TY - JOUR A1 - Dandekar, Thomas A1 - Eisenreich, Wolfgang T1 - Host-adapted metabolism and its regulation in bacterial pathogens JF - Frontiers in Cellular and Infection Microbiology N2 - No abstract available. KW - bacterial pathogens KW - enteric pathogens KW - metabolism KW - host-pathogen adaption KW - isotopolog profiling Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-196876 SN - 2235-2988 VL - 5 IS - 28 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 - 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 - Shityakov, Sergey A1 - Dandekar, Thomas A1 - Förster, Carola T1 - Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia JF - HIV/AIDS: Research and Palliative Care N2 - Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) between the samples from AIDS patients with and without apparent features of HIVE-induced dementia were identified. In addition, protein–protein interaction networks were constructed by mapping DEGs into protein–protein interaction data to identify the pathways that these DEGs are involved in. The results revealed that the expression of 1,528 DEGs is mainly involved in the immune response, regulation of cell proliferation, cellular response to inflammation, signal transduction, and viral replication cycle. Heat-shock protein alpha, class A member 1 (HSP90AA1), and fibronectin 1 were detected as hub nodes with degree values >130. In conclusion, the results indicate that HSP90A and fibronectin 1 play important roles in HIVE pathogenesis. KW - microarray KW - differentially expressed genes KW - protein-protein interaction network KW - gene ontology KW - encephalitis dementia KW - human immunodeficiency virus Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149494 VL - 7 ER - TY - JOUR A1 - Morriswood, Brooke T1 - Form, fabric, and function of a flagellum-associated cytoskeletal structure. JF - Cells N2 - Trypanosoma brucei is a uniflagellated protist and the causative agent of African trypanosomiasis, a neglected tropical disease. The single flagellum of T. brucei is essential to a number of cellular processes such as motility, and has been a longstanding focus of scientific enquiry. A number of cytoskeletal structures are associated with the flagellum in T. brucei, and one such structure—a multiprotein complex containing the repeat motif protein TbMORN1—is the focus of this review. The TbMORN1-containing complex, which was discovered less than ten years ago, is essential for the viability of the mammalian-infective form of T. brucei. The complex has an unusual asymmetric morphology, and is coiled around the flagellum to form a hook shape. Proteomic analysis using the proximity-dependent biotin identification (BioID) technique has elucidated a number of its components. Recent work has uncovered a role for TbMORN1 in facilitating protein entry into the cell, thus providing a link between the cytoskeleton and the endomembrane system. This review summarises the extant data on the complex, highlights the outstanding questions for future enquiry, and provides speculation as to its possible role in a size-exclusion mechanism for regulating protein entry. The review additionally clarifies the nomenclature associated with this topic, and proposes the adoption of the term “hook complex” to replace the former name “bilobe” to describe the complex. KW - BioID KW - Trypanosoma brucei KW - cytoskeleton KW - TbMORN1 KW - MORN-repeat Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149467 VL - 4 IS - 4 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 - Dandekar, Thomas A1 - Fieselmann, Astrid A1 - Fischer, Eva A1 - Popp, Jasmin A1 - Hensel, Michael A1 - Noster, Janina T1 - Salmonella - how a metabolic generalist adopts an intracellular lifestyle during infection JF - Frontiers in Cellular and Infection Microbiology N2 - The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology. KW - enterica serovar Typhimurium KW - bacterial invasion KW - mouse model KW - defenses KW - regulation KW - "-omics" KW - virulence KW - Salmonella-containing vacuole (SCV) KW - metabolism KW - nitric oxide Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-149029 VL - 4 IS - 191 ER - 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 - Paul, Mila M. A1 - Pauli, Martin A1 - Ehmann, Nadine A1 - Hallermann, Stefan A1 - Sauer, Markus A1 - Kittel, Robert J. A1 - Heckmann, Manfred T1 - Bruchpilot and Synaptotagmin collaborate to drive rapid glutamate release and active zone differentiation JF - Frontiers in Cellular Neuroscience N2 - The active zone (AZ) protein Bruchpilot (Brp) is essential for rapid glutamate release at Drosophila melanogaster neuromuscular junctions (NMJs). Quantal time course and measurements of action potential-waveform suggest that presynaptic fusion mechanisms are altered in brp null mutants (brp\(^{69}\)). This could account for their increased evoked excitatory postsynaptic current (EPSC) delay and rise time (by about 1 ms). To test the mechanism of release protraction at brp\(^{69}\) AZs, we performed knock-down of Synaptotagmin-1 (Syt) via RNAi (syt\(^{KD}\)) in wildtype (wt), brp\(^{69}\) and rab3 null mutants (rab3\(^{rup}\)), where Brp is concentrated at a small number of AZs. At wt and rab3\(^{rup}\) synapses, syt\(^{KD}\) lowered EPSC amplitude while increasing rise time and delay, consistent with the role of Syt as a release sensor. In contrast, syt\(^{KD}\) did not alter EPSC amplitude at brp\(^{69}\) synapses, but shortened delay and rise time. In fact, following syt\(^{KD}\), these kinetic properties were strikingly similar in wt and brp\(^{69}\), which supports the notion that Syt protracts release at brp\(^{69}\) synapses. To gain insight into this surprising role of Syt at brp\(^{69}\) AZs, we analyzed the structural and functional differentiation of synaptic boutons at the NMJ. At tonic type Ib motor neurons, distal boutons contain more AZs, more Brp proteins per AZ and show elevated and accelerated glutamate release compared to proximal boutons. The functional differentiation between proximal and distal boutons is Brp-dependent and reduced after syt\(^{KD}\). Notably, syt\(^{KD}\) boutons are smaller, contain fewer Brp positive AZs and these are of similar number in proximal and distal boutons. In addition, super-resolution imaging via dSTORM revealed that syt\(^{KD}\) increases the number and alters the spatial distribution of Brp molecules at AZs, while the gradient of Brp proteins per AZ is diminished. In summary, these data demonstrate that normal structural and functional differentiation of Drosophila AZs requires concerted action of Brp and Syt. KW - neuromuscular junction KW - Bruchpilot KW - synaptic delay KW - dSTORM KW - synaptotagmin KW - presynaptic differentiation KW - neurotransmitter release KW - active zone KW - synaptic transmission KW - fluorescent probes Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148988 VL - 9 IS - 29 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 - Leikam, C A1 - Hufnagel, AL A1 - Otto, C A1 - Murphy, DJ A1 - Mühling, B A1 - Kneitz, S A1 - Nanda, I A1 - Schmid, M A1 - Wagner, TU A1 - Haferkamp, S A1 - Bröcker, E-B A1 - Schartl, M A1 - Meierjohann, S T1 - In vitro evidence for senescent multinucleated melanocytes as a source for tumor-initiating cells JF - Cell Death and Disease N2 - Oncogenic signaling in melanocytes results in oncogene-induced senescence (OIS), a stable cell-cycle arrest frequently characterized by a bi-or multinuclear phenotype that is considered as a barrier to cancer progression. However, the long-sustained conviction that senescence is a truly irreversible process has recently been challenged. Still, it is not known whether cells driven into OIS can progress to cancer and thereby pose a potential threat. Here, we show that prolonged expression of the melanoma oncogene N-RAS\(^{61K}\) in pigment cells overcomes OIS by triggering the emergence of tumor-initiating mononucleated stem-like cells from senescent cells. This progeny is dedifferentiated, highly proliferative, anoikis-resistant and induces fast growing, metastatic tumors. Our data describe that differentiated cells, which are driven into senescence by an oncogene, use this senescence state as trigger for tumor transformation, giving rise to highly aggressive tumor-initiating cells. These observations provide the first experimental in vitro evidence for the evasion of OIS on the cellular level and ensuing transformation. KW - reactive oxygen KW - human melanoma KW - MITF KW - cancer KW - skin KW - DNA damage KW - kappa-B KW - oncogene-induced senescence KW - cellular senescence Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148718 VL - 6 IS - e1711 ER - TY - JOUR A1 - Scholz, Nicole A1 - Gehring, Jennifer A1 - Guan, Chonglin A1 - Ljaschenko, Dmitrij A1 - Fischer, Robin A1 - Lakshmanan, Vetrivel A1 - Kittel, Robert J. A1 - Langenhan, Tobias T1 - The adhesion GPCR Latrophilin/CIRL shapes mechanosensation JF - Cell Reports N2 - G-protein-coupled receptors (GPCRs) are typically regarded as chemosensors that control cellular states in response to soluble extracellular cues. However, the modality of stimuli recognized through adhesion GPCR (aGPCR), the second largest class of the GPCR superfamily, is unresolved. Our study characterizes the Drosophila aGPCR Latrophilin/dCirl, a prototype member of this enigmatic receptor class. We show that dCirl shapes the perception of tactile, proprioceptive, and auditory stimuli through chordotonal neurons, the principal mechanosensors of Drosophila. dCirl sensitizes these neurons for the detection of mechanical stimulation by amplifying their input-output function. Our results indicate that aGPCR may generally process and modulate the perception of mechanical signals, linking these important stimuli to the sensory canon of the GPCR superfamily. KW - \(\alpha\)-latrotoxin KW - chordotonal organs KW - Johnstons organ KW - ligand CD55 KW - hearing KW - binding KW - shear stress KW - protein-coupled receptors KW - drosophila larvae KW - domain Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148626 VL - 11 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 - Martin, Emily A. A1 - Reineking, Björn A1 - Seo, Bumsuk A1 - Steffan-Dewenter, Ingolf T1 - Pest control of aphids depends on landscape complexity and natural enemy interactions JF - PeerJ N2 - Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1) the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2) the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the effectiveness of aphid natural pest control. KW - insect populations KW - metaanalysis KW - biodiversity-ecosystem functioning KW - cabbage Brassica oleracea var. capitata KW - proportion of seminatural habitat KW - South Korea KW - land use intensification KW - trophic interactions KW - agroecosystems KW - biological control KW - agricultural landscapes KW - pest KW - biodiversity KW - herbivores Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148393 VL - 3 IS - e1095 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 - Remmele, Christian W. A1 - Luther, Christian H. A1 - Balkenhol, Johannes A1 - Dandekar, Thomas A1 - Müller, Tobias A1 - Dittrich, Marcus T. T1 - Integrated inference and evaluation of host-fungi interaction networks JF - Frontiers in Microbiology N2 - Fungal microorganisms frequently lead to life-threatening infections. Within this group of pathogens, the commensal Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of invasive mycoses in Europe. A key capability for host invasion and immune response evasion are specific molecular interactions between the fungal pathogen and its human host. Experimentally validated knowledge about these crucial interactions is rare in literature and even specialized host pathogen databases mainly focus on bacterial and viral interactions whereas information on fungi is still sparse. To establish large-scale host fungi interaction networks on a systems biology scale, we develop an extended inference approach based on protein orthology and data on gene functions. Using human and yeast intraspecies networks as template, we derive a large network of pathogen host interactions (PHI). Rigorous filtering and refinement steps based on cellular localization and pathogenicity information of predicted interactors yield a primary scaffold of fungi human and fungi mouse interaction networks. Specific enrichment of known pathogenicity-relevant genes indicates the biological relevance of the predicted PHI. A detailed inspection of functionally relevant subnetworks reveals novel host fungal interaction candidates such as the Candida virulence factor PLB1 and the anti-fungal host protein APP. Our results demonstrate the applicability of interolog-based prediction methods for host fungi interactions and underline the importance of filtering and refinement steps to attain biologically more relevant interactions. This integrated network framework can serve as a basis for future analyses of high-throughput host fungi transcriptome and proteome data. KW - candida genome database KW - computational prediction KW - potential role KW - network inference KW - bioinformatics and computational biology KW - protein interaction database KW - Aspergillus fumigatus KW - cell wall KW - functional modules KW - alzheimers disease KW - molecular cloning KW - Candida albicans KW - pathogen-host interaction (PHI) KW - protein-protein interaction KW - pathogenicity KW - interolog Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148278 VL - 6 IS - 764 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 - Wäldchen, Sina A1 - Lehmann, Julian A1 - Klein, Teresa A1 - van de Linde, Sebastian A1 - Sauer, Markus T1 - Light-induced cell damage in live-cell super-resolution microscopy JF - Scientific Reports N2 - Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20-24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of similar to 1 kW cm\(^{-2}\) at 640 nm for several minutes, the maximum dose at 405 nm is only similar to 50 J cm\(^{-2}\), emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities. KW - optical reconstruction microscopy KW - tag fusion proteins KW - localization microscopy KW - photodynamic therapy KW - diffraction limit KW - illumination microscopy KW - structured illumination KW - fluorescent probes KW - in vitro KW - dynamics Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-145207 VL - 5 IS - 15348 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 -