain inflammatory and chemotactic cytokines in M0, CAM, and AAM macrophage subsets. Conclusively, it was shown that silicone has the ability to induce a pro-inflammatory state to different magnitudes dependent on the macrophage subsets. This priming of the macrophage phenotype by silicone could explain the incidence of severe foreign body complications observed in vivo. KW - Biomaterials KW - silicone KW - macrophage subsets KW - cytokines/chemokines Y1 - 2015 U6 - https://doi.org/10.3233/CH-151991 SN - 1386-0291 SN - 1875-8622 VL - 61 IS - 2 SP - 119 EP - 133 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Bizic-Ionescu, Mina A1 - Zeder, Michael A1 - Ionescu, Danny A1 - Orlic, Sandi A1 - Fuchs, Bernhard M. A1 - Grossart, Hans-Peter A1 - Amann, Rudolf T1 - Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization JF - Environmental microbiology N2 - Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in-situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles >5 and >10m respectively. Limnic particles were more abundant (average: 1x10(7)l(-1)), smaller in size (average areas: 471 versus 2050m(2)) and more densely colonized (average densities: 7.3 versus 3.6 cells 100m(-2)) than marine ones. Limnic particle-associated (PA) bacteria harboured Alphaproteobacteria and Betaproteobacteria, and unlike previously suggested sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. Large differences in individual particle colonization could be detected. High-throughput sequencing revealed a significant overlap of PA and free-living (FL) bacteria highlighting an underestimated connectivity between both fractions. PA bacteria were in 14/21 cases more diverse than FL bacteria, reflecting a high heterogeneity in the particle microenvironment. We propose that a ratio of Chao 1 indices of PA/FL<1 indicates the presence of rather homogeneously colonized particles. The identification of different bacterial families enriched on either limnic or marine particles demonstrates that, despite the seemingly similar ecological niches, PA communities of both environments differ substantially. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12466 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 10 SP - 3500 EP - 3514 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Blankenburg, Stefanie A1 - Balfanz, Sabine A1 - Hayashi, Y. A1 - Shigenobu, S. A1 - Miura, T. A1 - Baumann, Otto A1 - Baumann, Arnd A1 - Blenau, Wolfgang T1 - Cockroach GABA(B) receptor subtypes: Molecular characterization, pharmacological properties and tissue distribution JF - Neuropharmacology N2 - gamma-aminobutyric acid (GABA) is the predominant inhibitory neurotransmitter in the central nervous system (CNS). Its effects are mediated by either ionotropic GABA(A) receptors or metabotropic GABA(B) receptors. GABA(B) receptors regulate, via Gi/o, G-proteins, ion channels, and adenylyl cyclases. In humans, GABA(B) receptor subtypes are involved in the etiology of neurologic and psychiatric disorders. In arthropods, however, these members of the G-protein-coupled receptor family are only inadequately characterized. Interestingly, physiological data have revealed important functions of GABA(B) receptors in the American cockroach, Periplaneta americana. We have cloned cDNAs coding for putative GABA(B) receptor subtypes 1 and 2 of P. americana (PeaGB1 and PeaGB2). When both receptor proteins are co-expressed in mammalian cells, activation of the receptor heteromer with GABA leads to a dose-dependent decrease in cAMP production. The pharmacological profile differs from that of mammalian and Drosophila GABA(B) receptors. Western blot analyses with polyclonal antibodies have revealed the expression of PeaGB1 and PeaGB2 in the CNS of the American cockroach. In addition to the widespread distribution in the brain, PeaGB1 is expressed in salivary glands and male accessory glands. Notably, PeaGB1-like immunoreactivity has been detected in the GABAergic salivary neuron 2, suggesting that GABA(B) receptors act as autoreceptors in this neuron. KW - GABA(B) receptor KW - G-protein-coupled receptor KW - Periplaneta americana KW - Central nervous system KW - Adenylyl cyclase KW - Salivary gland Y1 - 2015 U6 - https://doi.org/10.1016/j.neuropharm.2014.08.022 SN - 0028-3908 SN - 1873-7064 VL - 88 SP - 134 EP - 144 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Bogen, Oliver A1 - Bender, Olaf A1 - Loewe, Jana A1 - Blenau, Wolfgang A1 - Thevis, Beatrice A1 - Schroeder, Wolfgang A1 - Margolis, Richard U. A1 - Levine, Jon D. A1 - Hucho, Ferdinand T1 - Neuronally produced versican V2 renders C-fiber nociceptors IB4-positive JF - Journal of neurochemistry N2 - A subpopulation of nociceptors, the glial cell line-derived neurotrophic factor (GDNF)-dependent, non-peptidergic C-fibers, expresses a cell-surface glycoconjugate that can be selectively labeled with isolectin B4 (IB4), a homotetrameric plant lectin from Griffonia simplicifolia. We show that versican is an IB4-binding molecule in rat dorsal root ganglion neurons. Using reverse transcriptase polymerase chain reaction (RT-PCR), insitu hybridization and immunofluorescence experiments on rat lumbar dorsal root ganglion, we provide the first demonstration that versican is produced by neurons. In addition, by probing Western blots with splice variant-specific antibodies we show that the IB4-binding versican contains only the glycosaminoglycan alpha domain. Our data support V2 as the versican isoform that renders this subpopulation of nociceptors IB4-positive (+). A subset of nociceptors, the GDNF-dependent non-peptidergic C-fibers can be characterized by its reactivity for isolectin B4 (IB4), a plant lectin from Griffonia simplicifolia. We have previously demonstrated that versican V2 binds IB4 in a Ca2+-dependent manner. However, given that versican is thought to be the product of glial cells, it was questionable whether versican V2 can be accountable for the IB4-reactivity of this subset of nociceptors. The results presented here prove - for the first time - a neuronal origin of versican and suggest that versican V2 is the molecule that renders GDNF-dependent non-peptidergic C-fibers IB4-positive. KW - IB4 KW - nociceptors KW - pain KW - sensory neurons KW - V2 KW - versican Y1 - 2015 U6 - https://doi.org/10.1111/jnc.13113 SN - 0022-3042 SN - 1471-4159 VL - 134 IS - 1 SP - 147 EP - 155 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bordag, Natalie A1 - Klie, Sebastian A1 - Jürchott, Kathrin A1 - Vierheller, Janine A1 - Schiewe, Hajo A1 - Albrecht, Valerie A1 - Tonn, Jörg-Christian A1 - Schwartz, Christoph A1 - Schichor, Christian A1 - Selbig, Joachim T1 - Glucocorticoid (dexamethasone)-induced metabolome changes in healthy males suggest prediction of response and side effects JF - Scientific reports N2 - Glucocorticoids are indispensable anti-inflammatory and decongestant drugs with high prevalence of use at (similar to)0.9% of the adult population. Better holistic insights into glucocorticoid-induced changes are crucial for effective use as concurrent medication and management of adverse effects. The profiles of 214 metabolites from plasma of 20 male healthy volunteers were recorded prior to and after ingestion of a single dose of 4 mg dexamethasone (+20 mg pantoprazole). Samples were drawn at three predefined time points per day: seven untreated (day 1 midday - day 3 midday) and four treated (day 3 evening - day 4 evening) per volunteer. Statistical analysis revealed tremendous impact of dexamethasone on the metabolome with 150 of 214 metabolites being significantly deregulated on at least one time point after treatment (ANOVA, Benjamini-Hochberg corrected, q < 0.05). Inter-person variability was high and remained uninfluenced by treatment. The clearly visible circadian rhythm prior to treatment was almost completely suppressed and deregulated by dexamethasone. The results draw a holistic picture of the severe metabolic deregulation induced by single-dose, short-term glucocorticoid application. The observed metabolic changes suggest a potential for early detection of severe side effects, raising hope for personalized early countermeasures increasing quality of life and reducing health care costs. Y1 - 2015 U6 - https://doi.org/10.1038/srep15954 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Borschewski, Aljona T1 - Bedeutung der Interaktion von Calcineurin und SORLA für die Regulation des Na⁺,K⁺,2Cl⁻-Kotransporters (NKCC2) in der Niere T1 - Importance of the interaction between calcineurin and SORLA for the regulation of the renal Na⁺-K⁺-2Cl⁻−cotransporter (NKCC2) N2 - Der Na⁺-K⁺-2Cl⁻-Kotransporter (NKCC2) wird im distalen Nephron der Niere exprimiert. Seine Verteilung umfasst die Epithelien der medullären und kortikalen Teile der dicken aufsteigenden Henle-Schleife (Thick ascending limb, TAL) und die Macula densa. Resorptiver NaCl-Transport über den NKCC2 dient dem renalen Konzentrierungsmechanismus und reguliert systemisch auch Volumenstatus und Blutdruck. Die Aktivität des NKCC2 ist mit der Phosphorylierung seiner N-terminalen Aminosäurereste Serin 126 und Threonin 96/101 verbunden. Vermittelt wird diese durch die homologen Kinasen SPAK (SPS-related proline/alanine-rich kinase) und OSR1 (Oxidative stress responsive kinase 1), die hierzu ihrerseits phosphoryliert werden müssen. Der regulatorische Kontext dieser Kinasen ist mittlerweile gut charakterisiert. Über Mechanismen und Produkte, die den NKCC2 deaktivieren, war hingegen weniger bekannt. Ziel der Arbeit war daher zu untersuchen, welche Wege zur Deaktivierung des Transporters führen. Der intrazelluläre Sortierungsrezeptor SORLA (Sorting-protein-related receptor with A-type repeats) war zuvor in seiner Bedeutung für das Nephron charakterisiert worden. Ein SORLA-defizientes Mausmodell weist unter anderem eine stark verringerte NKCC2-Phosphorylierung auf. Unter osmotischem Stress können SORLA-defiziente Mäuse ihren Urin weniger effizient konzentrieren. Meine Resultate zeigen mit hochauflösender Technik, dass SORLA apikal im TAL lokalisiert ist und dass mit NKCC2 eine anteilige Kolokalisation besteht. Unter SORLA Defizienz war die für die NKCC2 Aktivität maßgebliche SPAK/OSR1-Phosphorylierung gegenüber dem Wildtyp nicht verändert. Jedoch war die ebenfalls im TAL exprimierte Phosphatase Calcineurin Aβ (CnAβ) per Western blot um das zweifache gesteigert. Parallel hierzu wurde immunhistochemisch die Kolokalisation von verstärktem CnAβ-Signal und NKCC2 bestätigt. Beide Befunde geben zusammen den Hinweis auf einen Bezug zwischen der reduzierten NKCC2-Phosphorylierung und der gesteigerten Präsenz von CnAβ bei SORLA Defizienz. Die parallel induzierte Überexpression von SORLA in HEK-Zellen zeigte entsprechend eine Halbierung der CnAβ Proteinmenge. SORLA steuert demzufolge sowohl die Abundanz als auch die zelluläre Verteilung der Phosphatase. Weiterhin ließ sich die Interaktion zwischen CnAβ und SORLA (intrazelluläre Domäne) mittels Co-Immunpräzipitation bzw. GST-pulldown assay nachweisen. Auch die Interaktion zwischen CnAβ und NKCC2 wurde auf diesem Weg belegt. Da allerdings weder SORLA noch NKCC2 ein spezifisches Bindungsmuster für CnAβ aufweisen, sind vermutlich intermediäre Adapterproteine bei ihrer Bindung involviert. Die pharmakologische Inhibition von CnAβ mittels Cyclosporin A (CsA; 1 h) führte bei SORLA Defizienz zur Normalisierung der NKCC2-Phosphorylierung. Entsprechend führte in vitro die Gabe von CsA bei TAL Zellen zu einer 7-fach gesteigerten NKCC2-Phosphorylierung. Zusammenfassend zeigen die Ergebnisse, dass die Phosphatase CnAβ über ihre Assoziation mit NKCC2 diesen im adluminalen Zellkompartiment deaktivieren kann. Gesteuert wird dieser Vorgang durch die Eigenschaft von SORLA, CnAβ apikal zu reduzieren und damit die adluminale Phosphorylierung und Aktivität von NKCC2 zu unterstützen. Da Calcineurin-Inhibitoren derzeit die Grundlage der immunsupprimierenden Therapie darstellen, haben die Ergebnisse eine klinische Relevanz. Angesichts der Co-Expression von SORLA und CnAβ in verschiedenen anderen Organen können die Ergebnisse auch über die Niere hinaus Bedeutung erlangen. N2 - The Na⁺-K⁺-2Cl⁻-cotransporter (NKCC2) of the thick ascending limb (TAL) is critical for renal salt handling. Activity of the cotransporter is facilitated by its phosphorylation at conserved N-terminal threonine and serine residues provided by homologous SPAK (SPS-related proline/alanine-rich kinase) and OSR1 (oxidative stress responsive kinase 1) kinases. The identification of factors which modulate the phosphorylation and hence, the activity of NKCC2 has received recent interest. SORLA (sorting-protein-related receptor with A-type repeats) is co-expressed with NKCC2 in TAL epithelium. Genetically engineered mice lacking SORLA show near-complete absence of NKCC2 phosphorylation at the SPAK/OSR1-dependent phosphoacceptors, indicating that SORLA acts as a mediator between these reaction partners, possibly by a cellular trafficking step involving additional molecules. The present study addresses molecular pathways modulating NKCC2 activity by phosphorylation or dephosphorylation reactions with a special focus on SORLA. Comparative evaluation of SORLA-deficient and wild-type mouse kidneys revealed similar levels of phosphorylated, catalytically active SPAK and OSR1 kinases, whereas abundance of the phosphatase calcineurin Aβ (CnAβ) was increased by approximately two-fold in the renal medulla of SORLA-deficient mice likely reflecting changes in TAL. In line with this, confocal microscopy revealed accumulation of CnAβ in the apical compartment of TAL in SORLA-deficient kidneys. In contrast, overexpression of SORLA in HEK cells resulted in approximately two-fold decreased CnAβ levels suggesting that SORLA modulates both the cellular abundance and distribution of the phosphatase. This data was further corroborated by co-immunoprecipitation and GST pull down assays which showed an interaction between the cytoplasmic tail of SORLA and CnAβ. Acute administration of the calcineurin inhibitor, cyclosporin A (CsA), for 1 h rapidly normalized NKCC2 phosphorylation in SORLA-deficient mice which demonstrates that the decrease in phospho-NKCC2 was functionally related with CnAβ. In sum, our data elucidate the role of calcineurin in the regulation of NKCC2 and establish SORLA as an endogenous regulator of the phosphatase. KW - Salztransport KW - Niere KW - Henlesche Schleife KW - Calcineurin KW - Phosphatase KW - SORLA KW - Calcineurin-Inhibitoren KW - Transporteraktivierung KW - Phosphorylierung KW - kidney KW - phosphorylation KW - thick ascending limb KW - epithelial salt transport KW - calcineurin inhibitors KW - cell signaling Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-89205 ER - TY - JOUR A1 - Breitkopf, Hendrik A1 - Onstein, Renske E. A1 - Cafasso, Donata A1 - Schlüter, Philipp M. A1 - Cozzolino, Salvatore T1 - Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids JF - New phytologist : international journal of plant science N2 - Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic. KW - Andrena KW - diversification rates KW - Eucera KW - Ophrys KW - pollination syndrome KW - pollinator shift KW - sexual deception (SD) KW - species radiation Y1 - 2015 U6 - https://doi.org/10.1111/nph.13219 SN - 0028-646X SN - 1469-8137 VL - 207 IS - 2 SP - 377 EP - 389 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Budzik, Karolina A. A1 - Zuwala, Krystyna A1 - Kupfer, Alexander A1 - Gower, David J. A1 - Wilkinson, Mark T1 - Diverse anatomy of the tongue and taste organs in five species of caecilian (Amphibia: Gymnophiona) JF - Zoologischer Anzeiger = Journal of comparative zoology : morphology, systematics, biogeography N2 - Limited previous studies on caecilian taste organs have demonstrated the presence of very few taste buds in the oral epithelium, while providing somewhat contradictory reports of their distribution within the oropharynx and across taxa. Here we report on the gross morphology of the tongue and explore the distribution, number and morphology of taste organs of five caecilian species representing five families, focusing upon variation within the group and investigating whether larvae and adults have the same type of taste organs. We find that taste buds are widespread in the oropharynx of caecilians and that they occur both in adults and larvae of a species with a biphasic life history. Thus Gymnophiona differ substantially from Batriachia, which have distinct larval and adult taste organs. KW - Amphibian KW - Number of taste organs KW - Sensory zone KW - Taste buds Y1 - 2015 U6 - https://doi.org/10.1016/j.jcz.2015.04.007 SN - 0044-5231 VL - 257 SP - 103 EP - 109 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Camargo, Rodolfo Gonzalez A1 - dos Reis Riccardi, Daniela Mendes A1 - Teixeira Ribeiro, Henrique Quintas A1 - Carnevali Junior, Luiz Carlos A1 - de Matos-Neto, Emidio Marques A1 - Enjiu, Lucas A1 - Neves, Rodrigo Xavier A1 - Carola Correia Lima, Joanna Darck A1 - Figueredo, Raquel Galvao A1 - Martins de Alcantara, Paulo Sergio A1 - Maximiano, Linda A1 - Otoch, Jose A1 - Batista Jr., Miguel Luiz A1 - Püschel, Gerhard Paul A1 - Seelaender, Marilia T1 - NF-kappa Bp65 and Expression of Its Pro-Inflammatory Target Genes Are Upregulated in the Subcutaneous Adipose Tissue of Cachectic Cancer Patients JF - Nutrients N2 - Cancer cachexia, of which the most notable symptom is severe and rapid weight loss, is present in the majority of patients with advanced cancer. Inflammatory mediators play an important role in the development of cachexia, envisaged as a chronic inflammatory syndrome. The white adipose tissue (WAT) is one of the first compartments affected in cancer cachexia and suffers a high rate of lipolysis. It secretes several cytokines capable of directly regulating intermediate metabolism. A common pathway in the regulation of the expression of pro-inflammatory cytokines in WAT is the activation of the nuclear transcription factor kappa-B (NF-B). We have examined the gene expression of the subunits NF-Bp65 and NF-Bp50, as well as NF-Bp65 and NF-Bp50 binding, the gene expression of pro-inflammatory mediators under NF-B control (IL-1, IL-6, INF-, TNF-, MCP-1), and its inhibitory protein, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IB-). The observational study involved 35 patients (control group, n = 12 and cancer group, n = 23, further divided into cachectic and non-cachectic). NF-Bp65 and its target genes expression (TNF-, IL-1, MCP-1 and IB-) were significantly higher in cachectic cancer patients. Moreover, NF-Bp65 gene expression correlated positively with the expression of its target genes. The results strongly suggest that the NF-B pathway plays a role in the promotion of WAT inflammation during cachexia. KW - cancer cachexia KW - inflammation KW - white adipose tissue KW - NF-B KW - IB Y1 - 2015 U6 - https://doi.org/10.3390/nu7064465 SN - 2072-6643 VL - 7 IS - 6 SP - 4465 EP - 4479 PB - MDPI CY - Basel 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 - Caron, Maria Mercedes A1 - De Frenne, P. A1 - Chabrerie, Olivier A1 - Cousins, S. A. O. A1 - De Backer, L. A1 - Decocq, G. A1 - Diekmann, M. A1 - Heinken, Thilo A1 - Kolb, A. A1 - Naaf, T. A1 - Plue, J. A1 - Selvi, F. A1 - Strimbeck, G. R. A1 - Wulf, M. A1 - Verheyen, Kris T1 - Impacts of warming and changes in precipitation frequency on the regeneration of two Acer species JF - Flora : morphology, distribution, functional ecology of plants KW - Seed provenance KW - Germination KW - Climate change KW - Interactive effects Y1 - 2015 U6 - https://doi.org/10.1016/j.flora.2015.05.005 SN - 0367-2530 SN - 1618-0585 VL - 214 SP - 24 EP - 33 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, Pieter A1 - Brunet, J. A1 - Chabrerie, Olivier A1 - Cousins, S. A. O. A1 - De Backer, L. A1 - Decocq, G. A1 - Diekmann, M. A1 - Heinken, Thilo A1 - Kolb, A. A1 - Naaf, T. A1 - Plue, J. A1 - Selvi, Federico A1 - Strimbeck, G. R. A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Interacting effects of warming and drought on regeneration and early growth of Acer pseudoplatanus and A. platanoides JF - Plant biology N2 - Climate change is acting on several aspects of plant life cycles, including the sexual reproductive stage, which is considered amongst the most sensitive life-cycle phases. In temperate forests, it is expected that climate change will lead to a compositional change in community structure due to changes in the dominance of currently more abundant forest tree species. Increasing our understanding of the effects of climate change on currently secondary tree species recruitment is therefore important to better understand and forecast population and community dynamics in forests. Here, we analyse the interactive effects of rising temperatures and soil moisture reduction on germination, seedling survival and early growth of two important secondary European tree species, Acer pseudoplatanus and A.platanoides. Additionally, we analyse the effect of the temperature experienced by the mother tree during seed production by collecting seeds of both species along a 2200-km long latitudinal gradient. For most of the responses, A.platanoides showed higher sensitivity to the treatments applied, and especially to its joint manipulation, which for some variables resulted in additive effects while for others only partial compensation. In both species, germination and survival decreased with rising temperatures and/or soil moisture reduction while early growth decreased with declining soil moisture content. We conclude that although A.platanoides germination and survival were more affected after the applied treatments, its initial higher germination and larger seedlings might allow this species to be relatively more successful than A.pseudoplatanus in the face of climate change. KW - Acer platanoides KW - Acer pseudoplatanus KW - climate change KW - drought KW - reproduction KW - seed KW - temperature Y1 - 2015 U6 - https://doi.org/10.1111/plb.12177 SN - 1435-8603 SN - 1438-8677 VL - 17 IS - 1 SP - 52 EP - 62 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Caron, Maria Mercedes A1 - De Frenne, Pieter A1 - Brunet, Jörg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Diekmann, Martin A1 - Graae, Bente Jessen A1 - Heinken, Thilo A1 - Kolb, Annette A1 - Lenoir, Jonathan A1 - Naaf, Tobias A1 - Plue, Jan A1 - Selvi, Federico A1 - Wulf, Monika A1 - Verheyen, Kris T1 - Divergent regeneration responses of two closely related tree species to direct abiotic and indirect biotic effects of climate change JF - Forest ecology and management N2 - Changing temperature and precipitation can strongly influence plant reproduction. However, also biotic interactions might indirectly affect the reproduction and recruitment success of plants in the context of climate change. Information about the interactive effects of changes in abiotic and biotic factors is essential, but still largely lacking, to better understand the potential effects of a changing climate on plant populations. Here we analyze the regeneration from seeds of Acer platanoides and Acer pseudoplatanus, two currently secondary forest tree species from seven regions along a 2200 km-wide latitudinal gradient in Europe. We assessed the germination, seedling survival and growth during two years in a common garden experiment where temperature, precipitation and competition with the understory vegetation were manipulated. A. platanoides was more sensitive to changes in biotic conditions while A. pseudoplatanus was affected by both abiotic and biotic changes. In general, competition reduced (in A. platanoides) and warming enhanced (in A. pseudoplatanus) germination and survival, respectively. Reduced competition strongly increased the growth of A. platanoides seedlings. Seedling responses were independent of the conditions experienced by the mother tree during seed production and maturation. Our results indicate that, due to the negative effects of competition on the regeneration of A. platanoides, it is likely that under stronger competition (projected under future climatic conditions) this species will be negatively affected in terms of germination, survival and seedling biomass. Climate-change experiments including both abiotic and biotic factors constitute a key step forward to better understand the response of tree species' regeneration to climate change. (C) 2015 Elsevier B.V. All rights reserved. KW - Acer KW - Regeneration KW - Latitudinal gradient KW - Temperature KW - Precipitation KW - Competition Y1 - 2015 U6 - https://doi.org/10.1016/j.foreco.2015.01.003 SN - 0378-1127 SN - 1872-7042 VL - 342 SP - 21 EP - 29 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Castellini, Alberto A1 - Paltrinieri, Daniele A1 - Manca, Vincenzo T1 - MP-GeneticSynth: inferring biological network regulations from time series JF - Bioinformatics N2 - MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis. Y1 - 2015 U6 - https://doi.org/10.1093/bioinformatics/btu694 SN - 1367-4803 SN - 1460-2059 VL - 31 IS - 5 SP - 785 EP - 787 PB - Oxford Univ. Press CY - Oxford ER - TY - INPR A1 - Chattopadhyay, Madhab K. A1 - Chakraborty, Ranadhir A1 - Grossart, Hans-Peter A1 - Reddy, Gundlapally S. A1 - Jagannadham, Medicharla V. T1 - Antibiotic resistance of bacteria T2 - BioMed research international Y1 - 2015 U6 - https://doi.org/10.1155/2015/501658 SN - 2314-6133 SN - 2314-6141 PB - Hindawi Publishing Corp. CY - New York ER - TY - JOUR A1 - Choi, Young-Joon A1 - Klosterman, Steven J. A1 - Kummer, Volker A1 - Voglmayr, Hermann A1 - Shin, Hyeon-Dong A1 - Thines, Marco T1 - Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach JF - Molecular phylogenetics and evolution N2 - Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. (C) 2015 Elsevier Inc. All rights reserved. KW - Cospeciation KW - Host shift KW - Multi-locus phylogeny KW - Oomycetes KW - Peronospora farinosa KW - Species tree Y1 - 2015 U6 - https://doi.org/10.1016/j.ympev.2015.03.003 SN - 1055-7903 SN - 1095-9513 VL - 86 SP - 24 EP - 34 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Cisek, Richard A1 - Tokarz, Danielle A1 - Steup, Martin A1 - Tetlow, Ian J. A1 - Emes, Michael J. A1 - Hebelstrup, Kim H. A1 - Blennow, Andreas A1 - Barzda, Virginijus T1 - Second harmonic generation microscopy investigation of the crystalline ultrastructure of three barley starch lines affected by hydration JF - Biomedical optics express N2 - Second harmonic generation (SHG) microscopy is employed to study changes in crystalline organization due to altered gene expression and hydration in barley starch granules. SHG intensity and susceptibility ratio values (R'(SHG)) are obtained using reduced Stokes-Mueller polarimetric microscopy. The maximum R'(SHG) values occur at moderate moisture indicating the narrowest orientation distribution of nonlinear dipoles from the cylindrical axis of glucan helices. The maximum SHG intensity occurs at the highest moisture and amylopectin content. These results support the hypothesis that SHG is caused by ordered hydrogen and hydroxyl bond networks which increase with hydration of starch granules. (C) 2015 Optical Society of America Y1 - 2015 U6 - https://doi.org/10.1364/BOE.6.003694 SN - 2156-7085 VL - 6 IS - 10 SP - 3694 EP - 3700 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Cochard, Roland A1 - Edwards, Peter J. A1 - Weber, Ewald T1 - Post-ranching tree-grass interactions in secondary Acacia zanzibarica woodlands in coastal Tanzania - an experimental study JF - Applied vegetation science : official organ of the International Association for Vegetation Science N2 - Questions: We studied a humid savanna rangeland., abandoned in 2000, where intensive cattle grazing had led to widespread encroachment by Acacia zanzibarica. We asked whether the acacia trees were able to regenerate in the absence of domesJic livestock, either beneath acacia canopies or in artificial clearings. Location: Tropical coastal Tanzania (former Mkwaja Ranch, now in Saadani National Park). Methods: We set out a total of 48 plots on four sites in November 2001, and assigned them to three treatments: trees felled (FN), trees felled and the stumps poisoned (FP) with Triclopyr, and no intervention (controls, NN). We analysed soils of plots for texture and nutrients. In two wet (July 2002 and 2003) and one dry (February 2003) seasons we assessed grass and tree leaf biomass and transpiration rates, and counted acacia seedlings and resprouts. The effects of treatments (controlled for site and other co-variables) on grass growth and acacia rectaiitment were determined statistically using general linear models (GLM). Results: Acacia leaves had a much higher stomatal conductance than grasses, with the consequence that total evapotranspiration in woodland was higher than in clearings. In the wet seasons, grass biomass and seedling densities were significantly higher in clearings than in control plots, which we attributed to more.favourable moisture conditions, In the dry season, by contrast, we found no differences, and all seedlings had died. On FN plots, 71% of stumps, and on FP plots, 11% resprouted (coppicing), but only a quarter of these shoots survived until July 2003. Root suckering occurred spontaneously at low densities. No root suckers or resprouts grew beyond the grass layer. Conclusions: Acacia woodlands do not regenerate in the absence of cattle grazing, and tree cutting in combination with appropriate fire management could potentially accelerate re-establishment of open grassland. However, regeneration might occur in the future due to the increasing wildlife populations within the new national park. KW - Bush encroachment KW - Clearing formation KW - Grass flush KW - Savanna rangeland dynamics KW - Sprouting KW - Tree recruitment Y1 - 2015 U6 - https://doi.org/10.1111/avsc.12134 SN - 1402-2001 SN - 1654-109X VL - 18 IS - 2 SP - 297 EP - 310 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Coelho, Catarina A1 - Foti, Alessandro A1 - Hartmann, Tobias A1 - Santos-Silva, Teresa A1 - Leimkühler, Silke A1 - Romao, Maria Joao T1 - Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase JF - Nature chemical biology N2 - Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-angstrom resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-angstrom resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs. Y1 - 2015 U6 - https://doi.org/10.1038/NCHEMBIO.1895 SN - 1552-4450 SN - 1552-4469 VL - 11 IS - 10 SP - 779 EP - + PB - Nature Publ. Group CY - New York ER - TY - JOUR A1 - Contin, Andrea A1 - Frasca, Stefano A1 - Vivekananthan, Jeevanthi A1 - Leimkühler, Silke A1 - Wollenberger, Ursula A1 - Plumere, Nicolas A1 - Schuhmann, Wolfgang T1 - A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation. KW - pH responsive hydrogel KW - External stimuli KW - Biofuel cell KW - Self-powered biosensor KW - Solvation Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400621 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 4 SP - 938 EP - 944 PB - Wiley-VCH CY - Weinheim 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 - Corno, Gianluca A1 - Salka, Ivette A1 - Pohlmann, Kirsten A1 - Hall, Alex R. A1 - Grossart, Hans-Peter T1 - Interspecific interactions drive chitin and cellulose degradation by aquatic microorganisms JF - Aquatic microbial ecology : international journal N2 - Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems. KW - Aggregation KW - Flagellate grazing KW - Ecological interactions KW - Microbial carbon transfer KW - Polymer degradation KW - System ecology Y1 - 2015 U6 - https://doi.org/10.3354/ame01765 SN - 0948-3055 SN - 1616-1564 VL - 76 IS - 1 SP - 27 EP - + PB - Institute of Mathematical Statistics CY - Oldendorf Luhe ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Czesnick, Hjördis A1 - Lenhard, Michael T1 - Size Control in Plants-Lessons from Leaves and Flowers JF - Cold Spring Harbor perspectives in biology N2 - To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed. Y1 - 2015 U6 - https://doi.org/10.1101/cshperspect.a019190 SN - 1943-0264 VL - 7 IS - 8 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - JOUR A1 - Dammhahn, Melanie A1 - Rakotondramanana, Claude Fabienne A1 - Goodman, Steven M. T1 - Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar: stable isotopes reveal fine-grained niche differentiation among cryptic species JF - Journal of tropical ecology N2 - Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0% in delta N-15, i.e. two trophic levels, and 4.2% in delta C-13 with a community mean of 11.3% in delta N-15 and - 21.0% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4%, delta C-13: 1.0%) with a community mean of 8.0% delta N-15 and - 21.7% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa. KW - Chiroptera KW - community structure KW - congeneric species KW - ecological niches KW - migration KW - Neoromicia KW - Pipistrellus KW - Scotophilus KW - stable carbon KW - stable nitrogen Y1 - 2015 U6 - https://doi.org/10.1017/S0266467414000741 SN - 0266-4674 SN - 1469-7831 VL - 31 SP - 153 EP - 164 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Del Campo, Cristian A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Ignatova, Zoya T1 - Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005613 SN - 1553-7404 VL - 11 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Di Giacomo, Adrian S. A1 - Di Giacomo, Alejandro G. A1 - Kliger, Rafi A1 - Reboreda, Juan C. A1 - Tiedemann, Ralph A1 - Mahler, Bettina T1 - No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed Tyrant Alectrurus risora, an endangered grassland species JF - Bird conservation international N2 - The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Ibera wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (Phi(ST) = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations. Y1 - 2015 U6 - https://doi.org/10.1017/S0959270914000203 SN - 0959-2709 SN - 1474-0001 VL - 25 IS - 2 SP - 127 EP - 138 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Diekmann, Martin A1 - Müller, Josef A1 - Heinken, Thilo A1 - Dupre, Cecilia T1 - Survey and statistical analysis of plant reintroductions in Germany JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Aim - Plant reintroductions and other forms of targeted species translocations will in the future gain growing importance for nature conservation. In fragmented habitats, species reintroductions offer one of the most efficient tools for preserving or restoring plant diversity. In our study, we have compiled available data about plant reintroduction projects in Germany to answer the following questions: (1) What are the characteristics, habitat preferences and ecological strategies of species considered in plant reintroduction trials, and are these representative of the entire class of threatened species in Germany? (2) Is the judgment of the success or failure of plant reintroductions biased by the choice of species used in the experiments? (3) Do reintroduction efforts focus on those species for which Germany has a particularly high responsibility for conservation? Methods - Information about reintroduction projects in Germany were obtained from published and internet sources as well as unpublished reports. In our search we focused on single-species trials in the framework of scientific or conservation projects. For all threatened species included in our database, we compiled information on their systematics, life form, ecological strategies and habitat preferences. A list of all species being threatened nationally or regionally, comprising both reintroduced and not reintroduced species, served as a reference for statistical analysis. Results - The list of vascular plants used in conservation-oriented reintroductions consisted of 196 taxa. Species of families with large and conspicuous, mostly insect-pollinated flowers (for example, Orchidaceae) were over-represented among the reintroduced species compared to those threatened species not included in reintroduction trials. Species considered were also more often than expected found in semi-natural open habitats such as heathlands and grasslands. Notably, many projects focused on calcareous grasslands, characterized by dry, high-pH and infertile soils. In contrast, species of more near-natural vegetation (alpine and rocky formations, forests) were under-represented. About 25% of the species that were reintroduced are not threatened on the national scale. Out of 150 species for which Germany has a particularly high responsibility for conservation, only 14 (9.3%) were reintroduced. For only about 1/3 of all reintroduction attempts, success or failure were documented; whereas the success rate appears to be relatively low in nutrient-poor environments, trials with nutrient-demanding and competitive species were more successful. Conclusions - We conclude that conservation-oriented reintroduction attempts should focus more on species for which the country or a region has a particular high responsibility. Reintroductions, to a larger extent than at present, also need to consider the different chances of success in different habitat types and environments. KW - conservation responsibility KW - Ellenberg indicator values KW - Grime strategy KW - habitat type KW - life form KW - red list Y1 - 2015 SN - 0722-494X IS - 35 SP - 249 EP - 265 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen 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 - CHAP A1 - Donohue, Patrick A1 - Smith, Mychal Daijon A1 - Bröker, Nina Kristin A1 - Doering, Carolin A1 - Mattos, Carla A1 - Barbirz, Stefanie T1 - Multiple Solvent Crystal Structures of phage P22 tailspike protein: An analysis of binding site hot spots and surface hydration T2 - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology Y1 - 2015 SN - 0892-6638 SN - 1530-6860 VL - 29 PB - Federation of American Societies for Experimental Biology CY - Bethesda ER - TY - JOUR A1 - Dubovskaya, Olga P. A1 - Tang, Kam W. A1 - Gladyshev, Michail I. A1 - Kirillin, Georgiy A1 - Buseva, Zhanna A1 - Kasprzak, Peter A1 - Tolomeev, Aleksandr P. A1 - Grossart, Hans-Peter T1 - Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check JF - PLoS one N2 - Background Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. Objectives and Results We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d(-1), whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d(-1), which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Ecological implications Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0131431 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Eggers, Ute A1 - Arens, Michael A1 - Firla, Mario A1 - Wallschläger, Hans-Dieter T1 - To fledge or not to fledge: factors influencing the number of eggs and the eggs-to-fledglings rate in White Storks Ciconia ciconia in an agricultural environment JF - Journal of ornithology N2 - Numerous studies have explored the relationship between environmental factors and White Stork Ciconia ciconia reproduction, mainly expressing breeding success as the number of fledglings. Nonetheless, one of the most critical life-history stages in birds falls between egg-laying and fledging, and identifying the factors causing offspring mortality during this period provides valuable knowledge. We quantified the number of laid White Stork eggs and the proportion of eggs that turned into fledglings in an agriculture-dominated region in Eastern Germany. Moreover, we identified the factors among land cover, weather and arrival dates, which influenced these two reproductive measures the most, and analysed the monitored mortality causes. On average, four eggs were laid per nest, and 57.8 % of the eggs turned into fledglings. The number of eggs laid was best explained by the negative effect of the arrival date of the second stork, while the percentage of eggs that turned into fledglings was more dependent on weather: most important parameters were mean temperature in the fifth and seventh weeks after the assumed breeding start (i.e. around the assumed hatching date), and the number of consecutive days with precipitation when nestlings are assumed to be approximately 3 weeks old. In an agricultural environment, weather effects that potentially disturb food availability might be more important than effects directly affecting the survival of White Stork offspring. The most frequent observed mortality cause, nest fights, furthermore revealed the relevance of intraspecific competition in the study population. KW - Breeding success KW - Clutch size KW - Mortality causes KW - Weather impact KW - Land use KW - Arrival dates Y1 - 2015 U6 - https://doi.org/10.1007/s10336-015-1182-9 SN - 0021-8375 SN - 1439-0361 VL - 156 IS - 3 SP - 711 EP - 723 PB - Springer CY - New York ER - TY - JOUR A1 - Elsner, Julia A1 - Schibler, Joerg A1 - Hofreiter, Michael A1 - Schlumbaum, Angela T1 - Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland JF - Archaeological and anthropological sciences N2 - Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the-inevitable-heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions. KW - Ancient DNA KW - DNA preservation KW - Horse KW - Cave KW - Switzerland Y1 - 2015 U6 - https://doi.org/10.1007/s12520-014-0213-4 SN - 1866-9557 SN - 1866-9565 VL - 7 IS - 4 SP - 505 EP - 515 PB - Springer CY - Heidelberg ER - TY - GEN A1 - Elsner, Julia A1 - Schibler, Jörg A1 - Hofreiter, Michael A1 - Schlumbaum, Angela T1 - Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 727 KW - ancient DNA KW - DNA preservation KW - horse KW - cave KW - Switzerland Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429763 SN - 1866-8372 IS - 727 SP - 505 EP - 515 ER - TY - JOUR A1 - Engqvist, Martin K. M. A1 - Schmitz, Jessica A1 - Gertzmann, Anke A1 - Florian, Alexandra A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Maurino, Veronica G. T1 - GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.01003 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1042 EP - 1061 PB - American Society of Plant Physiologists CY - Rockville ER - TY - INPR A1 - Ensslin, Andreas A1 - Tschoepe, Okka A1 - Burkart, Michael A1 - Joshi, Jasmin Radha T1 - Fitness decline and adaptation to novel environments in ex situ plant collections: Current knowledge and future perspectives T2 - : an international journal N2 - The conservation of rare plant species as living collections in botanic gardens and arboreta has become an established tool in the battle against worldwide species' extinctions. However, the establishment of ex situ collections with a high conservation value requires a sound understanding of the evolutionary processes that may reduce the suitability of these collections for future reintroductions. Particularly, risks such as fitness decline of cultivated plants over time, trait shifts and loss of adaptation to the original habitat due to changes in selection regimes have rarely been addressed so far. Based on a literature review and results of our own project we show that genetic drift can lead to fitness decline in ex situ cultivated plants, but these drift effects strongly depend on the conditions and cultivation history in the ex situ facility. Furthermore, we provide evidence that shifts in traits such as germination and flowering time, and a decrease in stress tolerance to drought and competition can reduce the conservation value of ex situ collections. These threats associated with ex situ conditions require more attention by researchers, curators and conservationists. We need to increase knowledge on traits that are subject to novel selection pressures in ex situ collections, and to define population sizes that prevent genetic drift. Establishing conservation networks with replicated collections across gardens and balancing the seed contribution of mother plants to the next generation within a collection are suggested as first steps to increase the conservation value of ex situ plant collections. (C) 2015 Elsevier Ltd. All rights reserved. KW - Ex situ conservation KW - Botanic gardens KW - Artificial selection KW - Genetic drift KW - Adaptive evolution Y1 - 2015 U6 - https://doi.org/10.1016/j.biocon.2015.10.012 SN - 0006-3207 SN - 1873-2917 VL - 192 SP - 394 EP - 401 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Fettke, Jörg A1 - Fernie, Alisdair R. T1 - Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism JF - Trends in plant science N2 - In most plants, carbohydrates represent the major energy store as well as providing the building blocks for essential structural polymers. Although the major pathways for carbohydrate biosynthesis, degradation, and transport are well characterized, several key steps have only recently been discovered. In addition, several novel minor metabolic routes have been uncovered in the past few years. Here we review current studies of plant carbohydrate metabolism detailing the expanding compendium of functionally characterized transport proteins as well as our deeper comprehension of more minor and conditionally activated metabolic pathways. We additionally explore the pertinent questions that will allow us to enhance our understanding of the response of both major and minor carbohydrate fluxes to changing cellular circumstances. Y1 - 2015 U6 - https://doi.org/10.1016/j.tplants.2015.04.012 SN - 1360-1385 VL - 20 IS - 8 SP - 490 EP - 497 PB - Elsevier CY - London ER - TY - JOUR A1 - Frindte, Katharina A1 - Allgaier, Martin A1 - Grossart, Hans-Peter A1 - Eckert, Werner T1 - Microbial response to experimentally controlled redox transitions at the sediment water interface JF - PLoS one N2 - The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0143428 SN - 1932-6203 VL - 10 IS - 11 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Fuentes Taladriz, Paulina Andrea T1 - High-level production of the antimalarial drug precursor artemisinic acid in plastids and in vivo visualization of plastid-to-nucleus gene transfer Y1 - 2015 ER - TY - THES A1 - Fünfgeld, Maximilian T1 - Compartmentation of adenine nucleotide metabolism Y1 - 2015 ER - TY - JOUR A1 - Garapati, Prashanth A1 - Feil, Regina A1 - Lunn, John Edward A1 - Van Dijck, Patrick A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00917 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 1 SP - 379 EP - 390 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Garapati, Prashanth A1 - Xue, Gang-Ping A1 - Munne-Bosch, Sergi A1 - Balazadeh, Salma T1 - Transcription Factor ATAF1 in Arabidopsis Promotes Senescence by Direct Regulation of Key Chloroplast Maintenance and Senescence Transcriptional Cascades JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Senescence represents a fundamental process of late leaf development. Transcription factors (TFs) play an important role for expression reprogramming during senescence; however, the gene regulatory networks through which they exert their functions, and their physiological integration, are still largely unknown. Here, we identify the Arabidopsis (Arabidopsis thaliana) abscisic acid (ABA)- and hydrogen peroxide-activated TF Arabidopsis thaliana ACTIVATING FACTOR1 (ATAF1) as a novel upstream regulator of senescence. ATAF1 executes its physiological role by affecting both key chloroplast maintenance and senescence-promoting TFs, namely GOLDEN2-LIKE1 (GLK1) and ORESARA1 (ARABIDOPSIS NAC092), respectively. Notably, while ATAF1 activates ORESARA1, it represses GLK1 expression by directly binding to their promoters, thereby generating a transcriptional output that shifts the physiological balance toward the progression of senescence. We furthermore demonstrate a key role of ATAF1 for ABA- and hydrogen peroxide-induced senescence, in accordance with a direct regulatory effect on ABA homeostasis genes, including NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 involved in ABA biosynthesis and ABC TRANSPORTER G FAMILY MEMBER40, encoding an ABA transport protein. Thus, ATAF1 serves as a core transcriptional activator of senescence by coupling stress-related signaling with photosynthesis- and senescence-related transcriptional cascades. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00567 SN - 0032-0889 SN - 1532-2548 VL - 168 IS - 3 SP - 1122 EP - + PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Garcia, Sarahi L. A1 - Buck, Moritz A1 - McMahon, Katherine D. A1 - Grossart, Hans-Peter A1 - Eiler, Alexander A1 - Warnecke, Falk T1 - Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community JF - Molecular ecology N2 - Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature. KW - community KW - cultures KW - interactions KW - metagenomics KW - populations Y1 - 2015 U6 - https://doi.org/10.1111/mec.13319 SN - 0962-1083 SN - 1365-294X VL - 24 IS - 17 SP - 4449 EP - 4459 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Geissler, Peter A1 - Poyarkov, Nikolay A. A1 - Grismer, Lee A1 - Nguyen, Truong Q. A1 - An, Hang T. A1 - Neang, Thy A1 - Kupfer, Alexander A1 - Ziegler, Thomas A1 - Böhme, Wolfgang A1 - Müller, Hendrik T1 - New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969 JF - Organisms, diversity & evolution : official journal of the Gesellschaft für Biologische Systematik N2 - Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided. KW - Biogeography KW - Caecilians KW - Indochina KW - Cambodia KW - Laos KW - Thailand KW - Vietnam KW - mtDNA KW - Barcoding KW - COI KW - cyt b KW - Phylogeny KW - Integrative taxonomy Y1 - 2015 U6 - https://doi.org/10.1007/s13127-014-0190-6 SN - 1439-6092 SN - 1618-1077 VL - 15 IS - 1 SP - 143 EP - 174 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Germonpre, Mietje A1 - Sablin, Mikhail V. A1 - Laznickova-Galetova, Martina A1 - Despres, Viviane A1 - Stevens, Rhiannon E. A1 - Stiller, Mathias A1 - Hofreiter, Michael T1 - Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014) JF - Journal of archaeological science N2 - This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary. (C) 2014 Elsevier Ltd. All rights reserved. KW - Canid morphotype KW - Dog KW - Domestication KW - Palaeolithic KW - Pleistocene KW - Wolf Y1 - 2015 U6 - https://doi.org/10.1016/j.jas.2014.11.035 SN - 0305-4403 SN - 1095-9238 VL - 54 SP - 210 EP - 216 PB - Elsevier CY - London ER - TY - JOUR A1 - Geyer, Juliane A1 - Strixner, Lena A1 - Kreft, Stefan A1 - Jeltsch, Florian A1 - Ibisch, Pierre L. T1 - Adapting conservation to climate change: a case study on feasibility and implementation in Brandenburg, Germany JF - Regional environmental change N2 - Conservation actions need to account for global climate change and adapt to it. The body of the literature on adaptation options is growing rapidly, but their feasibility and current state of implementation are rarely assessed. We discussed the practicability of adaptation options with conservation managers analysing three fields of action: reducing the vulnerability of conservation management, reducing the vulnerability of conservation targets (i.e. biodiversity) and climate change mitigation. For all options, feasibility, current state of implementation and existing obstacles to implementation were analysed, using the Federal State of Brandenburg, Germany, as a case study. Practitioners considered a large number of options useful, most of which have already been implemented at least in part. Those options considered broadly implemented resemble mainly conventional measures of conservation without direct relation to climate change. Managers are facing several obstacles for adapting to climate change, including political reluctance to change, financial and staff shortages in conservation administrations and conflictive EU funding schemes in agriculture. A certain reluctance to act, due to the high degree of uncertainty with regard to climate change scenarios and impacts, is widespread. A lack of knowledge of appropriate methods such as adaptive management often inhibits the implementation of adaptation options in the field of planning and management. Based on the findings for Brandenburg, we generally conclude that it is necessary to focus in particular on options that help to reduce vulnerability of conservation management itself, i.e. those that enhance management effectiveness. For instance, adaptive and proactive risk management can be applied as a no-regrets option, independently from specific climate change scenarios or impacts, strengthening action under uncertainty. KW - Climate change KW - Adaptation options KW - Nature conservation management KW - Vulnerability Y1 - 2015 U6 - https://doi.org/10.1007/s10113-014-0609-9 SN - 1436-3798 SN - 1436-378X VL - 15 IS - 1 SP - 139 EP - 153 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Glud, Ronnie N. A1 - Grossart, Hans-Peter A1 - Larsen, Morten A1 - Tang, Kam W. A1 - Arendt, Kristine E. A1 - Rysgaard, Soren A1 - Thamdrup, Bo A1 - Gissel Nielsen, Torkel T1 - Copepod carcasses as microbial hot spots for pelagic denitrification JF - Limnology and oceanography N2 - Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O-2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O-2 level. The extent of anoxia gradually expanded with decreasing ambient O-2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes (nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in (15)NO3-amended seawater demonstrated denitrification, of which on average 34%+/- 17% (n=28) was sustained by nitrification. However, the activity was highly variable and was strongly dependent on the ambient O-2 levels. While denitrification was present even at air-saturation (302 mol L-1), the average carcass specific activity increased several orders of magnitude to approximate to 1 nmol d(-1) at 20% air-saturation (55 mol O-2 L-1) at an ambient temperature of 7 degrees C. Sinking carcasses of C. finmarchicus therefore represent hotspots of pelagic denitrification, but the quantitative importance as a sink for bioavailable nitrogen is strongly dependent on the ambient O-2 level. The importance of carcass associated denitrification could be highly significant in O-2 depleted environments such as Oxygen Minimum Zones (OMZ). Y1 - 2015 U6 - https://doi.org/10.1002/lno.10149 SN - 0024-3590 SN - 1939-5590 VL - 60 IS - 6 SP - 2026 EP - 2036 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Gorochowski, Thomas E. A1 - Ignatova, Zoya A1 - Bovenberg, Roel A. L. A1 - Roubos, Johannes A. T1 - Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate JF - Nucleic acids research N2 - Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. Y1 - 2015 U6 - https://doi.org/10.1093/nar/gkv199 SN - 0305-1048 SN - 1362-4962 VL - 43 IS - 6 SP - 3022 EP - 3032 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Groeneveld, Jürgen A1 - Johst, Karin A1 - Kawaguchi, So A1 - Meyer, Bettina A1 - Teschke, Mathias A1 - Grimm, Volker T1 - How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - The Southern Ocean ecosystem is characterized by extreme seasonal changes in environmental factors such as day length, sea ice extent and food availability. The key species Antarctic krill (Euphausia superba) has evolved metabolic and behavioural seasonal rhythms to cope with these seasonal changes. We investigate the switch between a physiological less active and active period for adult krill, a rhythm which seems to be controlled by internal biological clocks. These biological clocks can be synchronized by environmental triggers such as day length and food availability. They have evolved for particular environmental regimes to synchronize predictable seasonal environmental changes with important life cycle functions of the species. In a changing environment the time when krill is metabolically active and the time of peak food availability may not overlap if krill's seasonal activity is solely determined by photoperiod (day length). This is especially true for the Atlantic sector of the Southern Ocean where the spatio-temporal ice cover dynamics are changing substantially with rising average temperatures. We developed an individual-based model for krill to explore the impact of photoperiod and food availability on the growth and demographics of krill. We simulated dynamics of local krill populations (with no movement of krill assumed) along a south-north gradient for different triggers of metabolic activity and different levels of food availability below the ice. We also observed the fate of larval krill which cannot switch to low metabolism and therefore are likely to overwinter under ice. Krill could only occupy the southern end of the gradient, where algae bloom only lasts for a short time, when alternative food supply under the ice was high and metabolic activity was triggered by photoperiod. The northern distribution was limited by lack of overwintering habitat for krill larvae due to short duration of sea ice cover even for high food content under the ice. The variability of the krill's length-frequency distributions varied for different triggers of metabolic activity, but did not depend on the sea ice extent. Our findings suggest a southward shift of krill populations due to reduction in the spatial sea ice extent, which is consistent with field observations. Overall, our results highlight the importance of the explicit consideration of spatio-temporal sea ice dynamics especially for larval krill together with temporal synchronization through internal clocks, triggered by environmental factors (photoperiod and food) in adult krill for the population modelling of krill. (C) 2015 Elsevier B.V. All rights reserved. KW - Dynamic energy budget theory KW - Individual based model KW - Southern Ocean KW - Sea ice KW - Climate change KW - Marine ecology Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.009 SN - 0304-3800 SN - 1872-7026 VL - 303 SP - 78 EP - 86 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Grune, Jana T1 - Effects of a novel non-steroidal mineralocorticoid receptor antagonist on cardiac hypertrophy Y1 - 2015 ER - TY - JOUR A1 - Gräf, Ralph A1 - Batsios, Petros A1 - Meyer, Irene T1 - Evolution of centrosomes and the nuclear lamina: Amoebozoan assets JF - European journal of cell biology N2 - The current eukaryotic tree of life groups most eukaryotes into one of five supergroups, the Opisthokonta, Amoebozoa, Archaeplastida, Excavata and SAR (Stramenopile, Alveolata, Rhizaria). Molecular and comparative morphological analyses revealed that the last eukaryotic common ancestor (LECA) already contained a rather sophisticated equipment of organelles including a mitochondrion, an endomembrane system, a nucleus with a lamina, a microtubule-organizing center (MTOC), and a flagellar apparatus. Recent studies of MTOCs, basal bodies/centrioles, and nuclear envelope organization of organisms in different supergroups have clarified our picture of how the nucleus and MTOCs co-evolved from LECA to extant eukaryotes. In this review we summarize these findings with special emphasis on valuable contributions of research on a lamin-like protein, nuclear envelope proteins, and the MTOC in the amoebozoan model organism Dictyostelium discoideum. (C) 2015 Elsevier GmbH. All rights reserved. KW - LINC complex KW - Sun1 KW - Nuclear lamina KW - Lamin KW - Nuclear envelope KW - Centrosome KW - Basal body KW - Centriole KW - LEM-domain Y1 - 2015 U6 - https://doi.org/10.1016/j.ejcb.2015.04.004 SN - 0171-9335 SN - 1618-1298 VL - 94 IS - 6 SP - 249 EP - 256 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Guha, S. A1 - Warsinke, Axel A1 - Tientcheu, Charles Merlin A1 - Schmalz, K. A1 - Meliani, C. A1 - Wenger, Ch. T1 - Label free sensing of creatinine using a 6 GHz CMOS near-field dielectric immunosensor JF - The analyst : the analytical journal of the Royal Society of Chemistry N2 - In this work we present a CMOS high frequency direct immunosensor operating at 6 GHz (C-band) for label free determination of creatinine. The sensor is fabricated in standard 0.13 mu m SiGe:C BiCMOS process. The report also demonstrates the ability to immobilize creatinine molecules on a Si3N4 passivation layer of the standard BiCMOS/CMOS process, therefore, evading any further need of cumbersome post processing of the fabricated sensor chip. The sensor is based on capacitive detection of the amount of non-creatinine bound antibodies binding to an immobilized creatinine layer on the passivated sensor. The chip bound antibody amount in turn corresponds indirectly to the creatinine concentration used in the incubation phase. The determination of creatinine in the concentration range of 0.88-880 mu M is successfully demonstrated in this work. A sensitivity of 35 MHz/10 fold increase in creatinine concentration (during incubation) at the centre frequency of 6 GHz is gained by the immunosensor. The results are compared with a standard optical measurement technique and the dynamic range and sensitivity is of the order of the established optical indication technique. The C-band immunosensor chip comprising an area of 0.3 mm(2) reduces the sensing area considerably, therefore, requiring a sample volume as low as 2 mu l. The small analyte sample volume and label free approach also reduce the experimental costs in addition to the low fabrication costs offered by the batch fabrication technique of CMOS/BiCMOS process. Y1 - 2015 U6 - https://doi.org/10.1039/c4an02194k SN - 0003-2654 SN - 1364-5528 VL - 140 IS - 9 SP - 3019 EP - 3027 PB - Royal Society of Chemistry CY - Cambridge ER - TY - INPR A1 - Hagelberg, Erika A1 - Hofreiter, Michael A1 - Keyser, Christine T1 - Ancient DNA: the first three decades T2 - Philosophical transactions of the Royal Society of London : B, Biological sciences KW - ancient DNA KW - human evolutionary genetics KW - palaeogenomics Y1 - 2015 U6 - https://doi.org/10.1098/rstb.2013.0371 SN - 0962-8436 SN - 1471-2970 VL - 370 IS - 1660 PB - Royal Society CY - London 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 - Hahn, Marc Benjamin A1 - Solomun, Tihomir A1 - Wellhausen, Robert A1 - Hermann, Sabrina A1 - Seitz, Harald A1 - Meyer, Susann A1 - Kunte, Hans-Jörg A1 - Zeman, Johannes A1 - Uhlig, Frank A1 - Smiatek, Jens A1 - Sturm, Heinz T1 - Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry N2 - Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-S-protein (G5P) to a single-stranded DNA (dT(25)). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonudeotide, which has important consequences for osmotic regulation mechanisms. Y1 - 2015 U6 - https://doi.org/10.1021/acs.jpcb.5b09506 SN - 1520-6106 VL - 119 IS - 49 SP - 15212 EP - 15220 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hamalainen, Anni A1 - Dammhahn, Melanie A1 - Aujard, Fabienne A1 - Kraus, Cornelia T1 - Losing grip: Senescent decline in physical strength in a small-bodied primate in captivity and in the wild JF - Experimental gerontology N2 - Muscle strength reflects physical functioning, declines at old age and predicts health and survival in humans and laboratory animals. Age-associated muscle deterioration causes loss of strength and may impair fitness of wild animals. However, the effects of age and life-history characteristics on muscle strength in wild animals are unknown. We investigated environment-and sex-specific patterns of physical functioning by measuring grip strength in wild and captive gray mouse lemurs. We expected more pronounced strength senescence in captivity due to condition-dependent, extrinsic mortality found in nature. Males were predicted to be stronger but potentially experience more severe senescence than females as predicted by life history theory. We found similar senescent declines in captive males and females as well as wild females, whereas wild males showed little decline, presumably due to their early mortality. Captive animals were generally weaker and showed earlier declines than wild animals. Unexpectedly, females tended to be stronger than males, especially in the reproductive season. Universal intrinsic mechanisms (e. g. sarcopenia) likely cause the similar patterns of strength loss across settings. The female advantage in muscle strength merits further study; it may follow higher reproductive investment by males, or be an adaptation associated with female social dominance. KW - Functional aging KW - Grip strength KW - Microcebus murinus KW - Natural population KW - Sarcopenia KW - Sex difference Y1 - 2015 U6 - https://doi.org/10.1016/j.exger.2014.11.017 SN - 0531-5565 SN - 1873-6815 VL - 61 SP - 54 EP - 61 PB - Elsevier CY - Oxford ER - TY - CHAP A1 - Hanke-Gogokhia, Christin A1 - Frederick, Jeanne M. A1 - Zhang, Houbin A1 - Baehr, Wolfgang T1 - ARL3 regulates transport of prenylated and acylated proteins to photoreceptor outer segment in mouse retina T2 - Investigative ophthalmology & visual science Y1 - 2015 SN - 0146-0404 SN - 1552-5783 VL - 56 IS - 7 PB - Association for Research in Vision and Opthalmology CY - Rockville ER - TY - GEN A1 - Hartmann, Stefanie A1 - Hasenkamp, Natascha A1 - Mayer, Jens A1 - Michaux, Johan A1 - Morand, Serge A1 - Mazzoni, Camila J. A1 - Roca, Alfred L. A1 - Greenwood, Alex D. T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1329 KW - murine leukemia virus KW - endogenous retrovirus KW - Xpr1 KW - XMRV KW - genomic evolution KW - Markov cluster algorithm Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431200 SN - 1866-8372 IS - 1329 ER - TY - JOUR A1 - Hartmann, Stefanie A1 - Hasenkamp, Natascha A1 - Mayer, Jens A1 - Michaux, Johan A1 - Morand, Serge A1 - Mazzoni, Camila J. A1 - Roca, Alfred L. A1 - Greenwood, Alex D. T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse JF - BMC genomics N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection. KW - Murine leukemia virus KW - Endogenous retrovirus KW - Xpr1 KW - XMRV KW - Genomic evolution KW - Markov cluster algorithm Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1766-z SN - 1471-2164 VL - 16 PB - BioMed Central CY - London 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 - Heinze, Johannes A1 - Bergmann, Joana A1 - Rillig, Matthias C. A1 - Joshi, Jasmin Radha T1 - Negative biotic soil-effects enhance biodiversity by restricting potentially dominant plant species in grasslands JF - Perspectives in plant ecology, evolution and systematics N2 - Interactions between soil microorganisms and plants can play a vital role for plant fitness and therefore also for plant community composition and biodiversity. However, little is known about how biotic plant soil interactions influence the local dominance and abundance of plant species and whether specific taxonomic or functional groups of plants are differentially affected by such biotic soil-effects. In two greenhouse experiments, we tested the biotic soil-effects of 33 grassland species differing in individual size and local abundance. We hypothesized that large plants that are not locally dominant (despite their size-related competitive advantage enabling them to potentially outshade competitors) are most strongly limited by negative biotic soil-effects. We sampled soils at the opposite ends of a gradient in land-use intensity in temperate grasslands to account for putative modulating effects of land-use intensity on biotic soil-effects. As hypothesized, large, but non-dominant species (especially grasses) experienced more negative biotic soil-effects compared with small and abundant plant species. Land-use intensity had contrasting effects on grasses and herbs resulting in more negative biotic soil-effects for grasses in less intensively managed grasslands. We conclude that biotic soil-effects contribute to the control of potentially dominant plants and hence enable species coexistence and biodiversity especially in species-rich less intensively managed grasslands. KW - Coexistence mechanisms KW - Plant soil feedbacks KW - Individual size KW - Local plant-abundance KW - Grassland diversity KW - Land-use intensity Y1 - 2015 U6 - https://doi.org/10.1016/j.ppees.2015.03.002 SN - 1433-8319 VL - 17 IS - 3 SP - 227 EP - 235 PB - Elsevier CY - Jena 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 - Henry, Brian D. A1 - Neill, Daniel R. A1 - Becker, Katrin Anne A1 - Gore, Suzanna A1 - Bricio-Moreno, Laura A1 - Ziobro, Regan A1 - Edwards, Michael J. A1 - Muehlemann, Kathrin A1 - Steinmann, Joerg A1 - Kleuser, Burkhard A1 - Japtok, Lukasz A1 - Luginbuehl, Miriam A1 - Wolfmeier, Heidi A1 - Scherag, Andre A1 - Gulbins, Erich A1 - Kadioglu, Aras A1 - Draeger, Annette A1 - Babiychuk, Eduard B. T1 - Engineered liposomes sequester bacterial exotoxins and protect from severe invasive infections in mice JF - Nature biotechnology : the science and business of biotechnology N2 - Gram-positive bacterial pathogens that secrete cytotoxic pore-forming toxins, such as Staphylococcus aureus and Streptococcus pneumoniae, cause a substantial burden of disease. Inspired by the principles that govern natural toxin-host interactions, we have engineered artificial liposomes that are tailored to effectively compete with host cells for toxin binding. Liposome-bound toxins are unable to lyse mammalian cells in vitro. We use these artificial liposomes as decoy targets to sequester bacterial toxins that are produced during active infection in vivo. Administration of artificial liposomes within 10 h after infection rescues mice from septicemia caused by S. aureus and S. pneumoniae, whereas untreated mice die within 24-33 h. Furthermore, liposomes protect mice against invasive pneumococcal pneumonia. Composed exclusively of naturally occurring lipids, tailored liposomes are not bactericidal and could be used therapeutically either alone or in conjunction with antibiotics to combat bacterial infections and to minimize toxin-induced tissue damage that occurs during bacterial clearance. Y1 - 2015 U6 - https://doi.org/10.1038/nbt.3037 SN - 1087-0156 SN - 1546-1696 VL - 33 IS - 1 SP - 81 EP - U295 PB - Nature Publ. Group CY - New York ER - TY - THES A1 - Herde, Antje T1 - Individual differences and seasonal variation in behaviour BT - Studies on common voles Y1 - 2015 ER - TY - JOUR A1 - Hermanussen, Michael A1 - Scheffler, Christiane A1 - Groth, Detlef A1 - Aßmann, Christian T1 - Height and skeletal morphology in relation to modern life style JF - Journal of physiological anthropology N2 - Height and skeletal morphology strongly relate to life style. Parallel to the decrease in physical activity and locomotion, modern people are slimmer in skeletal proportions. In German children and adolescents, elbow breadth and particularly relative pelvic breadth (50th centile of bicristal distance divided by body height) have significantly decreased in recent years. Even more evident than the changes in pelvic morphology are the rapid changes in body height in most modern countries since the end-19th and particularly since the mid-20th century. Modern Japanese mature earlier; the age at take-off (ATO, the age at which the adolescent growth spurt starts) decreases, and they are taller at all ages. Preece-Baines modelling of six national samples of Japanese children and adolescents, surveyed between 1955 and 2000, shows that this gain in height is largely an adolescent trend, whereas height at take-off (HTO) increased by less than 3 cm since 1955; adolescent growth (height gain between ATO and adult age) increased by 6 cm. The effect of globalization on the modern post-war Japanese society ("community effect in height") on adolescent growth is discussed. KW - Pelvic breadth KW - Elbow breadth KW - Growth KW - Adult height KW - Community effect in height Y1 - 2015 U6 - https://doi.org/10.1186/s40101-015-0080-4 SN - 1880-6805 VL - 34 PB - BioMed Central CY - London ER - TY - JOUR A1 - Herter, Susanne A1 - McKenna, Shane M. A1 - Frazer, Andrew R. A1 - Leimkühler, Silke A1 - Carnell, Andrew J. A1 - Turner, Nicholas J. T1 - Galactose Oxidase Variants for the Oxidation of Amino Alcohols in Enzyme Cascade Synthesis JF - ChemCatChem : heterogeneous & homogeneous & bio- & nano-catalysis ; a journal of ChemPubSoc Europe N2 - The use of selected engineered galactose oxidase (GOase) variants for the oxidation of amino alcohols to aldehydes under mild conditions in aqueous systems is reported. GOase variant F-2 catalyses the regioselective oxidation of N-carbobenzyloxy (Cbz)-protected 3-amino-1,2-propanediol to the corresponding -hydroxyaldehyde which was then used in an aldolase reaction. Another variant, M3-5, was found to exhibit activity towards free and N-Cbz-protected aliphatic and aromatic amino alcohols allowing the synthesis of lactams such as 3,4-dihydronaphthalen-1(2H)-one, 2-pyrrolidone and valerolactam in one-pot tandem reactions with xanthine dehydrogenase (XDH) or aldehyde oxidase (PaoABC). KW - aldehyde oxidase KW - amino alcohols KW - cascade reactions KW - enzyme catalysis KW - lactams Y1 - 2015 U6 - https://doi.org/10.1002/cctc.201500218 SN - 1867-3880 SN - 1867-3899 VL - 7 IS - 15 SP - 2313 EP - 2317 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hess, Anne-Katrin A1 - Saffert, Paul A1 - Liebeton, Klaus A1 - Ignatova, Zoya T1 - Optimization of Translation Profiles Enhances Protein Expression and Solubility JF - PLoS one N2 - mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5'-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0127039 SN - 1932-6203 VL - 10 IS - 5 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Heyneke, Elmien T1 - The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism Y1 - 2015 ER - TY - JOUR A1 - Hixson, Stefanie M. A1 - Sharma, Bhanu A1 - Kainz, Martin J. A1 - Wacker, Alexander A1 - Arts, Michael T. T1 - Production, distribution, and abundance of long-chain omega-3 polyunsaturated fatty acids: a fundamental dichotomy between freshwater and terrestrial ecosystems JF - Environmental reviews = Dossiers environnement N2 - Long-chain polyunsaturated fatty acids (LC-PUFA) are critical for the health of aquatic and terrestrial organisms; therefore, understanding the production, distribution, and abundance of these compounds is imperative. Although the dynamics of LC-PUFA production and distribution in aquatic environments has been well documented, a systematic and comprehensive comparison to LC-PUFA in terrestrial environments has not been rigorously investigated. Here we use a data synthesis approach to compare and contrast fatty acid profiles of 369 aquatic and terrestrial organisms. Habitat and trophic level were interacting factors that determined the proportion of individual omega-3 (n-3) or omega-6 (n-6) PUFA in aquatic and terrestrial organisms. Higher total n-3 content compared with n-6 PUFA and a strong prevalence of the n-3 PUFA eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) characterized aquatic versus terrestrial organisms. Conversely, terrestrial organisms had higher linoleic acid (LNA) and alpha-linolenic acid (ALA) contents than aquatic organisms; however, the ratio of ALA: LNA was higher in aquatic organisms. The EPA + DHA content was higher in aquatic animals than terrestrial organisms, and increased from algae to invertebrates to vertebrates in the aquatic environment. An analysis of covariance (ANCOVA) revealed that fatty acid composition was highly dependent on the interaction between habitat and trophic level. We conclude that freshwater ecosystems provide an essential service through the production of n-3 LC-PUFA that are required to maintain the health of terrestrial organisms including humans. KW - aquatic ecosystems KW - conservation KW - eicosapentaenoic acid KW - docosahexaenoic acid KW - food webs Y1 - 2015 U6 - https://doi.org/10.1139/er-2015-0029 SN - 1208-6053 SN - 1181-8700 VL - 23 IS - 4 SP - 414 EP - 424 PB - NRC Research Press CY - Ottawa ER - TY - CHAP A1 - Hofreiter, Michael A1 - Barlow, Axel A1 - Paijmans, Johanna L. A. A1 - Westbury, Michael V. T1 - Genomic analyses from highly degraded DNA T2 - Genome Y1 - 2015 SN - 0831-2796 SN - 1480-3321 VL - 58 IS - 5 SP - 228 EP - 228 PB - NRC Research Press CY - Ottawa ER - TY - JOUR A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. A1 - Goodchild, Helen A1 - Speller, Camilla F. A1 - Barlow, Axel A1 - González-Fortes, Gloria M. A1 - Thomas, Jessica A. A1 - Ludwig, Arne A1 - Collins, Matthew J. T1 - The future of ancient DNA: Technical advances and conceptual shifts JF - Bioessays : ideas that push the boundaries N2 - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. KW - ancient DNA KW - hybridisation capture KW - multi-locus data KW - next generation sequencing (NGS) KW - palaeogenomics KW - population genomics Y1 - 2015 U6 - https://doi.org/10.1002/bies.201400160 SN - 0265-9247 SN - 1521-1878 VL - 37 IS - 3 SP - 284 EP - 293 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Horn, Sebastian A1 - Hempel, Stefan A1 - Ristow, Michael A1 - Rillig, Matthias C. A1 - Kowarik, Ingo A1 - Caruso, Tancredi T1 - Plant community assembly at small scales: Spatial vs. environmental factors in a European grassland JF - Acta oecologica : international journal of ecology N2 - Dispersal limitation and environmental conditions are crucial drivers of plant species distribution and establishment. As these factors operate at different spatial scales, we asked: Do the environmental factors known to determine community assembly at broad scales operate at fine scales (few meters)? How much do these factors account for community variation at fine scales? In which way do biotic and abiotic interactions drive changes in species composition? We surveyed the plant community within a dry grassland along a very steep gradient of soil characteristics like pH and nutrients. We used a spatially explicit sampling design, based on three replicated macroplots of 15 x 15, 12 x 12 and 12 x 12 m in extent. Soil samples were taken to quantify several soil properties (carbon, nitrogen, plant available phosphorus, pH, water content and dehydrogenase activity as a proxy for overall microbial activity). We performed variance partitioning to assess the effect of these variables on plant composition and statistically controlled for spatial autocorrelation via eigenvector mapping. We also applied null model analysis to test for non-random patterns in species co-occurrence using randomization schemes that account for patterns expected under species interactions. At a fine spatial scale, environmental factors explained 18% of variation when controlling for spatial autocorrelation in the distribution of plant species, whereas purely spatial processes accounted for 14% variation. Null model analysis showed that species spatially segregated in a non-random way and these spatial patterns could be due to a combination of environmental filtering and biotic interactions. Our grassland study suggests that environmental factors found to be directly relevant in broad scale studies are present also at small scales, but are supplemented by spatial processes and more direct interactions like competition. (C) 2015 Elsevier Masson SAS. All rights reserved. KW - Assembly pattern KW - Dispersal limitation KW - Festuca brevipila KW - Niche partitioning KW - Null model KW - Plant community ecology KW - Variance partitioning Y1 - 2015 U6 - https://doi.org/10.1016/j.actao.2015.01.004 SN - 1146-609X SN - 1873-6238 VL - 63 SP - 56 EP - 62 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Hu, Chenlin A1 - Völler, Ginka A1 - Sussmuth, Roderich A1 - Dittmann-Thünemann, Elke A1 - Kehr, Jan-Christoph T1 - Functional assessment of mycosporine-like amino acids in Microcystis aeruginosa strain PCC 7806 JF - Environmental microbiology N2 - The biological role of the widespread mycosporine-like amino acids (MAAs) in cyanobacteria is under debate. Here, we have constructed and characterized two mutants impaired in MAA biosynthesis in the bloom-forming cyanobacterium Microcystis aeruginosaPCC 7806. We could identify shinorine as the sole MAA type of the strain, which is exclusively located in the extracellular matrix. Bioinformatic studies as wells as polymerase chain reaction screening revealed that the ability to produce MAAs is sporadically distributed within the genus. Growth experiments and reactive oxygen species quantification with wild-type and mutant strains did not support a role of shinorine in protection against UV or other stress conditions in M.aeruginosaPCC 7806. The shinorine content per dry weight of cells as well as transcription of the mys gene cluster was not significantly elevated in response to UV-A, UV-B or any other stress condition tested. Remarkably, both mutants exhibited pronounced morphological changes compared with the wild type. We observed an increased accumulation and an enhanced hydrophobicity of the extracellular matrix. Our study suggests that MAAs in Microcystis play a negligible role in protection against UV radiation but might be a strain-specific trait involved in extracellular matrix formation and cell-cell interaction. Y1 - 2015 U6 - https://doi.org/10.1111/1462-2920.12577 SN - 1462-2912 SN - 1462-2920 VL - 17 IS - 5 SP - 1548 EP - 1559 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hönicke, Christiane A1 - Bliss, Peter A1 - Moritz, Robin F. A. T1 - Effect of density on traffic and velocity on trunk trails of Formica pratensis JF - The science of nature N2 - The allocation of large numbers of workers facilitates the swift intake of locally available resources which is essential for ant colony survival. To organise the traffic between nest and food source, the black-meadow ant Formica pratensis establishes permanent trunk trails, which are maintained by the ants. To unravel the ant organisation and potential traffic rules on these trails, we analysed velocity and lane segregation under various densities by experimentally changing feeding regimes. Even under the highest ant densities achieved, we never observed any traffic jams. On the contrary, velocity increased after supplementary feeding despite an enhanced density. Furthermore, inbound ants returning to the nest had a higher velocity than those leaving the colony. Whilst at low and medium density the ants used the centre of the trail, they used the full width of the trail at high density. Outbound ants also showed some degree of lane segregation which contributes to traffic organisation. KW - Density KW - Trunk trail KW - Traffic KW - Lateralization KW - Formica pratensis Y1 - 2015 U6 - https://doi.org/10.1007/s00114-015-1267-6 SN - 0028-1042 SN - 1432-1904 VL - 102 IS - 3-4 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Hüttl, Christine A1 - Hettrich, Cornelia A1 - Riedel, Melanie A1 - Henklein, Petra A1 - Rawel, Harshadrai Manilal A1 - Bier, Frank Fabian T1 - Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition JF - Chemical biology & drug design N2 - A straightforward synthesis strategy to multimerize a peptide mimotopes for antibody B13-DE1 recognition is described based on lysine dendrons as multivalent scaffolds. Lysine dendrons that possess N-terminal alkyne residues at the periphery were quantitative functionalized with azido peptides using click chemistry. The solid-phase peptide synthesis (SPPS) allows preparing the peptide dendron in high purity and establishing the possibility of automation. The presented peptide dendron is a promising candidate as multivalent ligand and was used for antibody B13-DE1 recognition. The binding affinity increases with higher dendron generation without loss of specificity. The analysis of biospecific interaction between the synthesized peptide dendron and the antibody was done via surface plasmon resonance (SPR) technique. The presented results show a promising tool for investigations of antigen-antibody reactions. KW - click chemistry KW - lysine dendron KW - peptide mimotopes KW - solid-phase peptide synthesis KW - surface plasmon resonance Y1 - 2015 U6 - https://doi.org/10.1111/cbdd.12444 SN - 1747-0277 SN - 1747-0285 VL - 85 IS - 5 SP - 565 EP - 573 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Imholt, Christian A1 - Reil, Daniela A1 - Eccard, Jana A1 - Jacob, Daniela A1 - Hempelmann, Nils A1 - Jacob, Jens T1 - Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus) JF - Pest management science N2 - BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry KW - climate change KW - population dynamics KW - bank vole KW - regression tree KW - outbreak Y1 - 2015 U6 - https://doi.org/10.1002/ps.3838 SN - 1526-498X SN - 1526-4998 VL - 71 IS - 2 SP - 166 EP - 172 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Ionescu, Danny A1 - Bizic-Ionescu, Mina A1 - Khalili, Arzhang A1 - Malekmohammadi, Reza A1 - Morad, Reza Mohammad A1 - de Beer, Dirk A1 - Grossart, Hans-Peter T1 - A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect JF - Scientific reports N2 - Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods. Y1 - 2015 U6 - https://doi.org/10.1038/srep14706 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Ishida, Seiji A1 - Nozaki, Daiki A1 - Grossart, Hans-Peter A1 - Kagami, Maiko T1 - Novel basal, fungal lineages from freshwater phytoplankton and lake samples JF - Environmental microbiology reports N2 - Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems. Y1 - 2015 U6 - https://doi.org/10.1111/1758-2229.12268 SN - 1758-2229 VL - 7 IS - 3 SP - 435 EP - 441 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - 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 - THES A1 - Jin, Chenyu T1 - Theoretical and experimental study of capillary effect on melting Y1 - 2015 ER - TY - JOUR A1 - Johnson, Kim L. A1 - Ramm, Sascha A1 - Kappel, Christian A1 - Ward, Sally A1 - Leyser, Ottoline A1 - Sakamoto, Tomoaki A1 - Kurata, Tetsuya A1 - Bevan, Michael W. A1 - Lenhard, Michael T1 - The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis JF - PLoS one N2 - Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0131103 SN - 1932-6203 VL - 10 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Mueller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians JF - Nature Communications N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms9912 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER - TY - GEN A1 - Jones, Eppie R. A1 - González-Fortes, Gloria M. A1 - Connell, Sarah A1 - Siska, Veronika A1 - Eriksson, Anders A1 - Martiniano, Rui A1 - McLaughlin, Russell L. A1 - Llorente, Marcos Gallego A1 - Cassidy, Lara M. A1 - Gamba, Cristina A1 - Meshveliani, Tengiz A1 - Bar-Yosef, Ofer A1 - Müller, Werner A1 - Belfer-Cohen, Anna A1 - Matskevich, Zinovi A1 - Jakeli, Nino A1 - Higham, Thomas F. G. A1 - Currat, Mathias A1 - Lordkipanidze, David A1 - Hofreiter, Michael A1 - Manica, Andrea A1 - Pinhasi, Ron A1 - Bradley, Daniel G. T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1334 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439317 SN - 1866-8372 IS - 1334 ER -