TY  - JOUR
A1  - Ehmann, Nadine
A1  - Sauer, Markus
A1  - Kittel, Robert J.
T1  - Super-resolution microscopy of the synaptic active zone
JF  - Frontiers in Cellular Neuroscience
N2  - Brain function relies on accurate information transfer at chemical synapses. At the presynaptic active zone (AZ) a variety of specialized proteins are assembled to complex architectures, which set the basis for speed, precision and plasticity of synaptic transmission. Calcium channels are pivotal for the initiation of excitation-secretion coupling and, correspondingly, capture a central position at the AZ. Combining quantitative functional studies with modeling approaches has provided predictions of channel properties, numbers and even positions on the nanometer scale. However, elucidating the nanoscopic organization of the surrounding protein network requires direct ultrastructural access. Without this information, knowledge of molecular synaptic structure-function relationships remains incomplete. Recently, super-resolution microscopy (SRM) techniques have begun to enter the neurosciences. These approaches combine high spatial resolution with the molecular specificity of fluorescence microscopy. Here, we discuss how SRM can be used to obtain information on the organization of AZ proteins
KW  - excitation-secretion coupling
KW  - Ca\(^{2+}\) channels
KW  - structure-function relationships
KW  - super-resolution microscopy
KW  - active zone
KW  - presynaptic calcium
KW  - neurotransmitter release
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148997
VL  - 9
IS  - 7
ER  - 
TY  - JOUR
A1  - Elkon, Ran
A1  - Loayza-Puch, Fabricio
A1  - Korkmaz, Gozde
A1  - Lopes, Rui
A1  - van Breugel, Pieter C
A1  - Bleijerveld, Onno B
A1  - Altelaar, AF Maarten
A1  - Wolf, Elmar
A1  - Lorenzin, Francesca
A1  - Eilers, Martin
A1  - Agami, Reuven
T1  - Myc coordinates transcription and translation to enhance transformation and suppress invasiveness
JF  - EMBO reports
N2  - c‐Myc is one of the major human proto‐oncogenes and is often associated with tumor aggression and poor clinical outcome. Paradoxically, Myc was also reported as a suppressor of cell motility, invasiveness, and metastasis. Among the direct targets of Myc are many components of the protein synthesis machinery whose induction results in an overall increase in protein synthesis that empowers tumor cell growth. At present, it is largely unknown whether beyond the global enhancement of protein synthesis, Myc activation results in translation modulation of specific genes. Here, we measured Myc‐induced global changes in gene expression at the transcription, translation, and protein levels and uncovered extensive transcript‐specific regulation of protein translation. Particularly, we detected a broad coordination between regulation of transcription and translation upon modulation of Myc activity and showed the connection of these responses to mTOR signaling to enhance oncogenic transformation and to the TGFβ pathway to modulate cell migration and invasiveness. Our results elucidate novel facets of Myc‐induced cellular responses and provide a more comprehensive view of the consequences of its activation in cancer cells.
KW  - c‐Myc
KW  - transcriptional responses
KW  - translational regulation
KW  - transcription
KW  - transformation
KW  - metastasis
KW  - cancer
KW  - protein biosynthesis & quality control
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-150373
VL  - 16
IS  - 12
ER  - 
TY  - JOUR
A1  - Falibene, Agustina
A1  - Roces, Flavio
A1  - Rössler, Wolfgang
T1  - Long-term avoidance memory formation is associated with a transient increase in mushroom body synaptic complexes in leaf-cutting ants
JF  - Frontiers in Behavioral Neuroscience
N2  - Long-term behavioral changes related to learning and experience have been shown to be associated with structural remodeling in the brain. Leaf-cutting ants learn to avoid previously preferred plants after they have proved harmful for their symbiotic fungus, a process that involves long-term olfactory memory. We studied the dynamics of brain microarchitectural changes after long-term olfactory memory formation following avoidance learning in Acromyrmex ambiguus. After performing experiments to control for possible neuronal changes related to age and body size, we quantified synaptic complexes (microglomeruli, MG) in olfactory regions of the mushroom bodies (MBs) at different times after learning. Long-term avoidance memory formation was associated with a transient change in MG densities. Two days after learning, MG density was higher than before learning. At days 4 and 15 after learning—when ants still showed plant avoidance—MG densities had decreased to the initial state. The structural reorganization of MG triggered by long-term avoidance memory formation clearly differed from changes promoted by pure exposure to and collection of novel plants with distinct odors. Sensory exposure by the simultaneous collection of several, instead of one, non-harmful plant species resulted in a decrease in MG densities in the olfactory lip. We hypothesize that while sensory exposure leads to MG pruning in the MB olfactory lip, the formation of long-term avoidance memory involves an initial growth of new MG followed by subsequent pruning.
KW  - microglomeruli
KW  - olfaction
KW  - avoidance learning
KW  - leaf-cutting ants
KW  - acromyrmex ambiguus
KW  - synaptic plasticity
KW  - mushroom body
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125522
VL  - 9
IS  - 84
ER  - 
TY  - JOUR
A1  - Falibene, Augustina
A1  - Roces, Flavio
A1  - Rössler, Wolfgang
T1  - Long-term avoidance memory formation is associated with a transient increase in mushroom body synaptic complexes in leaf-cutting ants
JF  - Frontiers in Behavioural Neuroscience
N2  - Long-term behavioral changes related to learning and experience have been shown to be associated with structural remodeling in the brain. Leaf-cutting ants learn to avoid previously preferred plants after they have proved harmful for their symbiotic fungus, a process that involves long-term olfactory memory. We studied the dynamics of brain microarchitectural changes after long-term olfactory memory formation following avoidance learning in Acromyrmex ambiguus. After performing experiments to control for possible neuronal changes related to age and body size, we quantified synaptic complexes (microglomeruli, MG) in olfactory regions of the mushroom bodies (MB) at different times after learning. Long-term avoidance memory formation was associated with a transient change in MG densities. Two days after learning, MG density was higher than before learning. At days 4 and 15 after learning when ants still showed plant avoidance MG densities had decreased to the initial state. The structural reorganization of MG triggered by long-term avoidance memory formation clearly differed from changes promoted by pure exposure to and collection of novel plants with distinct odors. Sensory exposure by the simultaneous collection of several, instead of one, non-harmful plant species resulted in a decrease in MG densities in the olfactory lip. We hypothesize that while sensory exposure leads to MG pruning in the MB olfactory lip, the formation of long-term avoidance memory involves an initial growth of new MG followed by subsequent pruning.
KW  - Acromyrmex ambiguus
KW  - leaf-cutting ants
KW  - avoidance learning
KW  - olfaction
KW  - honeybee
KW  - microglomeruli
KW  - mushroom body
KW  - synaptic plasticity
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148763
VL  - 9
IS  - 84
ER  - 
TY  - JOUR
A1  - Floren, Andreas
A1  - Krüger, Dirk
A1  - Müller, Tobias
A1  - Dittrich, Marcus
A1  - Rudloff, Renate
A1  - Hoppe, Björn
A1  - Linsenmair, Karl Eduard
T1  - Diversity and interactions of wood-inhabiting fungi and beetles after deadwood enrichment
JF  - PLoS ONE
N2  - Freshly cut beech deadwood was enriched in the canopy and on the ground in three cultural landscapes in Germany (Swabian Alb, Hainich-Dun, Schorfheide-Chorin) in order to analyse the diversity, distribution and interaction of wood-inhabiting fungi and beetles. After two years of wood decay 83 MOTUs (Molecular Operational Taxonomic Units) from 28 wood samples were identified. Flight Interception Traps (FITs) installed adjacent to the deadwood enrichments captured 29.465 beetles which were sorted to 566 species. Geographical 'region' was the main factor determining both beetle and fungal assemblages. The proportions of species occurring in all regions were low. Statistic models suggest that assemblages of both taxa differed between stratum and management praxis but their strength varied among regions. Fungal assemblages in Hainich-Dun, for which the data was most comprehensive, discriminated unmanaged from extensively managed and age-class forests (even-aged timber management) while canopy communities differed not from those near the ground. In contrast, the beetle assemblages at the same sites showed the opposite pattern. We pursued an approach in the search for fungus-beetle associations by computing cross correlations and visualize significant links in a network graph. These correlations can be used to formulate hypotheses on mutualistic relationships for example in respect to beetles acting as vectors of fungal spores.
KW  - european beech forests
KW  - bark beetles
KW  - management
KW  - decay
KW  - ecology
KW  - norway spruce
KW  - substrate quality
KW  - communities
KW  - rare
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-145129
VL  - 10
IS  - 11
ER  - 
TY  - JOUR
A1  - Frank, Daniel O.
A1  - Dengjel, Jörn
A1  - Wilfling, Florian
A1  - Kozjak-Pavlovic, Vera
A1  - Häcker, Georg
A1  - Weber, Arnim
T1  - The Pro-Apoptotic BH3-Only Protein Bim Interacts with Components of the Translocase of the Outer Mitochondrial Membrane (TOM)
JF  - PLoS ONE
N2  - The pro-apoptotic Bcl-2-family protein Bim belongs to the BH3-only proteins known as initiators of apoptosis. Recent data show that Bim is constitutively inserted in the outer mitochondrial membrane via a C-terminal transmembrane anchor from where it can activate the effector of cytochrome c-release, Bax. To identify regulators of Bim-activity, we conducted a search for proteins interacting with Bim at mitochondria. We found an interaction of Bim with Tom70, Tom20 and more weakly with Tom40, all components of the Translocase of the Outer Membrane (TOM). In vitro import assays performed on tryptically digested yeast mitochondria showed reduced Bim insertion into the outer mitochondrial membrane (OMM) indicating that protein receptors may be involved in the import process. However, RNAi against components of TOM (Tom40, Tom70, Tom22 or Tom20) by siRNA, individually or in combination, did not consistently change the amount of Bim on HeLa mitochondria, either at steady state or upon de novo-induction. In support of this, the individual or combined knockdowns of TOM receptors also failed to alter the susceptibility of HeLa cells to Bim-induced apoptosis. In isolated yeast mitochondria, lack of Tom70 or the TOM-components Tom20 or Tom22 alone did not affect the import of Bim into the outer mitochondrial membrane. In yeast, expression of Bim can sensitize the cells to Bax-dependent killing. This sensitization was unaffected by the absence of Tom70 or by an experimental reduction in Tom40. Although thus the physiological role of the Bim-TOM-interaction remains unclear, TOM complex components do not seem to be essential for Bim insertion into the OMM. Nevertheless, this association should be noted and considered when the regulation of Bim in other cells and situations is investigated.
KW  - bax
KW  - preproteins
KW  - phosphorylation
KW  - proteomics
KW  - degradation
KW  - cells
KW  - family
KW  - import
KW  - BH3 domains
KW  - Bcl-2 proteins
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143301
VL  - 10
IS  - 4
ER  - 
TY  - JOUR
A1  - Galluzzi, L.
A1  - Bravo-San Pedro, J. M.
A1  - Vitale, I.
A1  - Aaronson, S. A.
A1  - Abrams, J. M.
A1  - Adam, D.
A1  - Alnemri, E. S.
A1  - Altucci, L.
A1  - Andrews, D.
A1  - Annicchiarico-Petruzelli, M.
A1  - Baehrecke, E. H.
A1  - Bazan, N. G.
A1  - Bertrand, M. J.
A1  - Bianchi, K.
A1  - Blagosklonny, M. V.
A1  - Blomgren, K.
A1  - Borner, C.
A1  - Bredesen, D. E.
A1  - Brenner, C.
A1  - Campanella, M.
A1  - Candi, E.
A1  - Cecconi, F.
A1  - Chan, F. K.
A1  - Chandel, N. S.
A1  - Cheng, E. H.
A1  - Chipuk, J. E.
A1  - Cidlowski, J. A.
A1  - Ciechanover, A.
A1  - Dawson, T. M.
A1  - Dawson, V. L.
A1  - De Laurenzi, V.
A1  - De Maria, R.
A1  - Debatin, K. M.
A1  - Di Daniele, N.
A1  - Dixit, V. M.
A1  - Dynlacht, B. D.
A1  - El-Deiry, W. S.
A1  - Fimia, G. M.
A1  - Flavell, R. A.
A1  - Fulda, S.
A1  - Garrido, C.
A1  - Gougeon, M. L.
A1  - Green, D. R.
A1  - Gronemeyer, H.
A1  - Hajnoczky, G.
A1  - Hardwick, J. M.
A1  - Hengartner, M. O.
A1  - Ichijo, H.
A1  - Joseph, B.
A1  - Jost, P. J.
A1  - Kaufmann, T.
A1  - Kepp, O.
A1  - Klionsky, D. J.
A1  - Knight, R. A.
A1  - Kumar, S.
A1  - Lemasters, J. J.
A1  - Levine, B.
A1  - Linkermann, A.
A1  - Lipton, S. A.
A1  - Lockshin, R. A.
A1  - López-Otín, C.
A1  - Lugli, E.
A1  - Madeo, F.
A1  - Malorni, W.
A1  - Marine, J. C.
A1  - Martin, S. J.
A1  - Martinou, J. C.
A1  - Medema, J. P.
A1  - Meier, P.
A1  - Melino, S.
A1  - Mizushima, N.
A1  - Moll, U.
A1  - Muñoz-Pinedo, C.
A1  - Nuñez, G.
A1  - Oberst, A.
A1  - Panaretakis, T.
A1  - Penninger, J. M.
A1  - Peter, M. E.
A1  - Piacentini, M.
A1  - Pinton, P.
A1  - Prehn, J. H.
A1  - Puthalakath, H.
A1  - Rabinovich, G. A.
A1  - Ravichandran, K. S.
A1  - Rizzuto, R.
A1  - Rodrigues, C. M.
A1  - Rubinsztein, D. C.
A1  - Rudel, T.
A1  - Shi, Y.
A1  - Simon, H. U.
A1  - Stockwell, B. R.
A1  - Szabadkai, G.
A1  - Tait, S. W.
A1  - Tang, H. L.
A1  - Tavernarakis, N.
A1  - Tsujimoto, Y.
A1  - Vanden Berghe, T.
A1  - Vandenabeele, P.
A1  - Villunger, A.
A1  - Wagner, E. F.
A1  - Walczak, H.
A1  - White, E.
A1  - Wood, W. G.
A1  - Yuan, J.
A1  - Zakeri, Z.
A1  - Zhivotovsky, B.
A1  - Melino, G.
A1  - Kroemer, G.
T1  - Essential versus accessory aspects of cell death: recommendations of the NCCD 2015
JF  - Cell Death and Differentiation
N2  - Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-121207
VL  - 22
ER  - 
TY  - JOUR
A1  - Gao, Shiqiang
A1  - Nagpal, Jatin
A1  - Schneider, Martin W.
A1  - Kozjak-Pavlovic, Vera
A1  - Nagel, Georg
A1  - Gottschalk, Alexander
T1  - Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp
JF  - Nature Communications
N2  - Cyclic GMP (cGMP) signalling regulates multiple biological functions through activation of protein kinase G and cyclic nucleotide-gated (CNG) channels. In sensory neurons, cGMP permits signal modulation, amplification and encoding, before depolarization. Here we implement a guanylyl cyclase rhodopsin from Blastocladiella emersonii as a new optogenetic tool (BeCyclOp), enabling rapid light-triggered cGMP increase in heterologous cells (Xenopus oocytes, HEK293T cells) and in Caenorhabditis elegans. Among five different fungal CyclOps, exhibiting unusual eight transmembrane topologies and cytosolic N-termini, BeCyclOp is the superior optogenetic tool (light/dark activity ratio: 5,000; no cAMP production; turnover (20 °C) ~17 cGMPs\(^{-1}\)). Via co-expressed CNG channels (OLF in oocytes, TAX-2/4 in C. elegans muscle), BeCyclOp photoactivation induces a rapid conductance increase and depolarization at very low light intensities. In O\(_2\)/CO\(_2\) sensory neurons of C. elegans, BeCyclOp activation evokes behavioural responses consistent with their normal sensory function. BeCyclOp therefore enables precise and rapid optogenetic manipulation of cGMP levels in cells and animals.
KW  - carbon dioxide avoidance
KW  - III adenylyl cyclases
KW  - rhodopsin
KW  - in vivo
KW  - optical control
KW  - Halobacterium halobium
KW  - C. elegans
KW  - cellular camp
KW  - Caenorhabditis elegans
KW  - nucleotide-gated channel
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148197
VL  - 6
IS  - 8046
ER  - 
TY  - JOUR
A1  - García-Martínez, Jorge
A1  - Brunk, Michael
A1  - Avalos, Javier
A1  - Terpitz, Ulrich
T1  - The CarO rhodopsin of the fungus Fusarium fujikuroi is a light-driven proton pump that retards spore germination
JF  - Scientific Reports
N2  - Rhodopsins are membrane-embedded photoreceptors found in all major taxonomic kingdoms using retinal as their chromophore. They play well-known functions in different biological systems, but their roles in fungi remain unknown. The filamentous fungus Fusarium fujikuroi contains two putative rhodopsins, CarO and OpsA. The gene carO is light-regulated, and the predicted polypeptide contains all conserved residues required for proton pumping. We aimed to elucidate the expression and cellular location of the fungal rhodopsin CarO, its presumed proton-pumping activity and the possible effect of such function on F. fujikuroi growth. In electrophysiology experiments we confirmed that CarO is a green-light driven proton pump. Visualization of fluorescent CarO-YFP expressed in F. fujikuroi under control of its native promoter revealed higher accumulation in spores (conidia) produced by light-exposed mycelia. Germination analyses of conidia from carO\(^{-}\) mutant and carO\(^{+}\) control strains showed a faster development of light-exposed carO-germlings. In conclusion, CarO is an active proton pump, abundant in light-formed conidia, whose activity slows down early hyphal development under light. Interestingly, CarO-related rhodopsins are typically found in plant-associated fungi, where green light dominates the phyllosphere. Our data provide the first reliable clue on a possible biological role of a fungal rhodopsin.
KW  - microbial rhodopsins
KW  - intracellular pH
KW  - membrane proteins
KW  - mutants
KW  - virulence
KW  - channelrhodopsin-2
KW  - growth
KW  - gene
KW  - expression
KW  - bacteriorhodopsin
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149049
VL  - 5
IS  - 7798
ER  - 
TY  - JOUR
A1  - Gupta, Shishir K.
A1  - Kupper, Maria
A1  - Ratzka, Carolin
A1  - Feldhaar, Heike
A1  - Vilcinskas, Andreas
A1  - Gross, Roy
A1  - Dandekar, Thomas
A1  - Förster, Frank
T1  - Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing
JF  - BMC Genomics
N2  - Background
Defence mechanisms of organisms are shaped by their lifestyle, environment and pathogen pressure. Carpenter ants are social insects which live in huge colonies comprising genetically closely related individuals in high densities within nests. This lifestyle potentially facilitates the rapid spread of pathogens between individuals. In concert with their innate immune system, social insects may apply external immune defences to manipulate the microbial community among individuals and within nests. Additionally, carpenter ants carry a mutualistic intracellular and obligate endosymbiotic bacterium, possibly maintained and regulated by the innate immune system. Thus, different selective forces could shape internal immune defences of Camponotus floridanus.

Results
The immune gene repertoire of C. floridanus was investigated by re-evaluating its genome sequence combined with a full transcriptome analysis of immune challenged and control animals using Illumina sequencing. The genome was re-annotated by mapping transcriptome reads and masking repeats. A total of 978 protein sequences were characterised further by annotating functional domains, leading to a change in their original annotation regarding function and domain composition in about 8 % of all proteins. Based on homology analysis with key components of major immune pathways of insects, the C. floridanus immune-related genes were compared to those of Drosophila melanogaster, Apis mellifera, and other hymenoptera. This analysis revealed that overall the immune system of carpenter ants comprises many components found in these insects. In addition, several C. floridanus specific genes of yet unknown functions but which are strongly induced after immune challenge were discovered. In contrast to solitary insects like Drosophila or the hymenopteran Nasonia vitripennis, the number of genes encoding pattern recognition receptors specific for bacterial peptidoglycan (PGN) and a variety of known antimicrobial peptide (AMP) genes is lower in C. floridanus. The comparative analysis of gene expression post immune-challenge in different developmental stages of C. floridanus suggests a stronger induction of immune gene expression in larvae in comparison to adults.

Conclusions
The comparison of the immune system of C. floridanus with that of other insects revealed the presence of a broad immune repertoire. However, the relatively low number of PGN recognition proteins and AMPs, the identification of Camponotus specific putative immune genes, and stage specific differences in immune gene regulation reflects Camponotus specific evolution including adaptations to its lifestyle.
KW  - immune system
KW  - transcriptome
KW  - carpenter ant
KW  - camponotus floridanus
KW  - re-annotation
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125279
VL  - 16
IS  - 540
ER  - 
TY  - JOUR
A1  - Gámez-Virués, Sagrario
A1  - Perović, David J.
A1  - Gossner, Martin M.
A1  - Börschig, Carmen
A1  - Blüthgen, Nico
A1  - de Jong, Heike
A1  - Simons, Nadja K.
A1  - Klein, Alexandra-Maria
A1  - Krauss, Jochen
A1  - Maier, Gwen
A1  - Scherber, Christoph
A1  - Steckel, Juliane
A1  - Rothenwöhrer, Christoph
A1  - Steffan-Dewenter, Ingolf
A1  - Weiner, Christiane N.
A1  - Weisser, Wolfgang
A1  - Werner, Michael
A1  - Tscharntke, Teja
A1  - Westphal, Catrin
T1  - Landscape simplification filters species traits and drives biotic homogenization
JF  - Nature Communications
N2  - Biodiversity loss can affect the viability of ecosystems by decreasing the ability of communities to respond to environmental change and disturbances. Agricultural intensification is a major driver of biodiversity loss and has multiple components operating at different spatial scales: from in-field management intensity to landscape-scale simplification. Here we show that landscape-level effects dominate functional community composition and can even buffer the effects of in-field management intensification on functional homogenization, and that animal communities in real-world managed landscapes show a unified response (across orders and guilds) to both landscape-scale simplification and in-field intensification. Adults and larvae with specialized feeding habits, species with shorter activity periods and relatively small body sizes are selected against in simplified landscapes with intense in-field management. Our results demonstrate that the diversity of land cover types at the landscape scale is critical for maintaining communities, which are functionally diverse, even in landscapes where in-field management intensity is high.
KW  - land-use intensity
KW  - community functional-responses
KW  - body-size
KW  - agricultural intensification
KW  - sustainable intensification
KW  - managed grasslands
KW  - biodiversity
KW  - diversity
KW  - heterogenity
KW  - butterflies
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-141925
VL  - 6
IS  - 8568
ER  - 
TY  - JOUR
A1  - Herter, Eva K.
A1  - Stauch, Maria
A1  - Gallant, Maria
A1  - Wolf, Elmar
A1  - Raabe, Thomas
A1  - Gallant, Peter
T1  - snoRNAs are a novel class of biologically relevant Myc targets
JF  - BMC Biology
N2  - Background
Myc proteins are essential regulators of animal growth during normal development, and their deregulation is one of the main driving factors of human malignancies. They function as transcription factors that (in vertebrates) control many growth- and proliferation-associated genes, and in some contexts contribute to global gene regulation.

Results
We combine chromatin immunoprecipitation-sequencing (ChIPseq) and RNAseq approaches in Drosophila tissue culture cells to identify a core set of less than 500 Myc target genes, whose salient function resides in the control of ribosome biogenesis. Among these genes we find the non-coding snoRNA genes as a large novel class of Myc targets. All assayed snoRNAs are affected by Myc, and many of them are subject to direct transcriptional activation by Myc, both in Drosophila and in vertebrates. The loss of snoRNAs impairs growth during normal development, whereas their overexpression increases tumor mass in a model for neuronal tumors.

Conclusions
This work shows that Myc acts as a master regulator of snoRNP biogenesis. In addition, in combination with recent observations of snoRNA involvement in human cancer, it raises the possibility that Myc’s transforming effects are partially mediated by this class of non-coding transcripts.
KW  - Drosophila
KW  - ribosome
KW  - snoRNA
KW  - Myc Transcription
KW  - growth
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124956
VL  - 13
IS  - 25
ER  - 
TY  - JOUR
A1  - Herweg, Jo-Ana
A1  - Hansmeier, Nicole
A1  - Otto, Andreas
A1  - Geffken, Anna C.
A1  - Subbarayal, Prema
A1  - Prusty, Bhupesh K.
A1  - Becher, Dörte
A1  - Hensel, Michael
A1  - Schaible, Ulrich E.
A1  - Rudel, Thomas
A1  - Hilbi, Hubert
T1  - Purification and proteomics of pathogen-modified vacuoles and membranes
JF  - Frontiers in Cellular and Infection Microbiology
N2  - Certain pathogenic bacteria adopt an intracellular lifestyle and proliferate in eukaryotic host cells. The intracellular niche protects the bacteria from cellular and humoral components of the mammalian immune system, and at the same time, allows the bacteria to gain access to otherwise restricted nutrient sources. Yet, intracellular protection and access to nutrients comes with a price, i.e., the bacteria need to overcome cell-autonomous defense mechanisms, such as the bactericidal endocytic pathway. While a few bacteria rupture the early phagosome and escape into the host cytoplasm, most intracellular pathogens form a distinct, degradation-resistant and replication-permissive membranous compartment. Intracellular bacteria that form unique pathogen vacuoles include Legionella, Mycobacterium, Chlamydia, Simkania, and Salmonella species. In order to understand the formation of these pathogen niches on a global scale and in a comprehensive and quantitative manner, an inventory of compartment-associated host factors is required. To this end, the intact pathogen compartments need to be isolated, purified and biochemically characterized. Here, we review recent progress on the isolation and purification of pathogen-modified vacuoles and membranes, as well as their proteomic characterization by mass spectrometry and different validation approaches. These studies provide the basis for further investigations on the specific mechanisms of pathogen-driven compartment formation.
KW  - spectrometry-based proteomics
KW  - Mycobacterium tuberculosis
KW  - Chlamydia
KW  - Salmonella
KW  - bacterium Legionella pneumophila
KW  - endocytic multivesicular bodies
KW  - phagosome maturation arrest
KW  - III secretion system
KW  - endoplasmic reticulum
KW  - Chlamydia trachomatis
KW  - Simkania negevensis
KW  - intracellular bacteria
KW  - host pathogen interactions
KW  - immuno-magnetic purification
KW  - Legionella
KW  - Mycobacterium
KW  - Simkania
KW  - pathogen vacuole
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151823
VL  - 5
IS  - 48
ER  - 
TY  - JOUR
A1  - Joschinski, Jens
A1  - Hovestadt, Thomas
A1  - Krauss, Jochen
T1  - Coping with shorter days: do phenology shifts constrain aphid fitness?
JF  - PeerJ
N2  - Climate change can alter the phenology of organisms. It may thus lead seasonal organisms to face different day lengths than in the past, and the fitness consequences of these changes are as yet unclear. To study such effects, we used the pea aphid Acyrthosiphon pisum as a model organism, as it has obligately asexual clones which can be used to study day length effects without eliciting a seasonal response. We recorded life-history traits under short and long days, both with two realistic temperature cycles with means differing by 2 °C. In addition, we measured the population growth of aphids on their host plant Pisum sativum. We show that short days reduce fecundity and the length of the reproductive period of aphids. Nevertheless, this does not translate into differences at the population level because the observed fitness costs only become apparent late in the individual's life. As expected, warm temperature shortens the development time by 0.7 days/°C, leading to faster generation times. We found no interaction of temperature and day length. We conclude that day length changes cause only relatively mild costs, which may not decelerate the increase in pest status due to climate change.
KW  - Homoptera aphididae
KW  - clock reproduction ecology
KW  - phenotypic plasticity
KW  - phenology shifts
KW  - insect timing
KW  - physiological constraints
KW  - day length
KW  - circadian rhythms
KW  - Acyrthosiphon pisum
KW  - climate change
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148382
VL  - 3
IS  - e1103
ER  - 
TY  - JOUR
A1  - Kang, Ji Hyoun
A1  - Manousaki, Tereza
A1  - Franchini, Paolo
A1  - Kneitz, Susanne
A1  - Schartl, Manfred
A1  - Meyer, Axel
T1  - Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin
JF  - Ecology and Evolution
N2  - Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the sword genes those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the older gonopodium than in the younger, and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
KW  - mouse testis differentiation
KW  - fishes Xiphophorus
KW  - beetle horns
KW  - gonopodium
KW  - RNA-Seq
KW  - swordtails
KW  - Xiphophorus
KW  - key innovation
KW  - male-specific traits
KW  - Co-option
KW  - genus Xiphophorus
KW  - hybrid origin
KW  - Drosophila melanogaster
KW  - expression analysis
KW  - cell proliferation
KW  - preexisting bias
KW  - sex combs
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144139
VL  - 5
IS  - 4
ER  - 
TY  - JOUR
A1  - Karl, Stefan
A1  - Dandekar, Thomas
T1  - Convergence behaviour and control in non-linear biological networks
JF  - Scientific Reports
N2  - Control of genetic regulatory networks is challenging to define and quantify. Previous control centrality metrics, which aim to capture the ability of individual nodes to control the system, have been found to suffer from plausibility and applicability problems. Here we present a new approach to control centrality based on network convergence behaviour, implemented as an extension of our genetic regulatory network simulation framework Jimena (http://stefan-karl.de/jimena). We distinguish three types of network control, and show how these mathematical concepts correspond to experimentally verified node functions and signalling pathways in immunity and cell differentiation: Total control centrality quantifies the impact of node mutations and identifies potential pharmacological targets such as genes involved in oncogenesis (e.g. zinc finger protein GLI2 or bone morphogenetic proteins in chondrocytes). Dynamic control centrality describes relaying functions as observed in signalling cascades (e.g. src kinase or Jak/Stat pathways). Value control centrality measures the direct influence of the value of the node on the network (e.g. Indian hedgehog as an essential regulator of proliferation in chondrocytes). Surveying random scale-free networks and biological networks, we find that control of the network resides in few high degree driver nodes and networks can be controlled best if they are sparsely connected.
KW  - complex networks
KW  - control profiles
KW  - differentiation
KW  - pathways
KW  - tumors
KW  - models
KW  - centrality
KW  - chondrosarcoma
KW  - transcriptional regulation
KW  - regulatory networks
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148510
VL  - 5
IS  - 09746
ER  - 
TY  - JOUR
A1  - Karulin, Alexey Y.
A1  - Caspell, Richard
A1  - Dittrich, Marcus
A1  - Lehmann, Paul V.
T1  - Normal distribution of CD8+ T-cell-derived ELISPOT counts within replicates justifies the reliance on parametric statistics for identifying positive responses
JF  - Cells
N2  - Accurate assessment of positive ELISPOT responses for low frequencies of antigen-specific T-cells is controversial. In particular, it is still unknown whether ELISPOT counts within replicate wells follow a theoretical distribution function, and thus whether high power parametric statistics can be used to discriminate between positive and negative wells. We studied experimental distributions of spot counts for up to 120 replicate wells of IFN-γ production by CD8+ T-cell responding to EBV LMP2A (426 – 434) peptide in human PBMC. The cells were tested in serial dilutions covering a wide range of average spot counts per condition, from just a few to hundreds of spots per well. Statistical analysis of the data using diagnostic Q-Q plots and the Shapiro-Wilk normality test showed that in the entire dynamic range of ELISPOT spot counts within replicate wells followed a normal distribution. This result implies that the Student t-Test and ANOVA are suited to identify positive responses. We also show experimentally that borderline responses can be reliably detected by involving more replicate wells, plating higher numbers of PBMC, addition of IL-7, or a combination of these. Furthermore, we have experimentally verified that the number of replicates needed for detection of weak responses can be calculated using parametric statistics.
KW  - ELISPOT
KW  - statistics
KW  - t-Test
KW  - ANOVA
KW  - T-cells
KW  - normal distribution
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149968
VL  - 4
IS  - 1
ER  - 
TY  - JOUR
A1  - Karulin, Alexey Y.
A1  - Karacsony, Kinga
A1  - Zhang, Wenji
A1  - Targoni, Oleg S.
A1  - Moldova, Ioana
A1  - Dittrich, Marcus
A1  - Sundararaman, Srividya
A1  - Lehmann, Paul V.
T1  - ELISPOTs produced by CD8 and CD4 cells follow Log Normal size distribution permitting objective counting
JF  - Cells
N2  - Each positive well in ELISPOT assays contains spots of variable sizes that can range from tens of micrometers up to a millimeter in diameter. Therefore, when it comes to counting these spots the decision on setting the lower and the upper spot size thresholds to discriminate between non-specific background noise, spots produced by individual T cells, and spots formed by T cell clusters is critical. If the spot sizes follow a known statistical distribution, precise predictions on minimal and maximal spot sizes, belonging to a given T cell population, can be made. We studied the size distributional properties of IFN-γ, IL-2, IL-4, IL-5 and IL-17 spots elicited in ELISPOT assays with PBMC from 172 healthy donors, upon stimulation with 32 individual viral peptides representing defined HLA Class I-restricted epitopes for CD8 cells, and with protein antigens of CMV and EBV activating CD4 cells. A total of 334 CD8 and 80 CD4 positive T cell responses were analyzed. In 99.7% of the test cases, spot size distributions followed Log Normal function. These data formally demonstrate that it is possible to establish objective, statistically validated parameters for counting T cell ELISPOTs.
KW  - ELISPOT
KW  - software
KW  - IFN-γ
KW  - IL-17
KW  - T cells
KW  - Normal Distribution
KW  - spot size
KW  - gating
KW  - cytokines
KW  - IL-2
KW  - IL-4
KW  - IL-5
KW  - CD8
KW  - CD4
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149648
VL  - 4
IS  - 1
ER  - 
TY  - JOUR
A1  - Klammert, Uwe
A1  - Müller, Thomas D.
A1  - Hellmann, Tina V.
A1  - Wuerzler, Kristian K.
A1  - Kotzsch, Alexander
A1  - Schliermann, Anna
A1  - Schmitz, Werner
A1  - Kuebler, Alexander C.
A1  - Sebald, Walter
A1  - Nickel, Joachim
T1  - GDF-5 can act as a context-dependent BMP-2 antagonist
JF  - BMC Biology
N2  - Background
Bone morphogenetic protein (BMP)-2 and growth and differentiation factor (GDF)-5 are two related transforming growth factor (TGF)-β family members with important functions in embryonic development and tissue homeostasis. BMP-2 is best known for its osteoinductive properties whereas GDF-5—as evident from its alternative name, cartilage derived morphogenetic protein 1—plays an important role in the formation of cartilage. In spite of these differences both factors signal by binding to the same subset of BMP receptors, raising the question how these different functionalities are generated. The largest difference in receptor binding is observed in the interaction with the type I receptor BMPR-IA. GDF-5, in contrast to BMP-2, shows preferential binding to the isoform BMPR-IB, which is abrogated by a single amino acid (A57R) substitution. The resulting variant, GDF-5 R57A, represents a “BMP-2 mimic” with respect to BMP receptor binding. In this study we thus wanted to analyze whether the two growth factors can induce distinct signals via an identically composed receptor.

Results
Unexpectedly and dependent on the cellular context, GDF-5 R57A showed clear differences in its activity compared to BMP-2. In ATDC-5 cells, both ligands induced alkaline phosphatase (ALP) expression with similar potency. But in C2C12 cells, the BMP-2 mimic GDF-5 R57A (and also wild-type GDF-5) clearly antagonized BMP-2-mediated ALP expression, despite signaling in both cell lines occurring solely via BMPR-IA. The BMP-2- antagonizing properties of GDF-5 and GDF-5 R57A could also be observed in vivo when implanting BMP-2 and either one of the two GDF-5 ligands simultaneously at heterotopic sites.

Conclusions
Although comparison of the crystal structures of the GDF-5 R57A:BMPR-IAEC- and BMP-2:BMPR-IAEC complex revealed small ligand-specific differences, these cannot account for the different signaling characteristics because the complexes seem identical in both differently reacting cell lines. We thus predict an additional component, most likely a not yet identified GDF-5-specific co-receptor, which alters the output of the signaling complexes. Hence the presence or absence of this component then switches GDF-5′s signaling capabilities to act either similar to BMP-2 or as a BMP-2 antagonist. These findings might shed new light on the role of GDF-5, e.g., in cartilage maintenance and/or limb development in that it might act as an inhibitor of signaling events initiated by other BMPs.
KW  - growth and differentiation factor 5
KW  - ligand-receptor complex
KW  - crystal structure
KW  - antagonist
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125550
VL  - 13
IS  - 77
ER  - 
TY  - JOUR
A1  - Kleijn, David
A1  - Winfree, Rachael
A1  - Bartomeus, Ignasi
A1  - Carvalheiro, Luísa G.
A1  - Henry, Mickael
A1  - Isaacs, Rufus
A1  - Klein, Alexandra-Maria
A1  - Kremen, Claire
A1  - M'Gonigle, Leithen K.
A1  - Rader, Romina
A1  - Ricketts, Taylor H.
A1  - Williams, Neal M.
A1  - Adamson, Nancy Lee
A1  - Ascher, John S.
A1  - Báldi, András
A1  - Batáry, Péter
A1  - Benjamin, Faye
A1  - Biesmeijer, Jacobus C.
A1  - Blitzer, Eleanor J.
A1  - Bommarco, Riccardo
A1  - Brand, Mariette R.
A1  - Bretagnolle, Vincent
A1  - Button, Lindsey
A1  - Cariveau, Daniel P.
A1  - Chifflet, Rémy
A1  - Colville, Jonathan F.
A1  - Danforth, Bryan N.
A1  - Elle, Elizabeth
A1  - Garratt, Michael P. D.
A1  - Herzog, Felix
A1  - Holzschuh, Andrea
A1  - Howlett, Brad G.
A1  - Jauker, Frank
A1  - Jha, Shalene
A1  - Knop, Eva
A1  - Krewenka, Kristin M.
A1  - Le Féon, Violette
A1  - Mandelik, Yael
A1  - May, Emily A.
A1  - Park, Mia G.
A1  - Pisanty, Gideon
A1  - Reemer, Menno
A1  - Riedinger, Verena
A1  - Rollin, Orianne
A1  - Rundlöf, Maj
A1  - Sardiñas, Hillary S.
A1  - Scheper, Jeroen
A1  - Sciligo, Amber R.
A1  - Smith, Henrik G.
A1  - Steffan-Dewenter, Ingolf
A1  - Thorp, Robbin
A1  - Tscharntke, Teja
A1  - Verhulst, Jort
A1  - Viana, Blandina F.
A1  - Vaissière, Bernard E.
A1  - Veldtman, Ruan
A1  - Ward, Kimiora L.
A1  - Westphal, Catrin
A1  - Potts, Simon G.
T1  - Delivery of crop pollination services is an insufficient argument for wild pollinator conservation
JF  - Nature Communications
N2  - There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost- effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost- effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.
KW  - ecosystem services
KW  - european countries
KW  - abundance
KW  - native bees
KW  - biodiversity conservation
KW  - plant diversity
KW  - fruit set
KW  - productivity
KW  - decline
KW  - pollen
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151879
VL  - 6
IS  - 7414
ER  -