TY - JOUR A1 - Thomas, H. J. D. A1 - Myers‐Smith, I. H. A1 - Bjorkman, A. D. A1 - Elmendorf, S. C. A1 - Blok, D. A1 - Cornelissen, J. H. C. A1 - Forbes, B. C. A1 - Hollister, R. D. A1 - Normand, S. A1 - Prevéy, J. S. A1 - Rixen, C. A1 - Schaepman‐Strub, G. A1 - Wilmking, M. A1 - Wipf, S. A1 - Cornwell, W. K. A1 - Kattge, J. A1 - Goetz, S. J. A1 - Guay, K. C. A1 - Alatalo, J. M. A1 - Anadon‐Rosell, A. A1 - Angers‐Blondin, S. A1 - Berner, L. T. A1 - Björk, R. G. A1 - Buchwal, A. A1 - Buras, A. A1 - Carbognani, M. A1 - Christie, K. A1 - Siegwart Collier, L. A1 - Cooper, E. J. A1 - Eskelinen, A. A1 - Frei, E. R. A1 - Grau, O. A1 - Grogan, P. A1 - Hallinger, M. A1 - Heijmans, M. M. P. D. A1 - Hermanutz, L. A1 - Hudson, J. M. G. A1 - Hülber, K. A1 - Iturrate‐Garcia, M. A1 - Iversen, C. M. A1 - Jaroszynska, F. A1 - Johnstone, J. F. A1 - Kaarlejärvi, E. A1 - Kulonen, A. A1 - Lamarque, L. J. A1 - Lévesque, E. A1 - Little, C. J. A1 - Michelsen, A. A1 - Milbau, A. A1 - Nabe‐Nielsen, J. A1 - Nielsen, S. S. A1 - Ninot, J. M. A1 - Oberbauer, S. F. A1 - Olofsson, J. A1 - Onipchenko, V. G. A1 - Petraglia, A. A1 - Rumpf, S. B. A1 - Semenchuk, P. R. A1 - Soudzilovskaia, N. A. A1 - Spasojevic, M. J. A1 - Speed, J. D. M. A1 - Tape, K. D. A1 - te Beest, M. A1 - Tomaselli, M. A1 - Trant, A. A1 - Treier, U. A. A1 - Venn, S. A1 - Vowles, T. A1 - Weijers, S. A1 - Zamin, T. A1 - Atkin, O. K. A1 - Bahn, M. A1 - Blonder, B. A1 - Campetella, G. A1 - Cerabolini, B. E. L. A1 - Chapin III, F. S. A1 - Dainese, M. A1 - de Vries, F. T. A1 - Díaz, S. A1 - Green, W. A1 - Jackson, R. B. A1 - Manning, P. A1 - Niinemets, Ü. A1 - Ozinga, W. A. A1 - Peñuelas, J. A1 - Reich, P. B. A1 - Schamp, B. A1 - Sheremetev, S. A1 - van Bodegom, P. M. T1 - Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome JF - Global Ecology and Biogeography N2 - Aim Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits. Location Tundra biome. Time period Data collected between 1964 and 2016. Major taxa studied 295 tundra vascular plant species. Methods We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits. Results Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression. Main conclusions Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra vegetation change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insights for ecological prediction and modelling. KW - cluster analysis KW - community composition KW - ecosystem function KW - plant functional groups KW - plant functional types KW - plant traits KW - tundra biome KW - vegetation change Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-241310 VL - 28 ER - TY - JOUR A1 - Müller, Jörg A1 - Noss, Reed F. A1 - Thorn, Simon A1 - Bässler, Claus A1 - Leverkus, Alexandro B. A1 - Lindenmayer, David T1 - Increasing disturbance demands new policies to conserve intact forest JF - Conservation Letters N2 - Ongoing controversy over logging the ancient Białowieża Forest in Poland symbolizes a global problem for policies and management of the increasing proportion of the earth's intact forest that is subject to postdisturbance logging. We review the extent of, and motivations for, postdisturbance logging in protected and unprotected forests globally. An unprecedented level of logging in protected areas and other places where green-tree harvest would not normally occur is driven by economic interests and a desire for pest control. To avoid failure of global initiatives dedicated to reducing the loss of species, five key policy reforms are necessary: (1) salvage logging must be banned from protected areas; (2) forest planning should address altered disturbance regimes for all intact forests to ensure that significant areas remain undisturbed by logging; (3) new kinds of integrated analyses are needed to assess the potential economic benefits of salvage logging against its ecological, economic, and social costs; (4) global and regional maps of natural disturbance regimes should be created to guide better spatiotemporal planning of protected areas and undisturbed forests outside reserves; and (5) improved education and communication programs are needed to correct widely held misconceptions about natural disturbances. KW - anthropogenic disturbance KW - forestry KW - FSC KW - natural disturbance KW - protected area management KW - sanitary logging Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224256 VL - 12 ER - TY - JOUR A1 - Bahram, Mohammad A1 - Anslan, Sten A1 - Hildebrand, Falk A1 - Bork, Peer A1 - Tedersoo, Leho T1 - Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment JF - Environmental Microbiology Reports N2 - High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221380 VL - 11 ER - TY - JOUR A1 - König, Kerstin A1 - Zundel, Petra A1 - Krimmer, Elena A1 - König, Christian A1 - Pollmann, Marie A1 - Gottlieb, Yuval A1 - Steidle, Johannes L. M. T1 - Reproductive isolation due to prezygotic isolation and postzygotic cytoplasmic incompatibility in parasitoid wasps JF - Ecology and Evolution N2 - The reproductive barriers that prevent gene flow between closely related species are a major topic in evolutionary research. Insect clades with parasitoid lifestyle are among the most species-rich insects and new species are constantly described, indicating that speciation occurs frequently in this group. However, there are only very few studies on speciation in parasitoids. We studied reproductive barriers in two lineages of Lariophagus distinguendus (Chalcidoidea: Hymenoptera), a parasitoid wasp of pest beetle larvae that occur in human environments. One of the two lineages occurs in households preferably attacking larvae of the drugstore beetle Stegobium paniceum (“DB-lineage”), the other in grain stores with larvae of the granary weevil Sitophilus granarius as main host (“GW-lineage”). Between two populations of the DB-lineage, we identified slight sexual isolation as intraspecific barrier. Between populations from both lineages, we found almost complete sexual isolation caused by female mate choice, and postzygotic isolation, which is partially caused by cytoplasmic incompatibility induced by so far undescribed endosymbionts which are not Wolbachia or Cardinium. Because separation between the two lineages is almost complete, they should be considered as separate species according to the biological species concept. This demonstrates that cryptic species within parasitoid Hymenoptera also occur in Central Europe in close contact to humans. KW - cytoplasmic incompatibility KW - endosymbiotic bacteria KW - Lariophagus distinguendus KW - parasitoid wasps KW - sexual isolation KW - speciation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222796 VL - 9 ER - TY - JOUR A1 - Hartke, Juliane A1 - Sprenger, Philipp P. A1 - Sahm, Jacqueline A1 - Winterberg, Helena A1 - Orivel, Jérôme A1 - Baur, Hannes A1 - Beuerle, Till A1 - Schmitt, Thomas A1 - Feldmeyer, Barbara A1 - Menzel, Florian T1 - Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association JF - Ecology and Evolution N2 - Upon advances in sequencing techniques, more and more morphologically identical organisms are identified as cryptic species. Often, mutualistic interactions are proposed as drivers of diversification. Species of the neotropical parabiotic ant association between Crematogaster levior and Camponotus femoratus are known for highly diverse cuticular hydrocarbon (CHC) profiles, which in insects serve as desiccation barrier but also as communication cues. In the present study, we investigated the association of the ants’ CHC profiles with genotypes and morphological traits, and discovered cryptic species pairs in both genera. To assess putative niche differentiation between the cryptic species, we conducted an environmental association study that included various climate variables, canopy cover, and mutualistic plant species. Although mostly sympatric, the two Camponotus species seem to prefer different climate niches. However in the two Crematogaster species, we could not detect any differences in niche preference. The strong differentiation in the CHC profiles may thus suggest a possible role during speciation itself either by inducing assortative mating or by reinforcing sexual selection after the speciation event. We did not detect any further niche differences in the environmental parameters tested. Thus, it remains open how the cryptic species avoid competitive exclusion, with scope for further investigations. KW - environmental association KW - integrative taxonomy KW - niche differentiation KW - population structure KW - sexual selection KW - speciation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-227857 VL - 9 ER - TY - JOUR A1 - Kendall, Liam K. A1 - Rader, Romina A1 - Gagic, Vesna A1 - Cariveau, Daniel P. A1 - Albrecht, Matthias A1 - Baldock, Katherine C. R. A1 - Freitas, Breno M. A1 - Hall, Mark A1 - Holzschuh, Andrea A1 - Molina, Francisco P. A1 - Morten, Joanne M. A1 - Pereira, Janaely S. A1 - Portman, Zachary M. A1 - Roberts, Stuart P. M. A1 - Rodriguez, Juanita A1 - Russo, Laura A1 - Sutter, Louis A1 - Vereecken, Nicolas J. A1 - Bartomeus, Ignasi T1 - Pollinator size and its consequences: Robust estimates of body size in pollinating insects JF - Ecology and Evolution N2 - Body size is an integral functional trait that underlies pollination-related ecological processes, yet it is often impractical to measure directly. Allometric scaling laws have been used to overcome this problem. However, most existing models rely upon small sample sizes, geographically restricted sampling and have limited applicability for non-bee taxa. Allometric models that consider biogeography, phylogenetic relatedness, and intraspecific variation are urgently required to ensure greater accuracy. We measured body size as dry weight and intertegular distance (ITD) of 391 bee species (4,035 specimens) and 103 hoverfly species (399 specimens) across four biogeographic regions: Australia, Europe, North America, and South America. We updated existing models within a Bayesian mixed-model framework to test the power of ITD to predict interspecific variation in pollinator dry weight in interaction with different co-variates: phylogeny or taxonomy, sexual dimorphism, and biogeographic region. In addition, we used ordinary least squares regression to assess intraspecific dry weight ~ ITD relationships for ten bees and five hoverfly species. Including co-variates led to more robust interspecific body size predictions for both bees and hoverflies relative to models with the ITD alone. In contrast, at the intraspecific level, our results demonstrate that the ITD is an inconsistent predictor of body size for bees and hoverflies. The use of allometric scaling laws to estimate body size is more suitable for interspecific comparative analyses than assessing intraspecific variation. Collectively, these models form the basis of the dynamic R package, “pollimetry,” which provides a comprehensive resource for allometric pollination research worldwide. KW - Apoidea KW - biogeography KW - body size KW - dry weight KW - pollimetry KW - pollination KW - predictive models KW - R package KW - Syrphidae Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-325705 VL - 9 ER - TY - JOUR A1 - Baluapuri, Apoorva A1 - Hofstetter, Julia A1 - Dudvarski Stankovic, Nevenka A1 - Endres, Theresa A1 - Bhandare, Pranjali A1 - Vos, Seychelle Monique A1 - Adhikari, Bikash A1 - Schwarz, Jessica Denise A1 - Narain, Ashwin A1 - Vogt, Markus A1 - Wang, Shuang-Yan A1 - Düster, Robert A1 - Jung, Lisa Anna A1 - Vanselow, Jens Thorsten A1 - Wiegering, Armin A1 - Geyer, Matthias A1 - Maric, Hans Michael A1 - Gallant, Peter A1 - Walz, Susanne A1 - Schlosser, Andreas A1 - Cramer, Patrick A1 - Eilers, Martin A1 - Wolf, Elmar T1 - MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation JF - Molecular Cell N2 - The MYC oncoprotein binds to promoter-proximal regions of virtually all transcribed genes and enhances RNA polymerase II (Pol II) function, but its precise mode of action is poorly understood. Using mass spectrometry of both MYC and Pol II complexes, we show here that MYC controls the assembly of Pol II with a small set of transcription elongation factors that includes SPT5, a subunit of the elongation factor DSIF. MYC directly binds SPT5, recruits SPT5 to promoters, and enables the CDK7-dependent transfer of SPT5 onto Pol II. Consistent with known functions of SPT5, MYC is required for fast and processive transcription elongation. Intriguingly, the high levels of MYC that are expressed in tumors sequester SPT5 into non-functional complexes, thereby decreasing the expression of growth-suppressive genes. Altogether, these results argue that MYC controls the productive assembly of processive Pol II elongation complexes and provide insight into how oncogenic levels of MYC permit uncontrolled cellular growth. KW - MYC KW - SPT5 KW - SUPT5H KW - SPT6 KW - RNA polymerase II KW - transcription KW - elongation rate KW - processivity KW - directionality KW - tumorigenesis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221438 VL - 74 ER - TY - JOUR A1 - Seitz, Nicola A1 - vanEngelsdorp, Dennis A1 - Leonhardt, Sara D. T1 - Conserving bees in destroyed landscapes: The potentials of reclaimed sand mines JF - Global Ecology and Conservation N2 - Sand mines represent anthropogenically impacted habitats found worldwide, which bear potential for bee conservation. Although floral resources can be limited at these habitats, vegetation free patches of open sandy soils and embankments may offer good nesting possibilities for sand restricted and other bees. We compared bee communities as found in three reclaimed sand mines and at adjacent roadside meadows in Maryland, USA, over two years. Both sand mines and roadsides hosted diverse bee communities with 111 and 88 bee species, respectively. Bee abundances as well as richness and Shannon diversity of bee species were higher in sand mines than at roadsides and negatively correlated with the percentage of vegetational ground cover. Species composition also differed significantly between habitats. Sand mines hosted a higher proportion of ground nesters, more uncommon and more ‘sand loving’ bees similar to natural sandy areas of Maryland. Despite the destruction of the original pre-mining habitat, sand mines thus appear to represent a unique habitat for wild bees, particularly when natural vegetation and open sand spots are encouraged. Considering habitat loss, the lack of natural disturbance regimes, and ongoing declines of wild bees, sand mines could add promising opportunities for bee conservation which has hitherto mainly focused on agricultural and urban habitats. KW - bee conservation KW - bee decline KW - habitat restoration KW - land use KW - wild bees KW - ground nesters Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235877 VL - 19 ER - TY - JOUR A1 - Hofrichter, Michaela A. H. A1 - Doll, Julia A1 - Habibi, Haleh A1 - Enayati, Samaneh A1 - Mehrjardi, Mohammad Yahya Vahidi A1 - Müller, Tobias A1 - Dittrich, Marcus A1 - Haaf, Thomas A1 - Vona, Barbara T1 - Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss JF - European Journal of Medical Genetics N2 - Pathogenic variants in COL9A1 are primarily associated with autosomal recessive Stickler syndrome. Patients with COL9A1-associated Stickler syndrome (STL) present hearing loss (HL), ophthalmic manifestations and skeletal abnormalities. However, the clinical spectrum of patients with COL9A1 variants can also include multiple epiphyseal dysplasia, as well as non-syndromic HL that was observed in one previously reported proband. Exome sequencing was performed on the genomic DNA of an Iranian patient and his affected brother who both report non-syndromic HL. A 44.6 kb homozygous in-frame deletion spanning exons 6 to 33 of COL9A1 was detected via exome-based copy number variation analysis. The deleted exons were confirmed by PCR in the patient and his affected brother, who both have non-syndromic HL. Segregation analysis via qPCR confirmed the parents as heterozygous deletion carriers. Breakpoint analysis mapped the homozygous deletion spanning introns 5 to 33 (g.70,948,188_70,997,277del, NM_001851.4(COL9A1):c.697–3754_2112+769del, p.(Phe233_Ser704del), with an additional 67 bp of inserted intronic sequence that may have originated due to a fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR) mechanism. This mechanism has not been previously implicated in HL or STL. This is also the first reported copy number variation in COL9A1 that was identified through an exome data set in an Iranian family with apparent non-syndromic HL. The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL. KW - COL9A1 KW - copy number variation KW - FoSTeS/MMBIR mechanism KW - non-syndromic hearing loss KW - Stickler syndrome Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-322008 VL - 62 ER - TY - JOUR A1 - Mooij, Wolf M A1 - van Wijk, Dianneke A1 - Beusen, Arthur HW A1 - Brederveld, Robert J A1 - Chang, Manqi A1 - Cobben, Marleen MP A1 - DeAngelis, Don L A1 - Downing, Andrea S A1 - Green, Pamela A1 - Gsell, Alena S A1 - Huttunen, Inese A1 - Janse, Jan H A1 - Janssen, Annette BG A1 - Hengeveld, Geerten M A1 - Kong, Xiangzhen A1 - Kramer, Lilith A1 - Kuiper, Jan J A1 - Langan, Simon J A1 - Nolet, Bart A A1 - Nuijten, Rascha JM A1 - Strokal, Maryna A1 - Troost, Tineke A A1 - van Dam, Anne A A1 - Teurlincx, Sven T1 - Modeling water quality in the Anthropocene: directions for the next-generation aquatic ecosystem models JF - Current Opinion in Environmental Sustainability N2 - “Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224173 VL - 36 ER - TY - JOUR A1 - Milanese, Alessio A1 - Mende, Daniel R A1 - Paoli, Lucas A1 - Salazar, Guillem A1 - Ruscheweyh, Hans-Joachim A1 - Cuenca, Miguelangel A1 - Hingamp, Pascal A1 - Alves, Renato A1 - Costea, Paul I A1 - Coelho, Luis Pedro A1 - Schmidt, Thomas S. B. A1 - Almeida, Alexandre A1 - Mitchell, Alex L A1 - Finn, Robert D. A1 - Huerta-Cepas, Jaime A1 - Bork, Peer A1 - Zeller, Georg A1 - Sunagawa, Shinichi T1 - Microbial abundance, activity and population genomic profiling with mOTUs2 JF - Nature Communications N2 - Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites). KW - microbiome KW - software Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224089 VL - 10 ER - TY - JOUR A1 - Krah, Franz-Sebastian A1 - Büntgen, Ulf A1 - Schaefer, Hanno A1 - Müller, Jörg A1 - Andrew, Carrie A1 - Boddy, Lynne A1 - Diez, Jeffrey A1 - Egli, Simon A1 - Freckleton, Robert A1 - Gange, Alan C. A1 - Halvorsen, Rune A1 - Heegaard, Einar A1 - Heideroth, Antje A1 - Heibl, Christoph A1 - Heilmann-Clausen, Jacob A1 - Høiland, Klaus A1 - Kar, Ritwika A1 - Kauserud, Håvard A1 - Kirk, Paul M. A1 - Kuyper, Thomas W. A1 - Krisai-Greilhuber, Irmgard A1 - Norden, Jenni A1 - Papastefanou, Phillip A1 - Senn-Irlet, Beatrice A1 - Bässler, Claus T1 - European mushroom assemblages are darker in cold climates JF - Nature Communications N2 - Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species’ geographical distributions will be critical in predicting ecosystem responses to global warming. KW - evolutionary ecology KW - fungal ecology KW - fungal evolution KW - macroecology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224815 VL - 10 ER - TY - JOUR A1 - Woodcock, B. A. A1 - Garratt, M. P. D. A1 - Powney, G. D. A1 - Shaw, R. F. A1 - Osborne, J. L. A1 - Soroka, J. A1 - Lindström, S. A. M. A1 - Stanley, D. A1 - Ouvrard, P. A1 - Edwards, M. E. A1 - Jauker, F. A1 - McCracken, M. E. A1 - Zou, Y. A1 - Potts, S. G. A1 - Rundlöf, M. A1 - Noriega, J. A. A1 - Greenop, A. A1 - Smith, H. G. A1 - Bommarco, R. A1 - van der Werf, W. A1 - Stout, J. C. A1 - Steffan-Dewenter, I. A1 - Morandin, L. A1 - Bullock, J. M. A1 - Pywell, R. F. T1 - Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield JF - Nature Communications N2 - How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture. KW - agroecology KW - agriculture KW - ecosystem services KW - environmental sciences Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-233787 VL - 10 ER - TY - JOUR A1 - Nerreter, Thomas A1 - Letschert, Sebastian A1 - Götz, Ralph A1 - Doose, Sören A1 - Danhof, Sophia A1 - Einsele, Hermann A1 - Sauer, Markus A1 - Hudecek, Michael T1 - Super-resolution microscopy reveals ultra-low CD19 expression on myeloma cells that triggers elimination by CD19 CAR-T JF - Nature Communications N2 - Immunotherapy with chimeric antigen receptor-engineered T-cells (CAR-T) is under investigation in multiple myeloma. There are reports of myeloma remission after CD19 CAR-T therapy, although CD19 is hardly detectable on myeloma cells by flow cytometry (FC). We apply single molecule-sensitive direct stochastic optical reconstruction microscopy (dSTORM), and demonstrate CD19 expression on a fraction of myeloma cells (10.3–80%) in 10 out of 14 patients (density: 13–5,000 molecules per cell). In contrast, FC detects CD19 in only 2 of these 10 patients, on a smaller fraction of cells. Treatment with CD19 CAR-T in vitro results in elimination of CD19-positive myeloma cells, including those with <100 CD19 molecules per cell. Similar data are obtained by dSTORM analyses of CD20 expression on myeloma cells and CD20 CAR-T. These data establish a sensitivity threshold for CAR-T and illustrate how super-resolution microscopy can guide patient selection in immunotherapy to exploit ultra-low density antigens. KW - cancer imaging KW - cancer immunotherapy KW - imaging Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232258 VL - 10 ER - TY - JOUR A1 - Mercier, Rebecca A1 - Wolmarans, Annemarie A1 - Schubert, Jonathan A1 - Neuweiler, Hannes A1 - Johnson, Jill L. A1 - LaPointe, Paul T1 - The conserved NxNNWHW motif in Aha-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation JF - Nature Communications N2 - Hsp90 is a dimeric molecular chaperone that is essential for the folding and activation of hundreds of client proteins. Co-chaperone proteins regulate the ATP-driven Hsp90 client activation cycle. Aha-type co-chaperones are the most potent stimulators of the Hsp90 ATPase activity but the relationship between ATPase regulation and in vivo activity is poorly understood. We report here that the most strongly conserved region of Aha-type co-chaperones, the N terminal NxNNWHW motif, modulates the apparent affinity of Hsp90 for nucleotide substrates. The ability of yeast Aha-type co-chaperones to act in vivo is ablated when the N terminal NxNNWHW motif is removed. This work suggests that nucleotide exchange during the Hsp90 functional cycle may be more important than rate of catalysis. KW - biophysics KW - cell growth KW - chaperones KW - enzymes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224007 VL - 10 ER - TY - JOUR A1 - Lübcke, Paul M. A1 - Ebbers, Meinolf N. B. A1 - Volzke, Johann A1 - Bull, Jana A1 - Kneitz, Susanne A1 - Engelmann, Robby A1 - Lang, Hermann A1 - Kreikemeyer, Bernd A1 - Müller-Hilke, Brigitte T1 - Periodontal treatment prevents arthritis in mice and methotrexate ameliorates periodontal bone loss JF - Scientific Reports N2 - Recent studies indicate a causal relationship between the periodontal pathogen P. gingivalis and rheumatoid arthritis involving the production of autoantibodies against citrullinated peptides. We therefore postulated that therapeutic eradication P. gingivalis may ameliorate rheumatoid arthritis development and here turned to a mouse model in order to challenge our hypothesis. F1 (DBA/1 x B10.Q) mice were orally inoculated with P. gingivalis before collagen-induced arthritis was provoked. Chlorhexidine or metronidazole were orally administered either before or during the induction phase of arthritis and their effects on arthritis progression and alveolar bone loss were compared to intraperitoneally injected methotrexate. Arthritis incidence and severity were macroscopically scored and alveolar bone loss was evaluated via microcomputed tomography. Serum antibody titres against P. gingivalis were quantified by ELISA and microbial dysbiosis following oral inoculation was monitored in stool samples via microbiome analyses. Both, oral chlorhexidine and metronidazole reduced the incidence and ameliorated the severity of collagen-induced arthritis comparable to methotrexate. Likewise, all three therapies attenuated alveolar bone loss. Relative abundance of Porphyromonadaceae was increased after oral inoculation with P. gingivalis and decreased after treatment. This is the first study to describe beneficial effects of non-surgical periodontal treatment on collagen-induced arthritis in mice and suggests that mouthwash with chlorhexidine or metronidazole may also be beneficial for patients with rheumatoid arthritis and a coexisting periodontitis. Methotrexate ameliorated periodontitis in mice, further raising the possibility that methotrexate may also positively impact on the tooth supporting tissues of patients with rheumatoid arthritis. KW - rheumatic diseases KW - rheumatology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-237355 VL - 9 ER - TY - JOUR A1 - Lu, Yuan A1 - Boswell, Wiliam A1 - Boswell, Mikki A1 - Klotz, Barbara A1 - Kneitz, Susanne A1 - Regneri, Janine A1 - Savage, Markita A1 - Mendoza, Cristina A1 - Postlethwait, John A1 - Warren, Wesley C. A1 - Schartl, Manfred A1 - Walter, Ronald B. T1 - Application of the Transcriptional Disease Signature (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish Model JF - Scientific Reports N2 - Cell culture and protein target-based compound screening strategies, though broadly utilized in selecting candidate compounds, often fail to eliminate candidate compounds with non-target effects and/or safety concerns until late in the drug developmental process. Phenotype screening using intact research animals is attractive because it can help identify small molecule candidate compounds that have a high probability of proceeding to clinical use. Most FDA approved, first-in-class small molecules were identified from phenotypic screening. However, phenotypic screening using rodent models is labor intensive, low-throughput, and very expensive. As a novel alternative for small molecule screening, we have been developing gene expression disease profiles, termed the Transcriptional Disease Signature (TDS), as readout of small molecule screens for therapeutic molecules. In this concept, compounds that can reverse, or otherwise affect known disease-associated gene expression patterns in whole animals may be rapidly identified for more detailed downstream direct testing of their efficacy and mode of action. To establish proof of concept for this screening strategy, we employed a transgenic strain of a small aquarium fish, medaka (Oryzias latipes), that overexpresses the malignant melanoma driver gene xmrk, a mutant egfr gene, that is driven by a pigment cell-specific mitf promoter. In this model, melanoma develops with 100% penetrance. Using the transgenic medaka malignant melanoma model, we established a screening system that employs the NanoString nCounter platform to quantify gene expression within custom sets of TDS gene targets that we had previously shown to exhibit differential transcription among xmrk-transgenic and wild-type medaka. Compound-modulated gene expression was identified using an internet-accessible custom-built data processing pipeline. The effect of a given drug on the entire TDS profile was estimated by comparing compound-modulated genes in the TDS using an activation Z-score and Kolmogorov-Smirnov statistics. TDS gene probes were designed that target common signaling pathways that include proliferation, development, toxicity, immune function, metabolism and detoxification. These pathways may be utilized to evaluate candidate compounds for potential favorable, or unfavorable, effects on melanoma-associated gene expression. Here we present the logistics of using medaka to screen compounds, as well as, the development of a user-friendly NanoString data analysis pipeline to support feasibility of this novel TDS drug-screening strategy. KW - bioinformatics KW - phenotypic screening Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-237322 VL - 9 ER - TY - JOUR A1 - Kraus, Amelie J. A1 - Brink, Benedikt G. A1 - Siegel, T. Nicolai T1 - Efficient and specific oligo-based depletion of rRNA JF - Scientific Reports N2 - In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available. KW - parasite biology KW - RNA sequencing KW - transcriptomics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224829 VL - 9 ER - TY - JOUR A1 - Kim, Bo-Mi A1 - Amores, Angel A1 - Kang, Seunghyun A1 - Ahn, Do-Hwan A1 - Kim, Jin-Hyoung A1 - Kim, Il-Chan A1 - Lee, Jun Hyuck A1 - Lee, Sung Gu A1 - Lee, Hyoungseok A1 - Lee, Jungeun A1 - Kim, Han-Woo A1 - Desvignes, Thomas A1 - Batzel, Peter A1 - Sydes, Jason A1 - Titus, Tom A1 - Wilson, Catherine A. A1 - Catchen, Julian M. A1 - Warren, Wesley C. A1 - Schartl, Manfred A1 - Detrich, H. William III A1 - Postlethwait, John H. A1 - Park, Hyun T1 - Antarctic blackfin icefish genome reveals adaptations to extreme environments JF - Nature Ecology & Evolution N2 - Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments. KW - animal physiology KW - evolutionary genetics KW - genomics KW - ichthyology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-325811 VL - 3 ER - TY - JOUR A1 - Dörk, Thilo A1 - Peterlongo, Peter A1 - Mannermaa, Arto A1 - Bolla, Manjeet K. A1 - Wang, Qin A1 - Dennis, Joe A1 - Ahearn, Thomas A1 - Andrulis, Irene L. A1 - Anton-Culver, Hoda A1 - Arndt, Volker A1 - Aronson, Kristan J. A1 - Augustinsson, Annelie A1 - Beane Freeman, Laura E. A1 - Beckmann, Matthias W. A1 - Beeghly-Fadiel, Alicia A1 - Behrens, Sabine A1 - Bermisheva, Marina A1 - Blomqvist, Carl A1 - Bogdanova, Natalia V. A1 - Bojesen, Stig E. A1 - Brauch, Hiltrud A1 - Brenner, Hermann A1 - Burwinkel, Barbara A1 - Canzian, Federico A1 - Chan, Tsun L. A1 - Chang-Claude, Jenny A1 - Chanock, Stephen J. A1 - Choi, Ji-Yeob A1 - Christiansen, Hans A1 - Clarke, Christine L. A1 - Couch, Fergus J. A1 - Czene, Kamila A1 - Daly, Mary B. A1 - dos-Santos-Silva, Isabel A1 - Dwek, Miriam A1 - Eccles, Diana M. A1 - Ekici, Arif B. A1 - Eriksson, Mikael A1 - Evans, D. Gareth A1 - Fasching, Peter A. A1 - Figueroa, Jonine A1 - Flyger, Henrik A1 - Fritschi, Lin A1 - Gabrielson, Marike A1 - Gago-Dominguez, Manuela A1 - Gao, Chi A1 - Gapstur, Susan M. A1 - García-Closas, Montserrat A1 - García-Sáenz, José A. A1 - Gaudet, Mia M. A1 - Giles, Graham G. A1 - Goldberg, Mark S. A1 - Goldgar, David E. A1 - Guenél, Pascal A1 - Haeberle, Lothar A1 - Haimann, Christopher A. A1 - Håkansson, Niclas A1 - Hall, Per A1 - Hamann, Ute A1 - Hartman, Mikael A1 - Hauke, Jan A1 - Hein, Alexander A1 - Hillemanns, Peter A1 - Hogervorst, Frans B. L. A1 - Hooning, Maartje J. A1 - Hopper, John L. A1 - Howell, Tony A1 - Huo, Dezheng A1 - Ito, Hidemi A1 - Iwasaki, Motoki A1 - Jakubowska, Anna A1 - Janni, Wolfgang A1 - John, Esther M. A1 - Jung, Audrey A1 - Kaaks, Rudolf A1 - Kang, Daehee A1 - Kapoor, Pooja Middha A1 - Khusnutdinova, Elza A1 - Kim, Sung-Won A1 - Kitahara, Cari M. A1 - Koutros, Stella A1 - Kraft, Peter A1 - Kristensen, Vessela N. A1 - Kwong, Ava A1 - Lambrechts, Diether A1 - Le Marchand, Loic A1 - Li, Jingmei A1 - Lindström, Sara A1 - Linet, Martha A1 - Lo, Wing-Yee A1 - Long, Jirong A1 - Lophatananon, Artitaya A1 - Lubiński, Jan A1 - Manoochehri, Mehdi A1 - Manoukian, Siranoush A1 - Margolin, Sara A1 - Martinez, Elena A1 - Matsuo, Keitaro A1 - Mavroudis, Dimitris A1 - Meindl, Alfons A1 - Menon, Usha A1 - Milne, Roger L. A1 - Mohd Taib, Nur Aishah A1 - Muir, Kenneth A1 - Mulligan, Anna Marie A1 - Neuhausen, Susan L. A1 - Nevanlinna, Heli A1 - Neven, Patrick A1 - Newman, William G. A1 - Offit, Kenneth A1 - Olopade, Olufunmilayo I. A1 - Olshan, Andrew F. A1 - Olson, Janet E. A1 - Olsson, Håkan A1 - Park, Sue K. A1 - Park-Simon, Tjoung-Won A1 - Peto, Julian A1 - Plaseska-Karanfilska, Dijana A1 - Pohl-Rescigno, Esther A1 - Presneau, Nadege A1 - Rack, Brigitte A1 - Radice, Paolo A1 - Rashid, Muhammad U. A1 - Rennert, Gad A1 - Rennert, Hedy S. A1 - Romero, Atocha A1 - Ruebner, Matthias A1 - Saloustros, Emmanouil A1 - Schmidt, Marjanka K. A1 - Schmutzler, Rita K. A1 - Schneider, Michael O. A1 - Schoemaker, Minouk J. A1 - Scott, Christopher A1 - Shen, Chen-Yang A1 - Shu, Xiao-Ou A1 - Simard, Jaques A1 - Slager, Susan A1 - Smichkoska, Snezhana A1 - Southey, Melissa C. A1 - Spinelli, John J. A1 - Stone, Jennifer A1 - Surowy, Harald A1 - Swerdlow, Anthony J. A1 - Tamimi, Rulla M. A1 - Tapper, William J. A1 - Teo, Soo H. A1 - Terry, Mary Beth A1 - Toland, Amanda E. A1 - Tollenaar, Rob A. E. M. A1 - Torres, Diana A1 - Torres-Mejía, Gabriela A1 - Troester, Melissa A. A1 - Truong, Thérèse A1 - Tsugane, Shoichiro A1 - Untch, Michael A1 - Vachon, Celine M. A1 - van den Ouweland, Ans M. W. A1 - van Veen, Elke M. A1 - Vijai, Joseph A1 - Wendt, Camilla A1 - Wolk, Alicja A1 - Yu, Jyh-Cherng A1 - Zheng, Wei A1 - Ziogas, Argyrios A1 - Ziv, Elad A1 - Dunnig, Alison A1 - Pharaoh, Paul D. P. A1 - Schindler, Detlev A1 - Devilee, Peter A1 - Easton, Douglas F. T1 - Two truncating variants in FANCC and breast cancer risk JF - Scientific Reports N2 - Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants. KW - oncology KW - risk factors Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222838 VL - 9 ER -