@article{MuellerNossThornetal.2019, author = {M{\"u}ller, J{\"o}rg and Noss, Reed F. and Thorn, Simon and B{\"a}ssler, Claus and Leverkus, Alexandro B. and Lindenmayer, David}, title = {Increasing disturbance demands new policies to conserve intact forest}, series = {Conservation Letters}, volume = {12}, journal = {Conservation Letters}, doi = {10.1111/conl.12449}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-224256}, year = {2019}, abstract = {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.}, language = {en} } @article{BahramAnslanHildebrandetal.2019, author = {Bahram, Mohammad and Anslan, Sten and Hildebrand, Falk and Bork, Peer and Tedersoo, Leho}, title = {Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment}, series = {Environmental Microbiology Reports}, volume = {11}, journal = {Environmental Microbiology Reports}, doi = {10.1111/1758-2229.12684}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221380}, pages = {487-494}, year = {2019}, abstract = {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.}, language = {en} } @article{MollKellnerLeonhardtetal.2018, author = {Moll, Julia and Kellner, Harald and Leonhardt, Sabrina and Stengel, Elisa and Dahl, Andreas and B{\"a}ssler, Claus and Buscot, Fran{\c{c}}ois and Hofrichter, Martin and Hoppe, Bj{\"o}rn}, title = {Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood}, series = {Environmental Microbiology}, volume = {20}, journal = {Environmental Microbiology}, doi = {10.1111/1462-2920.14376}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-224168}, pages = {3744-3756}, year = {2018}, abstract = {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.}, language = {en} } @article{HilmersFriessBaessleretal.2018, author = {Hilmers, Torben and Friess, Nicolas and B{\"a}ssler, Claus and Heurich, Marco and Brandl, Roland and Pretzsch, Hans and Seidl, Rupert and M{\"u}ller, J{\"o}rg}, title = {Biodiversity along temperate forest succession}, series = {Journal of Applied Ecology}, volume = {55}, journal = {Journal of Applied Ecology}, doi = {10.1111/1365-2664.13238}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-320632}, pages = {2756-2766}, year = {2018}, abstract = {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.}, language = {en} } @article{KoenigZundelKrimmeretal.2019, author = {K{\"o}nig, Kerstin and Zundel, Petra and Krimmer, Elena and K{\"o}nig, Christian and Pollmann, Marie and Gottlieb, Yuval and Steidle, Johannes L. M.}, title = {Reproductive isolation due to prezygotic isolation and postzygotic cytoplasmic incompatibility in parasitoid wasps}, series = {Ecology and Evolution}, volume = {9}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.5588}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-222796}, pages = {10694-10706}, year = {2019}, abstract = {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.}, language = {en} } @article{HartkeSprengerSahmetal.2019, author = {Hartke, Juliane and Sprenger, Philipp P. and Sahm, Jacqueline and Winterberg, Helena and Orivel, J{\´e}r{\^o}me and Baur, Hannes and Beuerle, Till and Schmitt, Thomas and Feldmeyer, Barbara and Menzel, Florian}, title = {Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association}, series = {Ecology and Evolution}, volume = {9}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.5464}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227857}, pages = {9160-9176}, year = {2019}, abstract = {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.}, language = {en} } @article{KendallRaderGagicetal.2019, author = {Kendall, Liam K. and Rader, Romina and Gagic, Vesna and Cariveau, Daniel P. and Albrecht, Matthias and Baldock, Katherine C. R. and Freitas, Breno M. and Hall, Mark and Holzschuh, Andrea and Molina, Francisco P. and Morten, Joanne M. and Pereira, Janaely S. and Portman, Zachary M. and Roberts, Stuart P. M. and Rodriguez, Juanita and Russo, Laura and Sutter, Louis and Vereecken, Nicolas J. and Bartomeus, Ignasi}, title = {Pollinator size and its consequences: Robust estimates of body size in pollinating insects}, series = {Ecology and Evolution}, volume = {9}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.4835}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325705}, pages = {1702-1714}, year = {2019}, abstract = {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.}, language = {en} } @article{HillaertHovestadtVandegehuchteetal.2018, author = {Hillaert, Jasmijn and Hovestadt, Thomas and Vandegehuchte, Martijn L. and Bonte, Dries}, title = {Size-dependent movement explains why bigger is better in fragmented landscapes}, series = {Ecology and Evolution}, volume = {8}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.4524}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-320322}, pages = {10754-10767}, year = {2018}, abstract = {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.}, language = {en} } @article{SteinStenchlyCoulibalyetal.2018, author = {Stein, Katharina and Stenchly, Kathrin and Coulibaly, Drissa and Pauly, Alain and Dimobe, Kangbeni and Steffan-Dewenter, Ingolf and Konat{\´e}, Souleymane and Goetze, Dethardt and Porembski, Stefan and Linsenmair, K. Eduard}, title = {Impact of human disturbance on bee pollinator communities in savanna and agricultural sites in Burkina Faso, West Africa}, series = {Ecology and Evolution}, volume = {8}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.4197}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239999}, pages = {6827-6838}, year = {2018}, abstract = {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.}, language = {en} } @article{MindenSchnetgerPufaletal.2018, author = {Minden, Vanessa and Schnetger, Bernhard and Pufal, Gesine and Leonhardt, Sara D.}, title = {Antibiotic-induced effects on scaling relationships and on plant element contents in herbs and grasses}, series = {Ecology and Evolution}, volume = {8}, journal = {Ecology and Evolution}, doi = {10.1002/ece3.4168}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-224094}, pages = {6699-6713}, year = {2018}, abstract = {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.}, language = {en} } @article{SchubertHagedornYoshiietal.2018, author = {Schubert, Frank K. and Hagedorn, Nicolas and Yoshii, Taishi and Helfrich-F{\"o}rster, Charlotte and Rieger, Dirk}, title = {Neuroanatomical details of the lateral neurons of Drosophila melanogaster support their functional role in the circadian system}, series = {Journal of Comparative Neurology}, volume = {526}, journal = {Journal of Comparative Neurology}, doi = {10.1002/cne.24406}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-234477}, pages = {1209-1231}, year = {2018}, abstract = {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.}, language = {en} } @article{FlunkertMaierhoferDittrichetal.2018, author = {Flunkert, Julia and Maierhofer, Anna and Dittrich, Marcus and M{\"u}ller, Tobias and Horvath, Steve and Nanda, Indrajit and Haaf, Thomas}, title = {Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts}, series = {Experimental Cell Research}, volume = {370}, journal = {Experimental Cell Research}, doi = {10.1016/j.yexcr.2018.06.034}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228177}, pages = {322-332}, year = {2018}, abstract = {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.}, language = {en} } @article{BaluapuriHofstetterDudvarskiStankovicetal.2019, author = {Baluapuri, Apoorva and Hofstetter, Julia and Dudvarski Stankovic, Nevenka and Endres, Theresa and Bhandare, Pranjali and Vos, Seychelle Monique and Adhikari, Bikash and Schwarz, Jessica Denise and Narain, Ashwin and Vogt, Markus and Wang, Shuang-Yan and D{\"u}ster, Robert and Jung, Lisa Anna and Vanselow, Jens Thorsten and Wiegering, Armin and Geyer, Matthias and Maric, Hans Michael and Gallant, Peter and Walz, Susanne and Schlosser, Andreas and Cramer, Patrick and Eilers, Martin and Wolf, Elmar}, title = {MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation}, series = {Molecular Cell}, volume = {74}, journal = {Molecular Cell}, doi = {10.1016/j.molcel.2019.02.031}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221438}, pages = {674-687}, year = {2019}, abstract = {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.}, language = {en} } @article{GoettlichKunzZappetal.2018, author = {G{\"o}ttlich, Claudia and Kunz, Meik and Zapp, Cornelia and Nietzer, Sarah L. and Walles, Heike and Dandekar, Thomas and Dandekar, Gudrun}, title = {A combined tissue-engineered/in silico signature tool patient stratification in lung cancer}, series = {Molecular Oncology}, volume = {12}, journal = {Molecular Oncology}, doi = {10.1002/1878-0261.12323}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-233137}, pages = {1264-1285}, year = {2018}, abstract = {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.}, language = {en} } @article{SeitzvanEngelsdorpLeonhardt2019, author = {Seitz, Nicola and vanEngelsdorp, Dennis and Leonhardt, Sara D.}, title = {Conserving bees in destroyed landscapes: The potentials of reclaimed sand mines}, series = {Global Ecology and Conservation}, volume = {19}, journal = {Global Ecology and Conservation}, doi = {10.1016/j.gecco.2019.e00642}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-235877}, year = {2019}, abstract = {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.}, language = {en} } @article{vandePeppelAanenBiedermann2018, author = {van de Peppel, L. J. J. and Aanen, D. K. and Biedermann, P. H. W.}, title = {Low intraspecific genetic diversity indicates asexuality and vertical transmission in the fungal cultivars of ambrosia beetles}, series = {Fungal Ecology}, volume = {32}, journal = {Fungal Ecology}, doi = {10.1016/j.funeco.2017.11.010}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-232161}, pages = {57-64}, year = {2018}, abstract = {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.}, language = {en} } @article{GrebinykGrebinykPrylutskaetal.2018, author = {Grebinyk, Anna and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {C60 fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy}, series = {Free Radical Biology and Medicine}, volume = {124}, journal = {Free Radical Biology and Medicine}, doi = {10.1016/j.freeradbiomed.2018.06.022}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228245}, pages = {319-327}, year = {2018}, abstract = {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.}, language = {en} } @article{HofrichterDollHabibietal.2019, author = {Hofrichter, Michaela A. H. and Doll, Julia and Habibi, Haleh and Enayati, Samaneh and Mehrjardi, Mohammad Yahya Vahidi and M{\"u}ller, Tobias and Dittrich, Marcus and Haaf, Thomas and Vona, Barbara}, title = {Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss}, series = {European Journal of Medical Genetics}, volume = {62}, journal = {European Journal of Medical Genetics}, doi = {10.1016/j.ejmg.2019.103724}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-322008}, year = {2019}, abstract = {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.}, language = {en} } @article{ChenLuChenetal.2017, author = {Chen, Wei-Hua and Lu, Guanting and Chen, Xiao and Zhao, Xing-Ming and Bork, Peer}, title = {OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {D1}, doi = {10.1093/nar/gkw1013}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-181334}, pages = {D940-D944}, year = {2017}, abstract = {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.}, language = {en} } @article{LinkPaouneskouVelkovaetal.2018, author = {Link, Jana and Paouneskou, Dimitra and Velkova, Maria and Daryabeigi, Anahita and Laos, Triin and Labella, Sara and Barroso, Consuelo and Pacheco Pi{\~n}ol, Sarai and Montoya, Alex and Kramer, Holger and Woglar, Alexander and Baudrimont, Antoine and Markert, Sebastian Mathias and Stigloher, Christian and Martinez-Perez, Enrique and Dammermann, Alexander and Alsheimer, Manfred and Zetka, Monique and Jantsch, Verena}, title = {Transient and Partial Nuclear Lamina Disruption Promotes Chromosome Movement in Early Meiotic Prophase}, series = {Developmental Cell}, volume = {45}, journal = {Developmental Cell}, doi = {10.1016/j.devcel.2018.03.018}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-236901}, pages = {212-225}, year = {2018}, abstract = {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.}, language = {en} }