@article{DietzHasseFerrarisetal.2013, author = {Dietz, Mariana S. and Hasse, Daniel and Ferraris, Davide M. and G{\"o}hler, Antonia and Niemann, Hartmut H. and Heilemann, Mike}, title = {Single-molecule photobleaching reveals increased MET receptor dimerization upon ligand binding in intact cells}, series = {BMC Biophysics}, volume = {6}, journal = {BMC Biophysics}, number = {6}, issn = {2046-1682}, doi = {10.1186/2046-1682-6-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121835}, year = {2013}, abstract = {Background: The human receptor tyrosine kinase MET and its ligand hepatocyte growth factor/scatter factor are essential during embryonic development and play an important role during cancer metastasis and tissue regeneration. In addition, it was found that MET is also relevant for infectious diseases and is the target of different bacteria, amongst them Listeria monocytogenes that induces bacterial uptake through the surface protein internalin B. Binding of ligand to the MET receptor is proposed to lead to receptor dimerization. However, it is also discussed whether preformed MET dimers exist on the cell membrane. Results: To address these issues we used single-molecule fluorescence microscopy techniques. Our photobleaching experiments show that MET exists in dimers on the membrane of cells in the absence of ligand and that the proportion of MET dimers increases significantly upon ligand binding. Conclusions: Our results indicate that partially preformed MET dimers may play a role in ligand binding or MET signaling. The addition of the bacterial ligand internalin B leads to an increase of MET dimers which is in agreement with the model of ligand-induced dimerization of receptor tyrosine kinases.}, language = {en} } @article{ChenGerber2014, author = {Chen, Yi-chun and Gerber, Bertram}, title = {Generalization and discrimination tasks yield concordant measures of perceived distance between odours and their binary mixtures in larval Drosophila}, series = {The Journal of Experimental Biology}, volume = {217}, journal = {The Journal of Experimental Biology}, number = {12}, doi = {10.1242/jeb.100966}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121625}, pages = {2071-7}, year = {2014}, abstract = {Similarity between odours is notoriously difficult to measure. Widely used behavioural approaches in insect olfaction research are cross-adaptation, masking, as well as associative tasks based on olfactory learning and the subsequent testing for how specific the established memory is. A concern with such memory-based approaches is that the learning process required to establish an odour memory may alter the way the odour is processed, such that measures of perception taken at the test are distorted. The present study was therefore designed to see whether behavioural judgements of perceptual distance are different for two different memory-based tasks, namely generalization and discrimination. We used odour-reward learning in larval Drosophila as a study case. In order to challenge the larvae's olfactory system, we chose to work with binary mixtures and their elements (1-octanol, n-amyl acetate, 3-octanol, benzaldehyde and hexyl acetate). We determined the perceptual distance between each mixture and its elements, first in a generalization task, and then in a discrimination task. It turns out that scores of perceptual distance are correlated between both tasks. A re-analysis of published studies looking at element-to-element perceptual distances in larval reward learning and in adult punishment learning confirms this result. We therefore suggest that across a given set of olfactory stimuli, associative training does not grossly alter the pattern of perceptual distances.}, language = {en} } @article{StefanovicBarnettvanDuijvenbodenetal.2014, author = {Stefanovic, Sonia and Barnett, Phil and van Duijvenboden, Karel and Weber, David and Gessler, Manfred and Christoffels, Vincent M.}, title = {GATA-dependent regulatory switches establish atrioventricular canal specificity during heart development}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, number = {3680}, issn = {2041-1723}, doi = {10.1038/ncomms4680}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121437}, year = {2014}, abstract = {The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. Here we assess the transcriptional mechanism underlying this localized differentiation process. We show that atrioventricular canal-specific enhancers are GATA-binding site-dependent and act as switches that repress gene activity in the chambers. We find that atrioventricular canal-specific gene loci are enriched in H3K27ac, a marker of active enhancers, in atrioventricular canal tissue and depleted in H3K27ac in chamber tissue. In the atrioventricular canal, Gata4 activates the enhancers in synergy with Bmp2/Smad signalling, leading to H3K27 acetylation. In contrast, in chambers, Gata4 cooperates with pan-cardiac Hdac1 and Hdac2 and chamber-specific Hey1 and Hey2, leading to H3K27 deacetylation and repression. We conclude that atrioventricular canal-specific enhancers are platforms integrating cardiac transcription factors, broadly active histone modification enzymes and localized co-factors to drive atrioventricular canal-specific gene activity.}, language = {en} } @article{BogdanSchultzGrosshans2013, author = {Bogdan, Sven and Schultz, J{\"o}rg and Grosshans, J{\"o}rg}, title = {Formin' cellular structures: Physiological roles of Diaphanous (Dia) in actin dynamics}, series = {Communicative \& Integrative Biology}, volume = {6}, journal = {Communicative \& Integrative Biology}, number = {e27634}, doi = {10.4161/cib.27634}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121305}, year = {2013}, abstract = {Members of the Diaphanous (Dia) protein family are key regulators of fundamental actin driven cellular processes, which are conserved from yeast to humans. Researchers have uncovered diverse physiological roles in cell morphology, cell motility, cell polarity, and cell division, which are involved in shaping cells into tissues and organs. The identification of numerous binding partners led to substantial progress in our understanding of the differential functions of Dia proteins. Genetic approaches and new microscopy techniques allow important new insights into their localization, activity, and molecular principles of regulation.}, language = {en} } @article{McCarthyMooreKraussetal.2014, author = {McCarthy, Michael A. and Moore, Alana L. and Krauss, Jochen and Morgan, John W. and Clements, Christopher F.}, title = {Linking Indices for Biodiversity Monitoring to Extinction Risk Theory}, series = {Conservation Biology}, volume = {28}, journal = {Conservation Biology}, number = {6}, doi = {10.1111/cobi.12308}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121218}, pages = {1575-83}, year = {2014}, abstract = {Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management objectives that a monitoring program aims to support. For example, the Convention on Biological Diversity requires reporting about extinction rates, so simple indices that reflect extinction risk would be valuable. We developed 3 biodiversity indices that are based on simple models of population viability that relate extinction risk to abundance. We based the first index on the geometric mean abundance of species and the second on a more general power mean. In a third index, we integrated the geometric mean abundance and trend. These indices require the same data as previous indices, but they also relate directly to extinction risk. Field data for butterflies and woodland plants and experimental studies of protozoan communities show that the indices correlate with local extinction rates. Applying the index based on the geometric mean to global data on changes in avian abundance suggested that the average extinction probability of birds has increased approximately 1\% from 1970 to 2009.}, language = {en} } @article{GalluzziBravoSanPedroVitaleetal.2015, author = {Galluzzi, L. and Bravo-San Pedro, J. M. and Vitale, I. and Aaronson, S. A. and Abrams, J. M. and Adam, D. and Alnemri, E. S. and Altucci, L. and Andrews, D. and Annicchiarico-Petruzelli, M. and Baehrecke, E. H. and Bazan, N. G. and Bertrand, M. J. and Bianchi, K. and Blagosklonny, M. V. and Blomgren, K. and Borner, C. and Bredesen, D. E. and Brenner, C. and Campanella, M. and Candi, E. and Cecconi, F. and Chan, F. K. and Chandel, N. S. and Cheng, E. H. and Chipuk, J. E. and Cidlowski, J. A. and Ciechanover, A. and Dawson, T. M. and Dawson, V. L. and De Laurenzi, V. and De Maria, R. and Debatin, K. M. and Di Daniele, N. and Dixit, V. M. and Dynlacht, B. D. and El-Deiry, W. S. and Fimia, G. M. and Flavell, R. A. and Fulda, S. and Garrido, C. and Gougeon, M. L. and Green, D. R. and Gronemeyer, H. and Hajnoczky, G. and Hardwick, J. M. and Hengartner, M. O. and Ichijo, H. and Joseph, B. and Jost, P. J. and Kaufmann, T. and Kepp, O. and Klionsky, D. J. and Knight, R. A. and Kumar, S. and Lemasters, J. J. and Levine, B. and Linkermann, A. and Lipton, S. A. and Lockshin, R. A. and L{\´o}pez-Ot{\´i}n, C. and Lugli, E. and Madeo, F. and Malorni, W. and Marine, J. C. and Martin, S. J. and Martinou, J. C. and Medema, J. P. and Meier, P. and Melino, S. and Mizushima, N. and Moll, U. and Mu{\~n}oz-Pinedo, C. and Nu{\~n}ez, G. and Oberst, A. and Panaretakis, T. and Penninger, J. M. and Peter, M. E. and Piacentini, M. and Pinton, P. and Prehn, J. H. and Puthalakath, H. and Rabinovich, G. A. and Ravichandran, K. S. and Rizzuto, R. and Rodrigues, C. M. and Rubinsztein, D. C. and Rudel, T. and Shi, Y. and Simon, H. U. and Stockwell, B. R. and Szabadkai, G. and Tait, S. W. and Tang, H. L. and Tavernarakis, N. and Tsujimoto, Y. and Vanden Berghe, T. and Vandenabeele, P. and Villunger, A. and Wagner, E. F. and Walczak, H. and White, E. and Wood, W. G. and Yuan, J. and Zakeri, Z. and Zhivotovsky, B. and Melino, G. and Kroemer, G.}, title = {Essential versus accessory aspects of cell death: recommendations of the NCCD 2015}, series = {Cell Death and Differentiation}, volume = {22}, journal = {Cell Death and Differentiation}, doi = {10.1038/cdd.2014.137}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121207}, pages = {58-73}, year = {2015}, abstract = {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.}, language = {en} } @article{ZhanStanciauskasStigloheretal.2014, author = {Zhan, Hong and Stanciauskas, Ramunas and Stigloher, Christian and Dizon, Kevin K. and Jospin, Maelle and Bessereau, Jean-Luis and Pinaud, Fabien}, title = {In vivo single-molecule imaging identifies altered dynamics of calcium channels in dystrophin-mutant C. elegans}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, number = {4974}, doi = {10.1038/ncomms5974}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121125}, year = {2014}, abstract = {Single-molecule (SM) fluorescence microscopy allows the imaging of biomolecules in cultured cells with a precision of a few nanometres but has yet to be implemented in living adult animals. Here we used split-GFP (green fluorescent protein) fusions and complementation-activated light microscopy (CALM) for subresolution imaging of individual membrane proteins in live Caenorhabditis elegans (C. elegans). In vivo tissue-specific SM tracking of transmembrane CD4 and voltage-dependent Ca(2+) channels (VDCC) was achieved with a precision of 30 nm within neuromuscular synapses and at the surface of muscle cells in normal and dystrophin-mutant worms. Through diffusion analyses, we reveal that dystrophin is involved in modulating the confinement of VDCC within sarcolemmal membrane nanodomains in response to varying tonus of C. elegans body-wall muscles. CALM expands the applications of SM imaging techniques beyond the petri dish and opens the possibility to explore the molecular basis of homeostatic and pathological cellular processes with subresolution precision, directly in live animals.}, language = {en} } @article{WirthGlushakovaScheuermayeretal.2014, author = {Wirth, Christine C. and Glushakova, Svetlana and Scheuermayer, Matthias and Repnik, Urska and Garg, Swatl and Schaack, Dominik and Kachman, Marika M. and Weißbach, Tim and Zimmerberg, Joshua and Dandekar, Thomas and Griffiths, Gareth and Chitnis, Chetan E. and Singh, Shallja and Fischer, Rainer and Pradel, Gabriele}, title = {Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes}, series = {Cellular Microbiology}, volume = {16}, journal = {Cellular Microbiology}, number = {5}, doi = {10.1111/cmi.12288}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120895}, pages = {709-33}, year = {2014}, abstract = {Egress of malaria parasites from the host cell requires the concerted rupture of its enveloping membranes. Hence, we investigated the role of the plasmodial perforin-like protein PPLP2 in the egress of Plasmodium falciparum from erythrocytes. PPLP2 is expressed in blood stage schizonts and mature gametocytes. The protein localizes in vesicular structures, which in activated gametocytes discharge PPLP2 in a calcium-dependent manner. PPLP2 comprises a MACPF domain and recombinant PPLP2 has haemolytic activities towards erythrocytes. PPLP2-deficient [PPLP2(-)] merozoites show normal egress dynamics during the erythrocytic replication cycle, but activated PPLP2(-) gametocytes were unable to leave erythrocytes and stayed trapped within these cells. While the parasitophorous vacuole membrane ruptured normally, the activated PPLP2(-) gametocytes were unable to permeabilize the erythrocyte membrane and to release the erythrocyte cytoplasm. In consequence, transmission of PPLP2(-) parasites to the Anopheles vector was reduced. Pore-forming equinatoxin II rescued both PPLP2(-) gametocyte exflagellation and parasite transmission. The pore sealant Tetronic 90R4, on the other hand, caused trapping of activated wild-type gametocytes within the enveloping erythrocytes, thus mimicking the PPLP2(-) loss-of-function phenotype. We propose that the haemolytic activity of PPLP2 is essential for gametocyte egress due to permeabilization of the erythrocyte membrane and depletion of the erythrocyte cytoplasm.}, language = {en} } @article{KlattHolzschuhWestphaletal.2014, author = {Klatt, Bj{\"o}rn K. and Holzschuh, Andrea and Westphal, Catrin and Clough, Yann and Smit, Inga and Pawelzik, Elke and Tscharntke, Teja}, title = {Bee pollination improves crop quality, shelf life and commercial value}, series = {Proceedings of the Royal Society B: Biological Sciences}, volume = {281}, journal = {Proceedings of the Royal Society B: Biological Sciences}, number = {1775}, doi = {10.1098/rspb.2013.2440}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120797}, year = {2014}, abstract = {Pollination improves the yield of most crop species and contributes to one-third of global crop production, but comprehensive benefits including crop quality are still unknown. Hence, pollination is underestimated by international policies, which is particularly alarming in times of agricultural intensification and diminishing pollination services. In this study, exclusion experiments with strawberries showed bee pollination to improve fruit quality, quantity and market value compared with wind and self-pollination. Bee-pollinated fruits were heavier, had less malformations and reached higher commercial grades. They had increased redness and reduced sugar-acid-ratios and were firmer, thus improving the commercially important shelf life. Longer shelf life reduced fruit loss by at least 11\%. This is accounting for 0.32 billion US\$ of the 1.44 billion US\$ provided by bee pollination to the total value of 2.90 billion US\$ made with strawberry selling in the European Union 2009. The fruit quality and yield effects are driven by the pollination-mediated production of hormonal growth regulators, which occur in several pollination-dependent crops. Thus, our comprehensive findings should be transferable to a wide range of crops and demonstrate bee pollination to be a hitherto underestimated but vital and economically important determinant of fruit quality.}, language = {en} } @article{DandekarFieselmannFischeretal.2014, author = {Dandekar, Thomas and Fieselmann, Astrid and Fischer, Eva and Popp, Jasmin and Hensel, Michael and Noster, Janina}, title = {Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {4}, journal = {Frontiers in Cellular and Infection Microbiology}, number = {191}, issn = {2235-2988}, doi = {10.3389/fcimb.2014.00191}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120686}, year = {2014}, abstract = {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.}, language = {en} }