TY - JOUR A1 - Nagy, Dóra A1 - Cusumano, Paola A1 - Andreatta, Gabriele A1 - Martin Anduaga, Ane A1 - Hermann-Luibl, Christiane A1 - Reinhard, Nils A1 - Gesto, João A1 - Wegener, Christian A1 - Mazzotta, Gabriella A1 - Rosato, Ezio A1 - Kyriacou, Charalambos P. A1 - Helfrich-Förster, Charlotte A1 - Costa, Rodolfo T1 - Peptidergic signaling from clock neurons regulates reproductive dormancy in Drosophila melanogaster JF - PLoS Genetics N2 - With the approach of winter, many insects switch to an alternative protective developmental program called diapause. Drosophila melanogaster females overwinter as adults by inducing a reproductive arrest that is characterized by inhibition of ovarian development at previtellogenic stages. The insulin producing cells (IPCs) are key regulators of this process, since they produce and release insulin-like peptides that act as diapause-antagonizing hormones. Here we show that in D. melanogaster two neuropeptides, Pigment Dispersing Factor (PDF) and short Neuropeptide F (sNPF) inhibit reproductive arrest, likely through modulation of the IPCs. In particular, genetic manipulations of the PDF-expressing neurons, which include the sNPF-producing small ventral Lateral Neurons (s-LNvs), modulated the levels of reproductive dormancy, suggesting the involvement of both neuropeptides. We expressed a genetically encoded cAMP sensor in the IPCs and challenged brain explants with synthetic PDF and sNPF. Bath applications of both neuropeptides increased cAMP levels in the IPCs, even more so when they were applied together, suggesting a synergistic effect. Bath application of sNPF additionally increased Ca2+ levels in the IPCs. Our results indicate that PDF and sNPF inhibit reproductive dormancy by maintaining the IPCs in an active state. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231681 VL - 15 ER - TY - JOUR A1 - Lu, Yuan A1 - Boswell, Mikki A1 - Boswell, William A1 - Kneitz, Susanne A1 - Klotz, Barbara A1 - Savage, Markita A1 - Salinas, Raquel A1 - Marks, Rebacca A1 - Regneri, Janine A1 - Postlethwait, John A1 - Warren, Wesley C. A1 - Schartl, Manfred A1 - Walter, Ronald T1 - Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model JF - PLoS Genetics N2 - Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F1 interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F1 interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-237318 VL - 14 ER - TY - JOUR A1 - Breitenbach, Tim A1 - Liang, Chunguang A1 - Beyersdorf, Niklas A1 - Dandekar, Thomas T1 - Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks JF - PLoS Computational Biology N2 - Once biological systems are modeled by regulatory networks, the next step is to include external stimuli, which model the experimental possibilities to affect the activity level of certain network’s nodes, in a mathematical framework. Then, this framework can be interpreted as a mathematical optimal control framework such that optimization algorithms can be used to determine external stimuli which cause a desired switch from an initial state of the network to another final state. These external stimuli are the intervention points for the corresponding biological experiment to obtain the desired outcome of the considered experiment. In this work, the model of regulatory networks is extended to controlled regulatory networks. For this purpose, external stimuli are considered which can affect the activity of the network’s nodes by activation or inhibition. A method is presented how to calculate a selection of external stimuli which causes a switch between two different steady states of a regulatory network. A software solution based on Jimena and Mathworks Matlab is provided. Furthermore, numerical examples are presented to demonstrate application and scope of the software on networks of 4 nodes, 11 nodes and 36 nodes. Moreover, we analyze the aggregation of platelets and the behavior of a basic T-helper cell protein-protein interaction network and its maturation towards Th0, Th1, Th2, Th17 and Treg cells in accordance with experimental data. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-220385 VL - 15 ER - TY - JOUR A1 - Herpin, Amaury A1 - Schmidt, Cornelia A1 - Kneitz, Susanne A1 - Gobé, Clara A1 - Regensburger, Martina A1 - Le Cam, Aurélie A1 - Montfort, Jérome A1 - Adolfi, Mateus C. A1 - Lillesaar, Christina A1 - Wilhelm, Dagmar A1 - Kraeussling, Michael A1 - Mourot, Brigitte A1 - Porcon, Béatrice A1 - Pannetier, Maëlle A1 - Pailhoux, Eric A1 - Ettwiller, Laurence A1 - Dolle, Dirk A1 - Guiguen, Yann A1 - Schartl, Manfred T1 - A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka JF - PLoS Biology N2 - Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka, a duplicate of dmrt1—acting as master sex-determining gene—has a tightly timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3′ UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka, two RNA-binding proteins with antagonizing properties target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. The D3U-box is also conserved in other germ-cell transcripts, making them responsive to the same RNA binding proteins. The evolutionary conservation of the D3U-box motif within dmrt1 genes of metazoans—together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells—suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-320011 VL - 17 ER - TY - JOUR A1 - Morgenstern, Marcel A1 - Peikert, Christian D. A1 - Lübbert, Philipp A1 - Suppanz, Ida A1 - Klemm, Cinzia A1 - Alka, Oliver A1 - Steiert, Conny A1 - Naumenko, Nataliia A1 - Schendzielorz, Alexander A1 - Melchionda, Laura A1 - Mühlhäuser, Wignand W. D. A1 - Knapp, Bettina A1 - Busch, Jakob D. A1 - Stiller, Sebastian B. A1 - Dannenmaier, Stefan A1 - Lindau, Caroline A1 - Licheva, Mariya A1 - Eickhorst, Christopher A1 - Galbusera, Riccardo A1 - Zerbes, Ralf M. A1 - Ryan, Michael T. A1 - Kraft, Claudine A1 - Kozjak-Pavlovic, Vera A1 - Drepper, Friedel A1 - Dennerlein, Sven A1 - Oeljeklaus, Silke A1 - Pfanner, Nikolaus A1 - Wiedemann, Nils A1 - Warscheid, Bettina T1 - Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context JF - Cell Metabolism N2 - Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality control and have been linked to various diseases. Different views exist on the composition of the human mitochondrial proteome. We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). We identified interactors of translocases, respiratory chain, and ATP synthase assembly factors. The abundance of MitoCoP proteins covers six orders of magnitude and amounts to 7% of the cellular proteome with the chaperones HSP60-HSP10 being the most abundant mitochondrial proteins. MitoCoP dynamics spans three orders of magnitudes, with half-lives from hours to months, and suggests a rapid regulation of biosynthesis and assembly processes. 460 MitoCoP genes are linked to human diseases with a strong prevalence for the central nervous system and metabolism. MitoCoP will provide a high-confidence resource for placing dynamics, functions, and dysfunctions of mitochondria into the cellular context. KW - mitochondria KW - human cells KW - high-confidence proteome KW - smORFs KW - copy numbers KW - half-lives KW - disease KW - complexome KW - protein translocation KW - respiratory chain Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-371114 VL - 33 ER - TY - JOUR A1 - Moreaux, Céline A1 - Meireles, Desirée A. L. A1 - Sonne, Jesper A1 - Badano, Ernesto I. A1 - Classen, Alice A1 - González-Chaves, Adrian A1 - Hipólito, Juliana A1 - Klein, Alexandra-Maria A1 - Maruyama, Pietro K. A1 - Metzger, Jean Paul A1 - Philpott, Stacy M. A1 - Rahbek, Carsten A1 - Saturni, Fernanda T. A1 - Sritongchuay, Tuanjit A1 - Tscharntke, Teja A1 - Uno, Shinsuke A1 - Vergara, Carlos H. A1 - Viana, Blandina F. A1 - Strange, Niels A1 - Dalsgaard, Bo T1 - The value of biotic pollination and dense forest for fruit set of Arabica coffee: A global assessment JF - Agriculture, Ecosystems & Environment N2 - Animal pollinators are globally threatened by anthropogenic land use change and agricultural intensification. The yield of many food crops is therefore negatively impacted because they benefit from biotic pollination. This is especially the case in the tropics. For instance, fruit set of Coffea arabica has been shown to increase by 10–30% in plantations with a high richness of bee species, possibly influenced by the availability of surrounding forest habitat. Here, we performed a global literature review to (1) assess how much animal pollination enhances coffee fruit set, and to (2) examine the importance of the amount of forest cover, distance to nearby forest and forest canopy density for bee species richness and coffee fruit set. Using a systematic literature review, we identified eleven case studies with a total of 182 samples where fruit set of C. arabica was assessed. We subsequently gathered forest data for all study sites from satellite imagery. We modelled the effects of open (all forest with a canopy density of ≥25%), closed (≥50%) and dense (≥75%) forests on pollinator richness and fruit set of coffee. Overall, we found that animal pollination increases coffee fruit set by ~18% on average. In only one of the case studies, regression results indicate a positive effect of dense forest on coffee fruit set, which increased with higher forest cover and shorter distance to the forest. Against expectations, forest cover and distance to open forest were not related to bee species richness and fruit set. In summary, we provide strong empirical support for the notion that animal pollinators increase coffee fruit set. Forest proximity had little overall influence on bee richness and coffee fruit set, except when farms were surrounded by dense tropical forests, potentially because these may provide high-quality habitats for bees pollinating coffee. We, therefore, advocate that more research is done to understand the biodiversity value of dense forest for pollinators, notably assessing the mechanisms underlying the importance of forest for pollinators and their pollination services. KW - bee richness KW - coffee KW - forest KW - pollination KW - remote sensing KW - systematic literature review Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-370982 VL - 323 ER - TY - JOUR A1 - Ma, Jie A1 - Gulbins, Erich A1 - Edwards, Michael J. A1 - Caldwell, Charles C. A1 - Fraunholz, Martin A1 - Becker, Katrin Anne T1 - Staphylococcus aureus α-toxin induces inflammatory cytokines via lysosomal acid sphingomyelinase and ceramides JF - Cellular Physiology and Biochemistry N2 - Staphylococcus aureus (S. aureus) infections are a major clinical problem and range from mild skin and soft-tissue infections to severe and even lethal infections such as pneumonia, endocarditis, sepsis, osteomyelitis, and toxic shock syndrome. Toxins that are released from S. aureus mediate many of these effects. Here, we aimed to identify molecular mechanisms how α-toxin, a major S. aureus toxin, induces inflammation. Methods: Macrophages were isolated from the bone marrow of wildtype and acid sphingomyelinase-deficient mice, stimulated with S. aureus α-toxin and activation of the acid sphingomyelinase was quantified. The subcellular formation of ceramides was determined by confocal microscopy. Release of cathepsins from lysosomes, activation of inflammasome proteins and formation of Interleukin-1β (IL-1β) and Tumor Necrosis Factor-α (TNF-α) were analyzed by western blotting, confocal microscopy and ELISA. Results: We demonstrate that S. aureus α-toxin activates the acid sphingomyelinase in ex vivo macrophages and triggers a release of ceramides. Ceramides induced by S. aureus α-toxin localize to lysosomes and mediate a release of cathepsin B and D from lysosomes into the cytoplasm. Cytosolic cathepsin B forms a complex with Nlrc4. Treatment of macrophages with α-toxin induces the formation of IL-1β and TNF-α. These events are reduced or abrogated, respectively, in cells lacking the acid sphingomyelinase and upon treatment of macrophages with amitriptyline, a functional inhibitor of acid sphingomyelinase. Pharmacological inhibition of cathepsin B prevented activation of the inflammasome measured as release of IL-1β, while the formation of TNF-α was independent of cathepsin B. Conclusion: We demonstrate a novel mechanism how bacterial toxins activate the inflammasome and mediate the formation and release of cytokines: S. aureus α-toxin triggers an activation of the acid sphingomyelinase and a release of ceramides resulting in the release of lysosomal cathepsin B and formation of pro-inflammatory cytokines. KW - Staphylococcus aureus KW - sphingomyelinase KW - ceramide KW - toxins KW - macrophages KW - cytokines Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181481 VL - 43 IS - 6 ER - TY - JOUR A1 - Szklarczyk, Damian A1 - Morris, John H. A1 - Cook, Helen A1 - Kuhn, Michael A1 - Wyder, Stefan A1 - Simonovic, Milan A1 - Santos, Aalberto A1 - Doncheva, Nadezhda T. A1 - Roth, Alexander A1 - Bork, Peer A1 - Jensen, Lars J. A1 - von Mering, Christian T1 - The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible JF - Nucleic Acids Research N2 - A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein–protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein–protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/. KW - string database KW - quality control KW - proteins KW - cellular function Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181445 VL - 45 IS - D1 ER - TY - JOUR A1 - Rhee, Jae-Sung A1 - Choi, Beom-Soon A1 - Kim, Jaebum A1 - Kim, Bo-Mi A1 - Lee, Young-Mi A1 - Kim, Il-Chan A1 - Kanamori, Akira A1 - Choi, Ik-Young A1 - Schartl, Manfred A1 - Lee, Jae-Seong T1 - Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus JF - Scientific Reports N2 - The Kryptolebias marmoratus is unique because it is the only selffertilizing hermaphroditic vertebrate, known to date. It primarily reproduces by internal self-fertilization in a mixed ovary/testis gonad. Here, we report on a high-quality genome assembly for the K. marmoratus South Korea (SK) strain highlighting the diversity and distribution of transposable elements (TEs). We find that K. marmoratus genome maintains number and composition of TEs. This can be an important genomic attribute promoting genome recombination in this selfing fish, while, in addition to a mixed mating strategy, it may also represent a mechanism contributing to the evolutionary adaptation to ecological pressure of the species. Future work should help clarify this point further once genomic information is gathered for other taxa of the family Rivulidae that do not self-fertilize. We provide a valuable genome resource that highlights the potential impact of TEs on the genome evolution of a fish species with an uncommon life cycle. KW - ecological genetics KW - evolutionary genetics KW - ichthyology KW - Kryptolebias marmoratus Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181329 VL - 7 ER - TY - JOUR A1 - Mannucci, Ilaria A1 - Dang, Nghi D. P. A1 - Huber, Hannes A1 - Murry, Jaclyn B. A1 - Abramson, Jeff A1 - Althoff, Thorsten A1 - Banka, Siddharth A1 - Baynam, Gareth A1 - Bearden, David A1 - Beleza-Meireles, Ana A1 - Benke, Paul J. A1 - Berland, Siren A1 - Bierhals, Tatjana A1 - Bilan, Frederic A1 - Bindoff, Laurence A. A1 - Braathen, Geir Julius A1 - Busk, Øyvind L. A1 - Chenbhanich, Jirat A1 - Denecke, Jonas A1 - Escobar, Luis F. A1 - Estes, Caroline A1 - Fleischer, Julie A1 - Groepper, Daniel A1 - Haaxma, Charlotte A. A1 - Hempel, Maja A1 - Holler-Managan, Yolanda A1 - Houge, Gunnar A1 - Jackson, Adam A1 - Kellogg, Laura A1 - Keren, Boris A1 - Kiraly-Borri, Catherine A1 - Kraus, Cornelia A1 - Kubisch, Christian A1 - Le Guyader, Gwenael A1 - Ljungblad, Ulf W. A1 - Brenman, Leslie Manace A1 - Martinez-Agosto, Julian A. A1 - Might, Matthew A1 - Miller, David T. A1 - Minks, Kelly Q. A1 - Moghaddam, Billur A1 - Nava, Caroline A1 - Nelson, Stanley F. A1 - Parant, John M. A1 - Prescott, Trine A1 - Rajabi, Farrah A1 - Randrianaivo, Hanitra A1 - Reiter, Simone F. A1 - Schuurs-Hoeijmakers, Janneke A1 - Shieh, Perry B. A1 - Slavotinek, Anne A1 - Smithson, Sarah A1 - Stegmann, Alexander P. A. A1 - Tomczak, Kinga A1 - Tveten, Kristian A1 - Wang, Jun A1 - Whitlock, Jordan H. A1 - Zweier, Christiane A1 - McWalter, Kirsty A1 - Juusola, Jane A1 - Quintero-Rivera, Fabiola A1 - Fischer, Utz A1 - Yeo, Nan Cher A1 - Kreienkamp, Hans-Jürgen A1 - Lessel, Davor T1 - Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders JF - Genome Medicine N2 - Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-306477 VL - 13 ER - TY - JOUR A1 - Maas, Bea A1 - Brandl, Manuela A1 - Hussain, Raja Imran A1 - Frank, Thomas A1 - Zulka, Klaus Peter A1 - Rabl, Dominik A1 - Walcher, Ronnie A1 - Moser, Dietmar T1 - Functional traits driving pollinator and predator responses to newly established grassland strips in agricultural landscapes JF - Journal of Applied Ecology N2 - Agricultural biodiversity and associated ecosystem functions are declining at alarming rates due to widespread land use intensification. They can only be maintained through targeted landscape management that supports species with different habitat preferences, dispersal capacities and other functional traits that determine their survival. However, we need better understanding whether short-term measures can already improve functional diversity in European agroecosystems. We investigated spatio-temporal responses of bees (solitary bees, bumblebees and honey bees), hoverflies, carabid beetles and spiders to newly established grassland strips in Lower Austria over 3 years, and along a distance gradient to old grasslands. Specifically, we asked if new grasslands, compared to old grasslands and cereal fields, serve as temporal dispersal habitat or corridor, and how species-specific traits affect dispersal patterns. Using a trait-based functional diversity approach, we investigated year and distance effects for nine selected key traits per taxon (e.g. body size, feeding guild and habitat preferences). Our results show that the functional diversity of predators and pollinators (i.e. functional richness and evenness), as well as community-weighted means of selected key traits in new grasslands significantly differed from adjacent cereal fields, but only slowly adjusted to adjacent old grasslands. These effects significantly decreased with increasing distance to old grasslands for carabids and spiders, but not for mobile bees and hoverflies. Synthesis and applications. Over 3 years, newly established grassland strips supported larger sized and actively foraging/hunting species in the agricultural landscape. Adjacent crops likely benefit from such measures through enhanced functional diversity and related ecosystem services. However, our results also suggest that 3-year period is too short to enhance the occurrence of pollinators and epigeic predators in new grasslands. Agri-environment measures need to be complemented by the conservation of permanent habitats to effectively maintain species and functional diversity. Our findings should be acknowledged by European policy and agricultural decision makers for the design of more effective agri-environment schemes, taking into account trait-dependent species responses to land use change. KW - agri-environment schemes KW - Common Agricultural Policy KW - ecosystem services; KW - Europe KW - functional diversity analysis; KW - pollination KW - predation KW - trait-based management Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369992 VL - 58 ER - TY - JOUR A1 - Lu, Yuan A1 - Bierbach, David A1 - Ormanns, Jenny A1 - Warren, Wesley C. A1 - Walter, Ronald B. A1 - Schartl, Manfred T1 - Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly JF - Genome Research N2 - The Amazon molly is a unique clonal fish species that originated from an interspecies hybrid between Poecilia species P. mexicana and P. latipinna. It reproduces by gynogenesis, which eliminates paternal genomic contribution to offspring. An earlier study showed that Amazon molly shows biallelic expression for a large portion of the genome, leading to two main questions: (1) Are the allelic expression patterns from the initial hybridization event stabilized or changed during establishment of the asexual species and its further evolution? (2) Is allelic expression biased toward one parental allele a stochastic or adaptive process? To answer these questions, the allelic expression of P. formosa siblings was assessed to investigate intra- and inter-cohort allelic expression variability. For comparison, interspecies hybrids between P. mexicana and P. latipinna were produced in the laboratory to represent the P. formosa ancestor. We have identified inter-cohort and intra-cohort variation in parental allelic expression. The existence of inter-cohort divergence suggests functional P. formosa allelic expression patterns do not simply reflect the atavistic situation of the first interspecies hybrid but potentially result from long-term selection of transcriptional fitness. In addition, clonal fish show a transcriptional trend representing minimal intra-clonal variability in allelic expression patterns compared to the corresponding hybrids. The intra-clonal similarity in gene expression translates to sophisticated genetic functional regulation at the individuum level. These findings suggest the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369578 VL - 31 ER - TY - JOUR A1 - Loza-Valdes, Angel A1 - Mayer, Alexander E A1 - Kassouf, Toufic A1 - Trujillo-Viera, Jonathan A1 - Schmitz, Werner A1 - Dziaczkowski, Filip A1 - Leitges, Michael A1 - Schlosser, Andreas A1 - Sumara, Grzegorz T1 - A phosphoproteomic approach reveals that PKD3 controls PKA-mediated glucose and tyrosine metabolism JF - Life Science Alliance N2 - Members of the protein kinase D (PKD) family (PKD1, 2, and 3) integrate hormonal and nutritional inputs to regulate complex cellular metabolism. Despite the fact that a number of functions have been annotated to particular PKDs, their molecular targets are relatively poorly explored. PKD3 promotes insulin sensitivity and suppresses lipogenesis in the liver of animals fed a high-fat diet. However, its substrates are largely unknown. Here we applied proteomic approaches to determine PKD3 targets. We identified more than 300 putative targets of PKD3. Furthermore, biochemical analysis revealed that PKD3 regulates cAMP-dependent PKA activity, a master regulator of the hepatic response to glucagon and fasting. PKA regulates glucose, lipid, and amino acid metabolism in the liver, by targeting key enzymes in the respective processes. Among them the PKA targets phenylalanine hydroxylase (PAH) catalyzes the conversion of phenylalanine to tyrosine. Consistently, we showed that PKD3 is activated by glucagon and promotes glucose and tyrosine levels in hepatocytes. Therefore, our data indicate that PKD3 might play a role in the hepatic response to glucagon. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369560 VL - 4 ER - TY - JOUR A1 - Li, Yuanyue A1 - Kuhn, Michael A1 - Zukowska-Kasprzyk, Joanna A1 - Hennrich, Marco L. A1 - Kastritis, Panagiotis L. A1 - O'Reilly, Francis J. A1 - Phapale, Prasad A1 - Beck, Martin A1 - Gavin, Anne-Claude A1 - Bork, Peer T1 - Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum JF - PLOS ONE N2 - Protein–metabolite interactions play an important role in the cell’s metabolism and many methods have been developed to screen them in vitro. However, few methods can be applied at a large scale and not alter biological state. Here we describe a proteometabolomic approach, using chromatography to generate cell fractions which are then analyzed with mass spectrometry for both protein and metabolite identification. Integrating the proteomic and metabolomic analyses makes it possible to identify protein-bound metabolites. Applying the concept to the thermophilic fungus Chaetomium thermophilum, we predict 461 likely protein-metabolite interactions, most of them novel. As a proof of principle, we experimentally validate a predicted interaction between the ribosome and isopentenyl adenine. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-364299 VL - 16 ER - TY - JOUR A1 - Li, Ming A1 - Zhang, Rui A1 - Fan, Guangyi A1 - Xu, Wenteng A1 - Zhou, Qian A1 - Wang, Lei A1 - Li, Wensheng A1 - Pang, Zunfang A1 - Yu, Mengjun A1 - Liu, Qun A1 - Liu, Xin A1 - Schartl, Manfred A1 - Chen, Songlin T1 - Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus JF - Molecular Biology and Evolution N2 - Sex chromosomes are a peculiar constituent of the genome because the evolutionary forces that fix the primary sex-determining gene cause genic degeneration and accumulation of junk DNA in the heterogametic partner. One of the most spectacular phenomena in sex chromosome evolution is the occurrence of neo-Y chromosomes, which lead to X1X2Y sex-determining systems. Such neo-sex chromosomes are critical for understanding the processes of sex chromosome evolution because they rejuvenate their total gene content. We assembled the male and female genomes at the chromosome level of the spotted knifejaw (Oplegnathus punctatus), which has a cytogenetically recognized neo-Y chromosome. The full assembly and annotation of all three sex chromosomes allowed us to reconstruct their evolutionary history. Contrary to other neo-Y chromosomes, the fusion to X2 is quite ancient, estimated at 48 Ma. Despite its old age and being even older in the X1 homologous region which carries a huge inversion that occurred as early as 55–48 Ma, genetic degeneration of the neo-Y appears to be only moderate. Transcriptomic analysis showed that sex chromosomes harbor 87 genes, which may serve important functions in the testis. The accumulation of such male-beneficial genes, a large inversion on the X1 homologous region and fusion to X2 appear to be the main drivers of neo-Y evolution in the spotted knifejaw. The availability of high-quality assemblies of the neo-Y and both X chromosomes make this fish an ideal model for a better understanding of the variability of sex determination mechanisms and of sex chromosome evolution. KW - neo-Y KW - evolution; KW - spotted knifejaw KW - genome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-364215 VL - 38 ER - TY - JOUR A1 - Letunic, Ivica A1 - Bork, Peer T1 - Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation JF - Nucleic Acids Research N2 - The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363803 VL - 49 ER - TY - JOUR A1 - Lehmann, Julian A1 - Jørgensen, Morten E. A1 - Fratz, Stefanie A1 - Müller, Heike M. A1 - Kusch, Jana A1 - Scherzer, Sönke A1 - Navarro-Retamal, Carlos A1 - Mayer, Dominik A1 - Böhm, Jennifer A1 - Konrad, Kai R. A1 - Terpitz, Ulrich A1 - Dreyer, Ingo A1 - Mueller, Thomas D. A1 - Sauer, Markus A1 - Hedrich, Rainer A1 - Geiger, Dietmar A1 - Maierhofer, Tobias T1 - Acidosis-induced activation of anion channel SLAH3 in the flooding-related stress response of Arabidopsis JF - Current Biology N2 - Plants, as sessile organisms, gained the ability to sense and respond to biotic and abiotic stressors to survive severe changes in their environments. The change in our climate comes with extreme dry periods but also episodes of flooding. The latter stress condition causes anaerobiosis-triggered cytosolic acidosis and impairs plant function. The molecular mechanism that enables plant cells to sense acidity and convey this signal via membrane depolarization was previously unknown. Here, we show that acidosis-induced anion efflux from Arabidopsis (Arabidopsis thaliana) roots is dependent on the S-type anion channel AtSLAH3. Heterologous expression of SLAH3 in Xenopus oocytes revealed that the anion channel is directly activated by a small, physiological drop in cytosolic pH. Acidosis-triggered activation of SLAH3 is mediated by protonation of histidine 330 and 454. Super-resolution microscopy analysis showed that the increase in cellular proton concentration switches SLAH3 from an electrically silent channel dimer into its active monomeric form. Our results show that, upon acidification, protons directly switch SLAH3 to its open configuration, bypassing kinase-dependent activation. Moreover, under flooding conditions, the stress response of Arabidopsis wild-type (WT) plants was significantly higher compared to SLAH3 loss-of-function mutants. Our genetic evidence of SLAH3 pH sensor function may guide the development of crop varieties with improved stress tolerance. KW - SLAH3 KW - S-type anion channel KW - hypoxia KW - pH KW - cytosolic acidification KW - flooding KW - PALM KW - stoichiometry Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363320 VL - 31 ER - TY - JOUR A1 - Le Provost, Gaëtane A1 - Thiele, Jan A1 - Westphal, Catrin A1 - Penone, Caterina A1 - Allan, Eric A1 - Neyret, Margot A1 - van der Plas, Fons A1 - Ayasse, Manfred A1 - Bardgett, Richard D. A1 - Birkhofer, Klaus A1 - Boch, Steffen A1 - Bonkowski, Michael A1 - Buscot, Francois A1 - Feldhaar, Heike A1 - Gaulton, Rachel A1 - Goldmann, Kezia A1 - Gossner, Martin M. A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Krauss, Jochen A1 - Renner, Swen A1 - Scherreiks, Pascal A1 - Sikorski, Johannes A1 - Baulechner, Dennis A1 - Blüthgen, Nico A1 - Bolliger, Ralph A1 - Börschig, Carmen A1 - Busch, Verena A1 - Chisté, Melanie A1 - Fiore-Donno, Anna Maria A1 - Fischer, Markus A1 - Arndt, Hartmut A1 - Hoelzel, Norbert A1 - John, Katharina A1 - Jung, Kirsten A1 - Lange, Markus A1 - Marzini, Carlo A1 - Overmann, Jörg A1 - Paŝalić, Esther A1 - Perović, David J. A1 - Prati, Daniel A1 - Schäfer, Deborah A1 - Schöning, Ingo A1 - Schrumpf, Marion A1 - Sonnemann, Ilja A1 - Steffan-Dewenter, Ingolf A1 - Tschapka, Marco A1 - Türke, Manfred A1 - Vogt, Juliane A1 - Wehner, Katja A1 - Weiner, Christiane A1 - Weisser, Wolfgang A1 - Wells, Konstans A1 - Werner, Michael A1 - Wolters, Volkmar A1 - Wubet, Tesfaye A1 - Wurst, Susanne A1 - Zaitsev, Andrey S. A1 - Manning, Peter T1 - Contrasting responses of above- and belowground diversity to multiple components of land-use intensity JF - Nature Communications N2 - Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity. KW - biodiversity KW - community ecology KW - grassland ecology Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-371552 VL - 12 ER - TY - JOUR A1 - Larrieu, Laurent A1 - Cabanettes, Alain A1 - Courbaud, Benoit A1 - Goulard, Michel A1 - Heintz, Wilfried A1 - Kozák, Daniel A1 - Kraus, Daniel A1 - Lachat, Thibault A1 - Ladet, Sylvie A1 - Müller, Jörg A1 - Paillet, Yoan A1 - Schuck, Andreas A1 - Stillhard, Jonas A1 - Svoboda, Miroslav T1 - Co-occurrence patterns of tree-related microhabitats: A method to simplify routine monitoring JF - Ecological Indicators N2 - A Tree-related Microhabitat (TreM) is a distinct, well-delineated morphological singularity occurring on living or standing dead trees, which constitutes a crucial substrate or life site for various species. TreMs are widely recognized as key features for biodiversity. Current TreM typology identifies 47 TreM types according to their morphology and their associated taxa. In order to provide a range of resolutions and make the typology more user-friendly, these 47 TreM types have been pooled into 15 groups and seven forms. Depending on the accuracy required and the time available, a user can now choose to describe TreMs at resolution levels corresponding to type, group or form. Another way to more easily record TreMs during routine management work would be to use co-occurrence patterns to reduce the number of observed TreMs required. Based on a large international TreM database (2052 plots; 70,958 individual trees; 78 tree species), we evaluated both the significance and the magnitude of TreM co-occurrence on living trees for 11 TreM groups. We highlighted 33 significant co-occurrences for broadleaves and nine for conifers. Bark loss, rot hole, crack and polypore had the highest number of positive co-occurrences (N = 8) with other TreMs on broadleaves; bark loss (N = 4) had the highest number for conifers. We found mutually exclusive occurrences only for conifers: Exposed Heartwood excluded both dendrotelm and sap run. Among the four variables we tested for their positive contribution to significant co-occurrences, tree diameter at breast height was the most consistent. Based on our results and practical considerations, we selected three TreM groups for broadleaves, and nine for conifers, and formed useful short lists to reduce the number of TreM groups to assess during routine forest management work in the field. In addition, detecting potential similarities or associations between TreMs has potential theoretical value, e.g. it may help researchers identify common factors favouring TreM formation or help managers select trees with multiple TreMs as candidates for retention. KW - TreM monitoring KW - biodiversity-friendly forest management Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363158 VL - 127 ER - TY - JOUR A1 - Kuhl, Heiner A1 - Guiguen, Yann A1 - Höhne, Christin A1 - Kreuz, Eva A1 - Du, Kang A1 - Klopp, Christophe A1 - Lopez-Roques,, Céline A1 - Yebra-Pimentel, Elena Santidrian A1 - Ciorpac, Mitica A1 - Gessner, Jörn A1 - Holostenco, Daniela A1 - Kleiner, Wibke A1 - Kohlmann, Klaus A1 - Lamatsch, Dunja K. A1 - Prokopov, Dmitry A1 - Bestin, Anastasia A1 - Bonpunt, Emmanuel A1 - Debeuf, Bastien A1 - Haffray, Pierrick A1 - Morvezen, Romain A1 - Patrice, Pierre A1 - Suciu, Radu A1 - Dirks, Ron A1 - Wuertz, Sven A1 - Kloas, Werner A1 - Schartl, Manfred A1 - Stöck, Matthias T1 - A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes JF - Philosophical Transactions of the Royal Society B N2 - Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’. KW - acipenseridae KW - sturgeon KW - sex chromosomes KW - female-specific KW - polyploidy KW - evolution Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363050 VL - 376 ER - 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 - Dornelas, Maria A1 - Antão, Laura H. A1 - Moyes, Faye A1 - Bates, Amanda E. A1 - Magurran, Anne E. A1 - Adam, Dušan A1 - Akhmetzhanova, Asem A. A1 - Appeltans, Ward A1 - Arcos, José Manuel A1 - Arnold, Haley A1 - Ayyappan, Narayanan A1 - Badihi, Gal A1 - Baird, Andrew H. A1 - Barbosa, Miguel A1 - Barreto, Tiago Egydio A1 - Bässler, Claus A1 - Bellgrove, Alecia A1 - Belmaker, Jonathan A1 - Benedetti-Cecchi, Lisandro A1 - Bett, Brian J. A1 - Bjorkman, Anne D. A1 - Błażewicz, Magdalena A1 - Blowes, Shane A. A1 - Bloch, Christopher P. Bloch A1 - Bonebrake, Timothy C. A1 - Boyd, Susan A1 - Bradford, Matt A1 - Brooks, Andrew J. A1 - Brown, James H. A1 - Bruelheide, Helge A1 - Budy, Phaedra A1 - Carvalho, Fernando A1 - Castañeda-Moya, Edward A1 - Chen, Chaolun Allen A1 - Chamblee, John F. A1 - Chase, Tory J. A1 - Siegwart Collier, Laura A1 - Collinge, Sharon K. A1 - Condit, Richard A1 - Cooper, Elisabeth J. A1 - Cornelissen, J. Hans C. A1 - Cotano, Unai A1 - Crow, Shannan Kyle A1 - Damasceno, Gabriella A1 - Davies, Claire H. A1 - Davis, Robert A. A1 - Day, Frank P. A1 - Degraer, Steven A1 - Doherty, Tim S. A1 - Dunn, Timothy E. A1 - Durigan, Giselda A1 - Duffy, J. Emmett A1 - Edelist, Dor A1 - Edgar, Graham J. A1 - Elahi, Robin A1 - Elmendorf, Sarah C. A1 - Enemar, Anders A1 - Ernest, S. K. Morgan A1 - Escribano, Rubén A1 - Estiarte, Marc A1 - Evans, Brian S. A1 - Fan, Tung-Yung A1 - Turini Farah, Fabiano A1 - Loureiro Fernandes, Luiz A1 - Farneda, Fábio Z. A1 - Fidelis, Alessandra A1 - Fitt, Robert A1 - Fosaa, Anna Maria A1 - Franco, Geraldo Antonio Daher Correa A1 - Frank, Grace E. A1 - Fraser, William R. A1 - García, Hernando A1 - Cazzolla Gatti, Roberto A1 - Givan, Or A1 - Gorgone-Barbosa, Elizabeth A1 - Gould, William A. A1 - Gries, Corinna A1 - Grossman, Gary D. A1 - Gutierréz, Julio R. A1 - Hale, Stephen A1 - Harmon, Mark E. A1 - Harte, John A1 - Haskins, Gary A1 - Henshaw, Donald L. A1 - Hermanutz, Luise A1 - Hidalgo, Pamela A1 - Higuchi, Pedro A1 - Hoey, Andrew A1 - Van Hoey, Gert A1 - Hofgaard, Annika A1 - Holeck, Kristen A1 - Hollister, Robert D. A1 - Holmes, Richard A1 - Hoogenboom, Mia A1 - Hsieh, Chih-hao A1 - Hubbell, Stephen P. A1 - Huettmann, Falk A1 - Huffard, Christine L. A1 - Hurlbert, Allen H. A1 - Ivanauskas, Natália Macedo A1 - Janík, David A1 - Jandt, Ute A1 - Jażdżewska, Anna A1 - Johannessen, Tore A1 - Johnstone, Jill A1 - Jones, Julia A1 - Jones, Faith A. M. A1 - Kang, Jungwon A1 - Kartawijaya, Tasrif A1 - Keeley, Erin C. A1 - Kelt, Douglas A. A1 - Kinnear, Rebecca A1 - Klanderud, Kari A1 - Knutsen, Halvor A1 - Koenig, Christopher C. A1 - Kortz, Alessandra R. A1 - Král, Kamil A1 - Kuhnz, Linda A. A1 - Kuo, Chao-Yang A1 - Kushner, David J. A1 - Laguionie-Marchais, Claire A1 - Lancaster, Lesley T. A1 - Lee, Cheol Min A1 - Lefcheck, Jonathan S. A1 - Lévesque, Esther A1 - Lightfoot, David A1 - Lloret, Francisco A1 - Lloyd, John D. A1 - López-Baucells, Adrià A1 - Louzao, Maite A1 - Madin, Joshua S. A1 - Magnússon, Borgþór A1 - Malamud, Shahar A1 - Matthews, Iain A1 - McFarland, Kent P. A1 - McGill, Brian A1 - McKnight, Diane A1 - McLarney, William O. A1 - Meador, Jason A1 - Meserve, Peter L. A1 - Metcalfe, Daniel J. A1 - Meyer, Christoph F. J. A1 - Michelsen, Anders A1 - Milchakova, Nataliya A1 - Moens, Tom A1 - Moland, Even A1 - Moore, Jon A1 - Moreira, Carolina Mathias A1 - Müller, Jörg A1 - Murphy, Grace A1 - Myers-Smith, Isla H. A1 - Myster, Randall W. A1 - Naumov, Andrew A1 - Neat, Francis A1 - Nelson, James A. A1 - Nelson, Michael Paul A1 - Newton, Stephen F. A1 - Norden, Natalia A1 - Oliver, Jeffrey C. A1 - Olsen, Esben M. A1 - Onipchenko, Vladimir G. A1 - Pabis, Krzysztof A1 - Pabst, Robert J. A1 - Paquette, Alain A1 - Pardede, Sinta A1 - Paterson, David M. A1 - Pélissier, Raphaël A1 - Peñuelas, Josep A1 - Pérez-Matus, Alejandro A1 - Pizarro, Oscar A1 - Pomati, Francesco A1 - Post, Eric A1 - Prins, Herbert H. T. A1 - Priscu, John C. A1 - Provoost, Pieter A1 - Prudic, Kathleen L. A1 - Pulliainen, Erkki A1 - Ramesh, B. R. A1 - Ramos, Olivia Mendivil A1 - Rassweiler, Andrew A1 - Rebelo, Jose Eduardo A1 - Reed, Daniel C. A1 - Reich, Peter B. A1 - Remillard, Suzanne M. A1 - Richardson, Anthony J. A1 - Richardson, J. Paul A1 - van Rijn, Itai A1 - Rocha, Ricardo A1 - Rivera-Monroy, Victor H. A1 - Rixen, Christian A1 - Robinson, Kevin P. A1 - Rodrigues, Ricardo Ribeiro A1 - de Cerqueira Rossa-Feres, Denise A1 - Rudstam, Lars A1 - Ruhl, Henry A1 - Ruz, Catalina S. A1 - Sampaio, Erica M. A1 - Rybicki, Nancy A1 - Rypel, Andrew A1 - Sal, Sofia A1 - Salgado, Beatriz A1 - Santos, Flavio A. M. A1 - Savassi-Coutinho, Ana Paula A1 - Scanga, Sara A1 - Schmidt, Jochen A1 - Schooley, Robert A1 - Setiawan, Fakhrizal A1 - Shao, Kwang-Tsao A1 - Shaver, Gaius R. A1 - Sherman, Sally A1 - Sherry, Thomas W. A1 - Siciński, Jacek A1 - Sievers, Caya A1 - da Silva, Ana Carolina A1 - da Silva, Fernando Rodrigues A1 - Silveira, Fabio L. A1 - Slingsby, Jasper A1 - Smart, Tracey A1 - Snell, Sara J. A1 - Soudzilovskaia, Nadejda A. A1 - Souza, Gabriel B. G. A1 - Souza, Flaviana Maluf A1 - Souza, Vinícius Castro A1 - Stallings, Christopher D. A1 - Stanforth, Rowan A1 - Stanley, Emily H. A1 - Sterza, José Mauro A1 - Stevens, Maarten A1 - Stuart-Smith, Rick A1 - Suarez, Yzel Rondon A1 - Supp, Sarah A1 - Tamashiro, Jorge Yoshio A1 - Tarigan, Sukmaraharja A1 - Thiede, Gary P. A1 - Thorn, Simon A1 - Tolvanen, Anne A1 - Toniato, Maria Teresa Zugliani A1 - Totland, Ørjan A1 - Twilley, Robert R. A1 - Vaitkus, Gediminas A1 - Valdivia, Nelson A1 - Vallejo, Martha Isabel A1 - Valone, Thomas J. A1 - Van Colen, Carl A1 - Vanaverbeke, Jan A1 - Venturoli, Fabio A1 - Verheye, Hans M. A1 - Vianna, Marcelo A1 - Vieira, Rui P. A1 - Vrška, Tomáš A1 - Vu, Con Quang A1 - Vu, Lien Van A1 - Waide, Robert B. A1 - Waldock, Conor A1 - Watts, Dave A1 - Webb, Sara A1 - Wesołowski, Tomasz A1 - White, Ethan P. A1 - Widdicombe, Claire E. A1 - Wilgers, Dustin A1 - Williams, Richard A1 - Williams, Stefan B. A1 - Williamson, Mark A1 - Willig, Michael R. A1 - Willis, Trevor J. A1 - Wipf, Sonja A1 - Woods, Kerry D. A1 - Woehler, Eric J. A1 - Zawada, Kyle A1 - Zettler, Michael L. T1 - BioTIME: A database of biodiversity time series for the Anthropocene JF - Global Ecology and Biogeography N2 - Motivation The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). Time period and grain BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. Software format .csv and .SQL. KW - biodiversity KW - global KW - spatial KW - species richness KW - temporal KW - turnover Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222846 VL - 27 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 - Moll, Julia A1 - Kellner, Harald A1 - Leonhardt, Sabrina A1 - Stengel, Elisa A1 - Dahl, Andreas A1 - Bässler, Claus A1 - Buscot, François A1 - Hofrichter, Martin A1 - Hoppe, Björn T1 - Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood JF - Environmental Microbiology N2 - Deadwood represents an important structural component of forest ecosystems, where it provides diverse niches for saproxylic biota. Although wood-inhabiting prokaryotes are involved in its degradation, knowledge about their diversity and the drivers of community structure is scarce. To explore the effect of deadwood substrate on microbial distribution, the present study focuses on the microbial communities of deadwood logs from 13 different tree species investigated using an amplicon based deep-sequencing analysis. Sapwood and heartwood communities were analysed separately and linked to various relevant wood physico-chemical parameters. Overall, Proteobacteria, Acidobacteria and Actinobacteria represented the most dominant phyla. Microbial OTU richness and community structure differed significantly between tree species and between sapwood and heartwood. These differences were more pronounced for heartwood than for sapwood. The pH value and water content were the most important drivers in both wood compartments. Overall, investigating numerous tree species and two compartments provided a remarkably comprehensive view of microbial diversity in deadwood. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224168 VL - 20 ER - TY - JOUR A1 - Hilmers, Torben A1 - Friess, Nicolas A1 - Bässler, Claus A1 - Heurich, Marco A1 - Brandl, Roland A1 - Pretzsch, Hans A1 - Seidl, Rupert A1 - Müller, Jörg T1 - Biodiversity along temperate forest succession JF - Journal of Applied Ecology N2 - 1. The successional dynamics of forests—from canopy openings to regeneration, maturation, and decay—influence the amount and heterogeneity of resources available for forest-dwelling organisms. Conservation has largely focused only on selected stages of forest succession (e.g., late-seral stages). However, to develop comprehensive conservation strategies and to understand the impact of forest management on biodiversity, a quantitative understanding of how different trophic groups vary over the course of succession is needed. 2. We classified mixed mountain forests in Central Europe into nine successional stages using airborne LiDAR. We analysed α- and β-diversity of six trophic groups encompassing approximately 3,000 species from three kingdoms. We quantified the effect of successional stage on the number of species with and without controlling for species abundances and tested whether the data fit the more-individuals hypothesis or the habitat heterogeneity hypothesis. Furthermore, we analysed the similarity of assemblages along successional development. 3. The abundance of producers, first-order consumers, and saprotrophic species showed a U-shaped response to forest succession. The number of species of producer and consumer groups generally followed this U-shaped pattern. In contrast to our expectation, the number of saprotrophic species did not change along succession. When we controlled for the effect of abundance, the number of producer and saproxylic beetle species increased linearly with forest succession, whereas the U-shaped response of the number of consumer species persisted. The analysis of assemblages indicated a large contribution of succession-mediated β-diversity to regional γ-diversity. 4. Synthesis and applications. Depending on the species group, our data supported both the more-individuals hypothesis and the habitat heterogeneity hypothesis. Our results highlight the strong influence of forest succession on biodiversity and underline the importance of controlling for successional dynamics when assessing biodiversity change in response to external drivers such as climate change. The successional stages with highest diversity (early and late successional stages) are currently strongly underrepresented in the forests of Central Europe. We thus recommend that conservation strategies aim at a more balanced representation of all successional stages. KW - biodiversity KW - forest dynamics KW - forest succession KW - habitat heterogeneity KW - LiDAR KW - species density KW - temperate forests KW - β-diversity Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-320632 VL - 55 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 - Hillaert, Jasmijn A1 - Hovestadt, Thomas A1 - Vandegehuchte, Martijn L. A1 - Bonte, Dries T1 - Size-dependent movement explains why bigger is better in fragmented landscapes JF - Ecology and Evolution N2 - Body size is a fundamental trait known to allometrically scale with metabolic rate and therefore a key determinant of individual development, life history, and consequently fitness. In spatially structured environments, movement is an equally important driver of fitness. Because movement is tightly coupled with body size, we expect habitat fragmentation to induce a strong selection pressure on size variation across and within species. Changes in body size distributions are then, in turn, expected to alter food web dynamics. However, no consensus has been reached on how spatial isolation and resource growth affect consumer body size distributions. Our aim was to investigate how these two factors shape the body size distribution of consumers under scenarios of size-dependent and size-independent consumer movement by applying a mechanistic, individual-based resource–consumer model. We also assessed the consequences of altered body size distributions for important ecosystem traits such as resource abundance and consumer stability. Finally, we determined those factors that explain most variation in size distributions. We demonstrate that decreasing connectivity and resource growth select for communities (or populations) consisting of larger species (or individuals) due to strong selection for the ability to move over longer distances if the movement is size-dependent. When including size-dependent movement, intermediate levels of connectivity result in increases in local size diversity. Due to this elevated functional diversity, resource uptake is maximized at the metapopulation or metacommunity level. At these intermediate levels of connectivity, size-dependent movement explains most of the observed variation in size distributions. Interestingly, local and spatial stability of consumer biomass is lowest when isolation and resource growth are high. Finally, we highlight that size-dependent movement is of vital importance for the survival of populations or communities within highly fragmented landscapes. Our results demonstrate that considering size-dependent movement is essential to understand how habitat fragmentation and resource growth shape body size distributions—and the resulting metapopulation or metacommunity dynamics—of consumers. KW - allometric scaling KW - body size distributions; KW - eco-evolutionary dynamics KW - habitat fragmentation KW - isolation KW - metabolic theory KW - optimal size KW - size-dependent movement Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-320322 VL - 8 ER - TY - JOUR A1 - Stein, Katharina A1 - Stenchly, Kathrin A1 - Coulibaly, Drissa A1 - Pauly, Alain A1 - Dimobe, Kangbeni A1 - Steffan-Dewenter, Ingolf A1 - Konaté, Souleymane A1 - Goetze, Dethardt A1 - Porembski, Stefan A1 - Linsenmair, K. Eduard T1 - Impact of human disturbance on bee pollinator communities in savanna and agricultural sites in Burkina Faso, West Africa JF - Ecology and Evolution N2 - All over the world, pollinators are threatened by land-use change involving degradation of seminatural habitats or conversion into agricultural land. Such disturbance often leads to lowered pollinator abundance and/or diversity, which might reduce crop yield in adjacent agricultural areas. For West Africa, changes in bee communities across disturbance gradients from savanna to agricultural land are mainly unknown. In this study, we monitored for the impact of human disturbance on bee communities in savanna and crop fields. We chose three savanna areas of varying disturbance intensity (low, medium, and high) in the South Sudanian zone of Burkina Faso, based on land-use/land cover data via Landsat images, and selected nearby cotton and sesame fields. During 21 months covering two rainy and two dry seasons in 2014 and 2015, we captured bees using pan traps. Spatial and temporal patterns of bee species abundance, richness, evenness and community structure were assessed. In total, 35,469 bee specimens were caught on 12 savanna sites and 22 fields, comprising 97 species of 32 genera. Bee abundance was highest at intermediate disturbance in the rainy season. Species richness and evenness did not differ significantly. Bee communities at medium and highly disturbed savanna sites comprised only subsets of those at low disturbed sites. An across-habitat spillover of bees (mostly abundant social bee species) from savanna into crop fields was observed during the rainy season when crops are mass-flowering, whereas most savanna plants are not in bloom. Despite disturbance intensification, our findings suggest that wild bee communities can persist in anthropogenic landscapes and that some species even benefitted disproportionally. West African areas of crop production such as for cotton and sesame may serve as important food resources for bee species in times when resources in the savanna are scarce and receive at the same time considerable pollination service. KW - bee communities KW - cotton KW - sesame KW - species spillover KW - sub-Saharan Africa Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-239999 VL - 8 ER - TY - JOUR A1 - Minden, Vanessa A1 - Schnetger, Bernhard A1 - Pufal, Gesine A1 - Leonhardt, Sara D. T1 - Antibiotic-induced effects on scaling relationships and on plant element contents in herbs and grasses JF - Ecology and Evolution N2 - Plant performance is correlated with element concentrations in plant tissue, which may be impacted by adverse chemical soil conditions. Antibiotics of veterinary origin can adversely affect plant performance. They are released to agricultural fields via grazing animals or manure, taken up by plants and may be stored, transformed or sequestered by plant metabolic processes. We studied the potential effects of three antibiotics (penicillin, sulfadiazine, and tetracycline) on plant element contents (macro- and microelements). Plant species included two herb species (Brassica napus and Capsella bursa-pastoris) and two grass species (Triticum aestivum and Apera spica-venti), representing two crop species and two noncrop species commonly found in field margins, respectively. Antibiotic concentrations were chosen as to reflect in vivo situations, that is, relatively low concentrations similar to those detected in soils. In a greenhouse experiment, plants were raised in soil spiked with antibiotics. After harvest, macro- and microelements in plant leaves, stems, and roots were determined (mg/g). Results indicate that antibiotics can affect element contents in plants. Penicillin exerted the greatest effect both on element contents and on scaling relationships of elements between plant organs. Roots responded strongest to antibiotics compared to stems and leaves. We conclude that antibiotics in the soil, even in low concentrations, lead to low-element homeostasis, altering the scaling relationships between roots and other plant organs, which may affect metabolic processes and ultimately the performance of a plant. KW - antibiotics KW - homeostasis KW - scaling relationships KW - standardized major axis regression KW - tissue nutrient contents Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224094 VL - 8 ER - TY - JOUR A1 - Schubert, Frank K. A1 - Hagedorn, Nicolas A1 - Yoshii, Taishi A1 - Helfrich-Förster, Charlotte A1 - Rieger, Dirk T1 - Neuroanatomical details of the lateral neurons of Drosophila melanogaster support their functional role in the circadian system JF - Journal of Comparative Neurology N2 - Drosophila melanogaster is a long-standing model organism in the circadian clock research. A major advantage is the relative small number of about 150 neurons, which built the circadian clock in Drosophila. In our recent work, we focused on the neuroanatomical properties of the lateral neurons of the clock network. By applying the multicolor-labeling technique Flybow we were able to identify the anatomical similarity of the previously described E2 subunit of the evening oscillator of the clock, which is built by the 5th small ventrolateral neuron (5th s-LNv) and one ITP positive dorsolateral neuron (LNd). These two clock neurons share the same spatial and functional properties. We found both neurons innervating the same brain areas with similar pre- and postsynaptic sites in the brain. Here the anatomical findings support their shared function as a main evening oscillator in the clock network like also found in previous studies. A second quite surprising finding addresses the large lateral ventral PDF-neurons (l-LNvs). We could show that the four hardly distinguishable l-LNvs consist of two subgroups with different innervation patterns. While three of the neurons reflect the well-known branching pattern reproduced by PDF immunohistochemistry, one neuron per brain hemisphere has a distinguished innervation profile and is restricted only to the proximal part of the medulla-surface. We named this neuron “extra” l-LNv (l-LNvx). We suggest the anatomical findings reflect different functional properties of the two l-LNv subgroups. KW - circadian clock neurons KW - Drosophila melanogaster KW - flybow KW - morphology KW - RRID: AB_760350 KW - RRID: AB_2315460 KW - RRID: AB_2314242 KW - RRID: AB_2315311 KW - RRID: AB_2314041 KW - RRID: AB_300798 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-234477 VL - 526 ER - TY - JOUR A1 - Flunkert, Julia A1 - Maierhofer, Anna A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Horvath, Steve A1 - Nanda, Indrajit A1 - Haaf, Thomas T1 - Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts JF - Experimental Cell Research N2 - To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for variation in radiation sensitivity, all experiments were performed with two different fibroblast strains. After a single X-ray dose of 2 Gy more than half of the irradiated clones exhibited radiation-induced genome instability (RIGI). Irradiated clones displayed an increased rate of loss of chromosome Y (LOY) and copy number variations (CNVs), compared to controls. CNV breakpoints clustered in specific chromosome regions, in particular 3p14.2 and 7q11.21, coinciding with common fragile sites. CNVs affecting the FHIT gene in FRA3B were observed in independent unstable clones and may drive RIGI. Bisulfite pyrosequencing of control clones and the respective primary culture revealed global hypomethylation of ALU, LINE-1, and alpha-satellite repeats as well as rDNA hypermethylation during in vitro ageing. Irradiated clones showed further reduced ALU and alpha-satellite methylation and increased rDNA methylation, compared to controls. Methylation arrays identified several hundred differentially methylated genes and several enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic (LOY and CNVs) and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis. We did not observe epigenetic differences between stable and unstable irradiated clones. The fact that the DNA methylation (DNAm) age of clones derived from the same primary culture varied greatly suggests that DNAm age of a single cell (represented by a clone) can be quite different from the DNAm age of a tissue. We propose that DNAm age reflects the emergent property of a large number of individual cells whose respective DNAm ages can be highly variable. KW - copy number variation (CNV) KW - delayed radiation effects KW - DNA methylation (DNAm) age KW - global DNA methylation KW - loss of chromosome Y (LOY); KW - methylation array analysis KW - radiation-induced genome instability (RIGI) Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228177 VL - 370 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 - Göttlich, Claudia A1 - Kunz, Meik A1 - Zapp, Cornelia A1 - Nietzer, Sarah L. A1 - Walles, Heike A1 - Dandekar, Thomas A1 - Dandekar, Gudrun T1 - A combined tissue-engineered/in silico signature tool patient stratification in lung cancer JF - Molecular Oncology N2 - Patient-tailored therapy based on tumor drivers is promising for lung cancer treatment. For this, we combined in vitro tissue models with in silico analyses. Using individual cell lines with specific mutations, we demonstrate a generic and rapid stratification pipeline for targeted tumor therapy. We improve in vitro models of tissue conditions by a biological matrix-based three-dimensional (3D) tissue culture that allows in vitro drug testing: It correctly shows a strong drug response upon gefitinib (Gef) treatment in a cell line harboring an EGFR-activating mutation (HCC827), but no clear drug response upon treatment with the HSP90 inhibitor 17AAG in two cell lines with KRAS mutations (H441, A549). In contrast, 2D testing implies wrongly KRAS as a biomarker for HSP90 inhibitor treatment, although this fails in clinical studies. Signaling analysis by phospho-arrays showed similar effects of EGFR inhibition by Gef in HCC827 cells, under both 2D and 3D conditions. Western blot analysis confirmed that for 3D conditions, HSP90 inhibitor treatment implies different p53 regulation and decreased MET inhibition in HCC827 and H441 cells. Using in vitro data (western, phospho-kinase array, proliferation, and apoptosis), we generated cell line-specific in silico topologies and condition-specific (2D, 3D) simulations of signaling correctly mirroring in vitro treatment responses. Networks predict drug targets considering key interactions and individual cell line mutations using the Human Protein Reference Database and the COSMIC database. A signature of potential biomarkers and matching drugs improve stratification and treatment in KRAS-mutated tumors. In silico screening and dynamic simulation of drug actions resulted in individual therapeutic suggestions, that is, targeting HIF1A in H441 and LKB1 in A549 cells. In conclusion, our in vitro tumor tissue model combined with an in silico tool improves drug effect prediction and patient stratification. Our tool is used in our comprehensive cancer center and is made now publicly available for targeted therapy decisions. KW - 3D lung tumor model KW - Boolean signaling network KW - chemoresistance KW - HSP90 inhibitor KW - insilico drug screening too KW - KRAS mutation signature Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-233137 VL - 12 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 - van de Peppel, L. J. J. A1 - Aanen, D. K. A1 - Biedermann, P. H. W. T1 - Low intraspecific genetic diversity indicates asexuality and vertical transmission in the fungal cultivars of ambrosia beetles JF - Fungal Ecology N2 - Ambrosia beetles farm ascomycetous fungi in tunnels within wood. These ambrosia fungi are regarded asexual, although population genetic proof is missing. Here we explored the intraspecific genetic diversity of Ambrosiella grosmanniae and Ambrosiella hartigii (Ascomycota: Microascales), the mutualists of the beetles Xylosandrus germanus and Anisandrus dispar. By sequencing five markers (ITS, LSU, TEF1α, RPB2, β-tubulin) from several fungal strains, we show that X. germanus cultivates the same two clones of A. grosmanniae in the USA and in Europe, whereas A. dispar is associated with a single A. hartigii clone across Europe. This low genetic diversity is consistent with predominantly asexual vertical transmission of Ambrosiella cultivars between beetle generations. This clonal agriculture is a remarkable case of convergence with fungus-farming ants, given that both groups have a completely different ecology and evolutionary history. KW - clonal fungiculture KW - ambrosia fungus KW - Ambrosiella KW - vertical transmission KW - symbiosis KW - Xylosandrus KW - Anisandrus KW - asexuality KW - genetic diversity Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232161 VL - 32 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Grebinyk, Sergii A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - C60 fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy JF - Free Radical Biology and Medicine N2 - Recent progress in nanobiotechnology has attracted interest to a biomedical application of the carbon nanostructure C60 fullerene since it possesses a unique structure and versatile biological activity. C60 fullerene potential application in the frame of cancer photodynamic therapy (PDT) relies on rapid development of new light sources as well as on better understanding of the fullerene interaction with cells. The aim of this study was to analyze C60 fullerene effects on human leukemic cells (CCRF-CEM) in combination with high power single chip light-emitting diodes (LEDs) light irradiation of different wavelengths: ultraviolet (UV, 365 nm), violet (405 nm), green (515 nm) and red (632 nm). The time-dependent accumulation of fullerene C60 in CCRF-CEM cells up to 250 ng/106 cells at 24 h with predominant localization within mitochondria was demonstrated with immunocytochemical staining and liquid chromatography mass spectrometry. In a cell viability assay we studied photoexcitation of the accumulated C60 nanostructures with ultraviolet or violet LEDs and could prove that significant phototoxic effects did arise. A less pronounced C60 fullerene phototoxic effect was observed after irradiation with green, and no effect was detected with red light. A C60 fullerene photoactivation with violet light induced substantial ROS generation and apoptotic cell death, confirmed by caspase3/7 activation and plasma membrane phosphatidylserine externalization. Our work proved C60 fullerene ability to induce apoptosis of leukemic cells after photoexcitation with high power single chip 405 nm LED as a light source. This underlined the potential for application of C60 nanostructure as a photosensitizer for anticancer therapy. KW - C-60 fullerene KW - photodanamic therapy KW - LEDs KW - leukemic cells KW - immunocytochemistry KW - HPLC-ESI-MS KW - apoptosis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228245 VL - 124 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 - Chen, Wei-Hua A1 - Lu, Guanting A1 - Chen, Xiao A1 - Zhao, Xing-Ming A1 - Bork, Peer T1 - OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines JF - Nucleic Acids Research N2 - OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased number of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info. KW - human cancer cell lines KW - gene essentiality database KW - OGEE v2 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-181334 VL - 45 IS - D1 ER - TY - JOUR A1 - Link, Jana A1 - Paouneskou, Dimitra A1 - Velkova, Maria A1 - Daryabeigi, Anahita A1 - Laos, Triin A1 - Labella, Sara A1 - Barroso, Consuelo A1 - Pacheco Piñol, Sarai A1 - Montoya, Alex A1 - Kramer, Holger A1 - Woglar, Alexander A1 - Baudrimont, Antoine A1 - Markert, Sebastian Mathias A1 - Stigloher, Christian A1 - Martinez-Perez, Enrique A1 - Dammermann, Alexander A1 - Alsheimer, Manfred A1 - Zetka, Monique A1 - Jantsch, Verena T1 - Transient and Partial Nuclear Lamina Disruption Promotes Chromosome Movement in Early Meiotic Prophase JF - Developmental Cell N2 - Meiotic chromosome movement is important for the pairwise alignment of homologous chromosomes, which is required for correct chromosome segregation. Movement is driven by cytoplasmic forces, transmitted to chromosome ends by nuclear membrane-spanning proteins. In animal cells, lamins form a prominent scaffold at the nuclear periphery, yet the role lamins play in meiotic chromosome movement is unclear. We show that chromosome movement correlates with reduced lamin association with the nuclear rim, which requires lamin phosphorylation at sites analogous to those that open lamina network crosslinks in mitosis. Failure to remodel the lamina results in delayed meiotic entry, altered chromatin organization, unpaired or interlocked chromosomes, and slowed chromosome movement. The remodeling kinases are delivered to lamins via chromosome ends coupled to the nuclear envelope, potentially enabling crosstalk between the lamina and chromosomal events. Thus, opening the lamina network plays a role in modulating contacts between chromosomes and the nuclear periphery during meiosis. KW - meiosis KW - C. elegans KW - chromosome movement KW - chromosome pairing KW - nuclear envelope KW - lamin Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-236901 VL - 45 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 - Becher, Isabelle A1 - Andrés-Pons, Amparo A1 - Romanov, Natalie A1 - Stein, Frank A1 - Schramm, Maike A1 - Baudin, Florence A1 - Helm, Dominic A1 - Kurzawa, Nils A1 - Mateus, André A1 - Mackmull, Marie-Therese A1 - Typas, Athanasios A1 - Müller, Christoph W. A1 - Bork, Peer A1 - Beck, Martin A1 - Savitski, Mikhail M. T1 - Pervasive Protein Thermal Stability Variation during the Cell Cycle JF - Cell N2 - Quantitative mass spectrometry has established proteome-wide regulation of protein abundance and post-translational modifications in various biological processes. Here, we used quantitative mass spectrometry to systematically analyze the thermal stability and solubility of proteins on a proteome-wide scale during the eukaryotic cell cycle. We demonstrate pervasive variation of these biophysical parameters with most changes occurring in mitosis and G1. Various cellular pathways and components vary in thermal stability, such as cell-cycle factors, polymerases, and chromatin remodelers. We demonstrate that protein thermal stability serves as a proxy for enzyme activity, DNA binding, and complex formation in situ. Strikingly, a large cohort of intrinsically disordered and mitotically phosphorylated proteins is stabilized and solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Our data represent a rich resource for cell, structural, and systems biologists interested in proteome regulation during biological transitions. KW - thermal proteome profiling KW - cell cycle KW - proteomics Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221565 VL - 173 ER - TY - THES A1 - Korte, Pamela T1 - Die funktionelle Bedeutung des Lipidstoffwechsels für die Stomataöffnung bei Hitzestress in \(Arabidopsis\) \(thaliana\) T1 - The functional significance of lipid metabolism for stomatal opening during heat stress in \(Arabidopsis\) \(thaliana\) N2 - Pflanzen sind verschiedenen Umweltbedingungen ausgesetzt, die zu suboptimalen Wachstumsbedingungen führen können. Dies gilt für eine Vielzahl von biotischen und abiotischen Faktoren. In der hier vorgelegten Arbeit wird der Effekt von erhöhten Temperaturen und Hitze genauer analysiert. Hitze ist einer der wichtigsten abiotischen Stressfaktoren, der das Pflanzenwachstum und die Reproduktion beeinflusst. Viele wichtige Kulturpflanzen zeigen immense Ertragseinbußen, die durch Hitze hervorgerufen werden. Durch den fortschreitenden Klimawandel werden jedoch Hitzeperioden immer häufiger und somit die Folgen für die Nahrungsproduktion immer gravierender. Zur Züchtung von Pflanzen die hitzetolerant sind und weniger hohe Ertragseinbußen unter diesem Stress aufweisen, ist es essenziell die grundlegenden molekularen Mechanismen der Hitzetoleranz zu verstehen. Es müssen die verschiedenen physiologischen und biochemischen Prozesse identifiziert werden, die es Pflanzen ermöglichen, sich anzupassen. Es ist bekannt, dass die Anpassungsmechanismen von Pflanzen komplex sind und sowohl Veränderungen auf zellulärer wie auch auf organismischer Ebene beinhalten. Ziel dieser Arbeit war es, weitere Erkenntnisse zu gewinnen, wie diese Anpassung vonstattengeht und welche molekularen Prozesse an ihr beteiligt sind. Ein Hauptaugenmerk lag dabei auf dem Einfluss des Lipidmetabolismus und den daran beteiligten Enzymen. Es konnte bereits gezeigt werden, dass die Akkumulation von Triacylglycerolen bei hohen Temperaturen die basale Thermotoleranz bei Arabidopsis thaliana erhöht. Wie jedoch der genaue Mechanismus dieser durch Triacylglycerole vermittelten Thermotoleranz funktioniert, war bis dato nicht bekannt. Ich konnte zeigen, dass die angesammelten Triacylglycerole genutzt werden können, um die Stomata während des Hitzestress zu öffnen. Dies führt zu einer erhöhten Transpiration und somit einer Kühlung der Blätter. Der Abbau von Triacylglycerolen und Stärke am Morgen ist notwendig, um die Stomata zu öffnen. Zusätzlich dient der Abbau der Aufrechterhaltung des Citratzyklus und somit der Energieversorgung. In weiteren Experimenten konnte ich durch Fütterung mit stabil markierter Laurinsäure zeigen, dass die Triacylglycerole auch dem Aufbau neuer Aminosäuren unter Stressbedingungen dienen. Die hier vorgestellten Arbeiten bieten die Grundlage, um den Mechanismus der Thermotoleranz besser zu verstehen. Das Verständnis der in dieser Arbeit beschriebenen molekularen Signalwege und Enzyme kann langfristig dazu beitragen hitzeresistentere Nutzpflanzen zu züchten. N2 - Plants are exposed to various environmental conditions that can lead to suboptimal growth conditions. This applies to a variety of biotic and abiotic factors. In the work presented here, the effect of elevated temperatures and heat is analyzed in more detail. Heat is one of the most important abiotic stress factors affecting plant growth and reproduction. Many important crops show immense yield losses caused by heat. However, as climate change progresses, periods of heat are becoming more frequent and the consequences for food production are becoming increasingly serious. Understanding the basic molecular mechanisms of heat tolerance is essential to breed plants that are heat tolerant and show less yield loss under this stress. The various physiological and biochemical processes that enable plants to adapt need to be identified. It is known that the adaptation mechanisms of plants are complex and involve changes at both the cellular and organismal level. The aim of this work was to gain further insights into how this adaptation takes place and which molecular processes are involved. The main focus was on the influence of lipid metabolism and the enzymes involved. It has already been shown that the accumulation of triacylglycerols at high temperatures increases basal thermotolerance in Arabidopsis thaliana. However, the exact mechanism of this triacylglycerol mediated thermotolerance was not known until now. I was able to show that the accumulated triacylglycerols can be used to open the stomata during heat stress. This leads to increased transpiration and thus cooling of the leaves. The degradation of triacylglycerols and starch in the morning is necessary to open the stomata. In addition, the degradation serves to maintain the citrate cycle and thus the energy supply. In further experiments, I was able to show by feeding stably labeled lauric acid that the triacylglycerols also serve to build up new amino acids under stress conditions. The work presented here provides the basis for a better understanding of the mechanism of thermotolerance. Understanding the molecular signaling pathways and enzymes described in this work could - in the long term - contribute to breeding of more heat-resistant crops. KW - Hitzestress KW - Ackerschmalwand KW - Arabidopsis thaliana KW - Triacylglycerol Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-370461 ER - TY - JOUR A1 - Too, Chin Chin A1 - Keller, Alexander A1 - Sickel, Wiebke A1 - Lee, Sui Mae A1 - Yule, Catherine M. T1 - Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth JF - Frontiers in Microbiology N2 - Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems. KW - tropical peat swamp forest KW - metabarcoding KW - microbial diversity and composition KW - tree species KW - depth KW - methanogens Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229000 VL - 9 ER - TY - JOUR A1 - Prusty, Bhupesh K. A1 - Gulve, Nitish A1 - Govind, Sheila A1 - Krueger, Gerhard R. F. A1 - Feichtinger, Julia A1 - Larcombe, Lee A1 - Aspinall, Richard A1 - Ablashi, Dharam V. A1 - Toro, Carla T. T1 - Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders JF - Frontiers in Microbiology N2 - Early-life infections and associated neuroinflammation is incriminated in the pathogenesis of various mood disorders. Infection with human roseoloviruses, HHV-6A and HHV-6B, allows viral latency in the central nervous system and other tissues, which can later be activated causing cognitive and behavioral disturbances. Hence, this study was designed to evaluate possible association of HHV-6A and HHV-6B activation with three different groups of psychiatric patients. DNA qPCR, immunofluorescence and FISH studies were carried out in post-mortem posterior cerebellum from 50 cases each of bipolar disorder (BPD), schizophrenia, 15 major depressive disorder (MDD) and 50 appropriate control samples obtained from two well-known brain collections (Stanley Medical Research Institute). HHV-6A and HHV-6B late proteins (indicating active infection) and viral DNA were detected more frequently (p < 0.001 for each virus) in human cerebellum in MDD and BPD relative to controls. These roseolovirus proteins and DNA were found less frequently in schizophrenia cases. Active HHV-6A and HHV-6B infection in cerebellar Purkinje cells were detected frequently in BPD and MDD cases. Furthermore, we found a significant association of HHV-6A infection with reduced Purkinje cell size, suggesting virus-mediated abnormal Purkinje cell function in these disorders. Finally, gene expression analysis of cerebellar tissue revealed changes in pathways reflecting an inflammatory response possibly to HHV-6A infection. Our results provide molecular evidence to support a role for active HHV-6A and HHV-6B infection in BPD and MDD. KW - HHV-6 KW - bipolar disorder KW - schizophrenia KW - major depressive disorder KW - Purkinje cells Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-369222 VL - 9 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 -