[{"has_accepted_license":"1","date_created":"2018-12-11T11:48:34Z","publication":"Plant and Cell Physiology","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"6854","article_processing_charge":"No","pubrep_id":"1009","external_id":{"pmid":["29016942"],"isi":["000413220400019"]},"volume":58,"quality_controlled":"1","pmid":1,"day":"21","author":[{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek"},{"first_name":"Yuki","last_name":"Matsuura","full_name":"Matsuura, Yuki"},{"full_name":"Santuari, Luca","last_name":"Santuari","first_name":"Luca"},{"first_name":"Hirotaka","last_name":"Kouno","full_name":"Kouno, Hirotaka"},{"first_name":"Kohei","last_name":"Arima","full_name":"Arima, Kohei"},{"full_name":"Hardtke, Christian","last_name":"Hardtke","first_name":"Christian"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Kakimoto, Tatsuo","last_name":"Kakimoto","first_name":"Tatsuo"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"}],"isi":1,"file":[{"file_id":"6333","checksum":"bd3e3a94d55416739cbb19624bb977f8","creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:48:06Z","file_name":"2017_PlantCellPhysio_Kitakura.pdf","date_created":"2019-04-17T07:52:34Z","relation":"main_file","content_type":"application/pdf","file_size":1352913}],"publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","publication_status":"published","doi":"10.1093/pcp/pcx118","oa_version":"Submitted Version","date_published":"2017-08-21T00:00:00Z","file_date_updated":"2020-07-14T12:48:06Z","scopus_import":"1","ddc":["581"],"intvolume":" 58","citation":{"short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118","ieee":"S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118"},"date_updated":"2023-09-27T11:00:19Z","abstract":[{"text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.","lang":"eng"}],"issue":"10","year":"2017","article_number":"1801-1811","_id":"799","status":"public","oa":1,"publication_identifier":{"issn":["00320781"]},"month":"08"},{"publication":"Nature Communications","date_created":"2018-12-11T11:48:34Z","has_accepted_license":"1","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"type":"journal_article","pubrep_id":"914","article_processing_charge":"No","publist_id":"6853","quality_controlled":"1","volume":8,"external_id":{"isi":["000412053100004"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"02","file":[{"access_level":"open_access","checksum":"7e2c7621afd5f802338e92e8619f024d","file_id":"5135","creator":"system","date_created":"2018-12-12T10:15:17Z","date_updated":"2020-07-14T12:48:07Z","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","file_size":4261832,"content_type":"application/pdf","relation":"main_file"}],"isi":1,"author":[{"full_name":"Strüber, Michael","first_name":"Michael","last_name":"Strüber"},{"full_name":"Sauer, Jonas","last_name":"Sauer","first_name":"Jonas"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"full_name":"Bartos, Marlene","last_name":"Bartos","first_name":"Marlene"}],"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"}],"title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1038/s41467-017-00936-3","publication_status":"published","date_published":"2017-10-02T00:00:00Z","oa_version":"Published Version","ddc":["571"],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:07Z","intvolume":" 8","citation":{"chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3.","apa":"Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3.","ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00936-3"},"year":"2017","issue":"1","abstract":[{"text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.","lang":"eng"}],"date_updated":"2023-09-27T10:59:41Z","_id":"800","article_number":"758","oa":1,"publication_identifier":{"issn":["20411723"]},"status":"public","ec_funded":1,"month":"10"},{"intvolume":" 96","citation":{"chicago":"Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.09.021.","mla":"Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity.” Neuron, vol. 96, no. 1, Elsevier, 2017, p. 177–189.e7, doi:10.1016/j.neuron.2017.09.021.","apa":"Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C., & Vogels, T. P. (2017). Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.09.021","ista":"Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017. Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. 96(1), 177–189.e7.","short":"R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels, Neuron 96 (2017) 177–189.e7.","ieee":"R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and T. P. Vogels, “Synaptic transmission optimization predicts expression loci of long-term plasticity,” Neuron, vol. 96, no. 1. Elsevier, p. 177–189.e7, 2017.","ama":"Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic transmission optimization predicts expression loci of long-term plasticity. Neuron. 2017;96(1):177-189.e7. doi:10.1016/j.neuron.2017.09.021"},"ddc":["570"],"file_date_updated":"2020-07-14T12:48:08Z","date_published":"2017-09-27T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.neuron.2017.09.021","publication_status":"published","month":"09","publication_identifier":{"issn":["0896-6273"]},"oa":1,"status":"public","_id":"8016","year":"2017","issue":"1","abstract":[{"lang":"eng","text":"Long-term modifications of neuronal connections are critical for reliable memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is highly variable. Here we introduce a theoretical framework in which long-term plasticity performs an optimization of the postsynaptic response statistics toward a given mean with minimal variance. Consequently, the state of the synapse at the time of plasticity induction determines the ratio of pre- and postsynaptic modifications. Our theory explains the experimentally observed expression loci of the hippocampal and neocortical synaptic potentiation studies we examined. Moreover, the theory predicts presynaptic expression of long-term depression, consistent with experimental observations. At inhibitory synapses, the theory suggests a statistically efficient excitatory-inhibitory balance in which changes in inhibitory postsynaptic response statistics specifically target the mean excitation. Our results provide a unifying theory for understanding the expression mechanisms and functions of long-term synaptic transmission plasticity."}],"date_updated":"2021-01-12T08:16:32Z","volume":96,"quality_controlled":"1","external_id":{"pmid":["28957667"]},"article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"type":"journal_article","publication":"Neuron","page":"177-189.e7","date_created":"2020-06-25T12:54:46Z","has_accepted_license":"1","title":"Synaptic transmission optimization predicts expression loci of long-term plasticity","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Elsevier","file":[{"date_created":"2020-07-09T09:42:49Z","date_updated":"2020-07-14T12:48:08Z","file_name":"2017_Neuron_Costa.pdf","access_level":"open_access","file_id":"8103","creator":"cziletti","checksum":"49fbca2821066c0965bd5678b32b6b48","file_size":7140149,"content_type":"application/pdf","relation":"main_file"}],"author":[{"last_name":"Costa","first_name":"Rui Ponte","full_name":"Costa, Rui Ponte"},{"full_name":"Padamsey, Zahid","last_name":"Padamsey","first_name":"Zahid"},{"full_name":"D’Amour, James A.","first_name":"James A.","last_name":"D’Amour"},{"last_name":"Emptage","first_name":"Nigel J.","full_name":"Emptage, Nigel J."},{"full_name":"Froemke, Robert C.","last_name":"Froemke","first_name":"Robert C."},{"full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"}],"extern":"1","day":"27","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1},{"_id":"8017","year":"2017","date_updated":"2021-01-12T08:16:32Z","abstract":[{"text":"nhibitory neurons, although relatively few in number, exert powerful control over brain circuits. They stabilize network activity in the face of strong feedback excitation and actively engage in computations. Recent studies reveal the importance of a precise balance of excitation and inhibition in neural circuits, which often requires exquisite fine-tuning of inhibitory connections. We review inhibitory synaptic plasticity and its roles in shaping both feedforward and feedback control. We discuss the necessity of complex, codependent plasticity mechanisms to build nontrivial, functioning networks, and we end by summarizing experimental evidence of such interactions.","lang":"eng"}],"issue":"1","month":"07","publication_identifier":{"issn":["0147-006X","1545-4126"]},"status":"public","date_published":"2017-07-01T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1146/annurev-neuro-072116-031005","intvolume":" 40","citation":{"short":"G. Hennequin, E.J. Agnes, T.P. Vogels, Annual Review of Neuroscience 40 (2017) 557–579.","ama":"Hennequin G, Agnes EJ, Vogels TP. Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. 2017;40(1):557-579. doi:10.1146/annurev-neuro-072116-031005","ieee":"G. Hennequin, E. J. Agnes, and T. P. Vogels, “Inhibitory plasticity: Balance, control, and codependence,” Annual Review of Neuroscience, vol. 40, no. 1. Annual Reviews, pp. 557–579, 2017.","chicago":"Hennequin, Guillaume, Everton J. Agnes, and Tim P Vogels. “Inhibitory Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience. Annual Reviews, 2017. https://doi.org/10.1146/annurev-neuro-072116-031005.","mla":"Hennequin, Guillaume, et al. “Inhibitory Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience, vol. 40, no. 1, Annual Reviews, 2017, pp. 557–79, doi:10.1146/annurev-neuro-072116-031005.","ista":"Hennequin G, Agnes EJ, Vogels TP. 2017. Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. 40(1), 557–579.","apa":"Hennequin, G., Agnes, E. J., & Vogels, T. P. (2017). Inhibitory plasticity: Balance, control, and codependence. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev-neuro-072116-031005"},"author":[{"full_name":"Hennequin, Guillaume","last_name":"Hennequin","first_name":"Guillaume"},{"last_name":"Agnes","first_name":"Everton J.","full_name":"Agnes, Everton J."},{"full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"}],"day":"01","extern":"1","pmid":1,"title":"Inhibitory plasticity: Balance, control, and codependence","publisher":"Annual Reviews","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"type":"journal_article","page":"557-579","date_created":"2020-06-25T12:55:53Z","publication":"Annual Review of Neuroscience","external_id":{"pmid":["28598717"]},"volume":40,"quality_controlled":"1","article_type":"original","article_processing_charge":"No"},{"year":"2017","date_updated":"2021-01-12T08:16:33Z","abstract":[{"text":"Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or \"engrams\" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched \"inhibitory engrams\" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. ","lang":"eng"}],"issue":"26","_id":"8018","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"status":"public","month":"06","publication_status":"published","doi":"10.1073/pnas.1701812114","date_published":"2017-06-27T00:00:00Z","oa_version":"Published Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/","open_access":"1"}],"intvolume":" 114","citation":{"short":"H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the National Academy of Sciences 114 (2017) 6666–6674.","ieee":"H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams in perception and memory,” Proceedings of the National Academy of Sciences, vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674, 2017.","ama":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 2017;114(26):6666-6674. doi:10.1073/pnas.1701812114","apa":"Barron, H. C., Vogels, T. P., Behrens, T. E., & Ramaswami, M. (2017). Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701812114","ista":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 114(26), 6666–6674.","mla":"Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” Proceedings of the National Academy of Sciences, vol. 114, no. 26, Proceedings of the National Academy of Sciences, 2017, pp. 6666–74, doi:10.1073/pnas.1701812114.","chicago":"Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami. “Inhibitory Engrams in Perception and Memory.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1701812114."},"day":"27","extern":"1","pmid":1,"author":[{"first_name":"Helen C.","last_name":"Barron","full_name":"Barron, Helen C."},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"last_name":"Behrens","first_name":"Timothy E.","full_name":"Behrens, Timothy E."},{"first_name":"Mani","last_name":"Ramaswami","full_name":"Ramaswami, Mani"}],"title":"Inhibitory engrams in perception and memory","publisher":"Proceedings of the National Academy of Sciences","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2020-06-25T12:56:58Z","page":"6666-6674","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","external_id":{"pmid":["28611219"]},"quality_controlled":"1","volume":114},{"intvolume":" 43","citation":{"ista":"Vogels TP, Griffith LC. 2017. Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. 43, A1–A5.","apa":"Vogels, T. P., & Griffith, L. C. (2017). Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.04.002","mla":"Vogels, Tim P., and Leslie C. Griffith. “Editorial Overview: Neurobiology of Learning and Plasticity 2017.” Current Opinion in Neurobiology, vol. 43, Elsevier, 2017, pp. A1–5, doi:10.1016/j.conb.2017.04.002.","chicago":"Vogels, Tim P, and Leslie C Griffith. “Editorial Overview: Neurobiology of Learning and Plasticity 2017.” Current Opinion in Neurobiology. Elsevier, 2017. https://doi.org/10.1016/j.conb.2017.04.002.","ieee":"T. P. Vogels and L. C. Griffith, “Editorial overview: Neurobiology of learning and plasticity 2017,” Current Opinion in Neurobiology, vol. 43. Elsevier, pp. A1–A5, 2017.","ama":"Vogels TP, Griffith LC. Editorial overview: Neurobiology of learning and plasticity 2017. Current Opinion in Neurobiology. 2017;43:A1-A5. doi:10.1016/j.conb.2017.04.002","short":"T.P. Vogels, L.C. Griffith, Current Opinion in Neurobiology 43 (2017) A1–A5."},"quality_controlled":"1","volume":43,"external_id":{"pmid":["28427877"]},"article_type":"letter_note","article_processing_charge":"No","date_published":"2017-04-17T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publication":"Current Opinion in Neurobiology","page":"A1-A5","date_created":"2020-06-25T13:03:30Z","doi":"10.1016/j.conb.2017.04.002","publication_status":"published","month":"04","publication_identifier":{"issn":["0959-4388"]},"title":"Editorial overview: Neurobiology of learning and plasticity 2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","status":"public","_id":"8019","author":[{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"full_name":"Griffith, Leslie C","first_name":"Leslie C","last_name":"Griffith"}],"extern":"1","year":"2017","day":"17","abstract":[{"text":"Synaptic plasticity is essential for the function of neural systems. It sets up initial circuitry and adjusts connection strengths according to the maintenance requirements of its host networks. Like all things biological, synaptic plasticity must rely on genetic programs to provide the molecular components of its machinery to integrate ongoing, often multi-sensory experience without destabilising effects. Because of its fundamental importance to healthy behaviour, understanding plasticity is thought to hold the key to understanding the brain. There are innumerable ways to approach this topic and a complete review of its status quo would be impossible. In the current issue we dig into some of the finer points of synaptic plasticity, starting small, at the level of genes, and slowly zooming out to synapses, populations of synapses, and finally entire systems and brain regions. At each level, we tried to represent different perspectives, different systems, and approaches to the same questions to give a broad sampling of how synaptic plasticity is being studied.","lang":"eng"}],"pmid":1,"date_updated":"2021-01-12T08:16:33Z"},{"citation":{"mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:10.1016/j.cell.2017.07.038.","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972.","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038.","ieee":"M. Samwer et al., “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972, 2017.","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038","short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972."},"intvolume":" 170","scopus_import":"1","file_date_updated":"2020-07-14T12:48:08Z","ddc":["570"],"oa_version":"Published Version","date_published":"2017-08-24T00:00:00Z","publication_status":"published","doi":"10.1016/j.cell.2017.07.038","month":"08","status":"public","publication_identifier":{"issn":["00928674"]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"}],"_id":"803","date_updated":"2023-09-27T10:59:14Z","abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"issue":"5","year":"2017","external_id":{"isi":["000408372400014"]},"volume":170,"quality_controlled":"1","publist_id":"6848","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"has_accepted_license":"1","page":"956 - 972","date_created":"2018-12-11T11:48:35Z","publication":"Cell","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Cell Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","isi":1,"author":[{"full_name":"Samwer, Matthias","last_name":"Samwer","first_name":"Matthias"},{"last_name":"Schneider","first_name":"Maximilian","full_name":"Schneider, Maximilian"},{"last_name":"Hoefler","first_name":"Rudolf","full_name":"Hoefler, Rudolf"},{"full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","first_name":"Philipp S","orcid":"0000-0002-5795-0133"},{"full_name":"Jude, Julian","first_name":"Julian","last_name":"Jude"},{"last_name":"Zuber","first_name":"Johannes","full_name":"Zuber, Johannes"},{"full_name":"Gerlic, Daniel","last_name":"Gerlic","first_name":"Daniel"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":17666637,"file_name":"2017_Cell_Samwer.pdf","date_updated":"2020-07-14T12:48:08Z","date_created":"2019-01-18T13:45:40Z","creator":"dernst","checksum":"64897b0c5373f22273f598e4672c60ff","file_id":"5852","access_level":"open_access"}],"day":"24","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"}},{"publication_status":"published","doi":"10.1021/acs.jctc.7b00374","date_published":"2017-10-10T00:00:00Z","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.03773"}],"scopus_import":"1","citation":{"chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation. American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., & Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:10.1021/acs.jctc.7b00374.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053."},"intvolume":" 13","year":"2017","date_updated":"2023-09-27T10:58:45Z","issue":"10","abstract":[{"text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides.","lang":"eng"}],"_id":"804","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["15499618"]},"oa":1,"status":"public","month":"10","page":"5039 - 5053","date_created":"2018-12-11T11:48:35Z","publication":"Journal of Chemical Theory and Computation","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"type":"journal_article","publist_id":"6847","article_processing_charge":"No","external_id":{"isi":["000412965700036"]},"volume":13,"quality_controlled":"1","day":"10","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","isi":1,"author":[{"full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","first_name":"Philipp S","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Deluweit, Felix","first_name":"Felix","last_name":"Deluweit"},{"last_name":"Scherrers","first_name":"Roger","full_name":"Scherrers, Roger"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K","full_name":"Sikora, Mateusz K"}],"title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","publisher":"American Chemical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","status":"public","publisher":"Company of Biologists","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","day":"31","year":"2017","date_updated":"2023-09-26T16:20:09Z","abstract":[{"text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2).","lang":"eng"}],"_id":"805","isi":1,"author":[{"full_name":"Pfurr, Sabrina","first_name":"Sabrina","last_name":"Pfurr"},{"full_name":"Chu, Yu","first_name":"Yu","last_name":"Chu"},{"first_name":"Christian","last_name":"Bohrer","full_name":"Bohrer, Christian"},{"last_name":"Greulich","first_name":"Franziska","full_name":"Greulich, Franziska"},{"last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J"},{"full_name":"Mammadzada, Könül","last_name":"Mammadzada","first_name":"Könül"},{"full_name":"Hils, Miriam","first_name":"Miriam","last_name":"Hils"},{"first_name":"Sebastian","last_name":"Arnold","full_name":"Arnold, Sebastian"},{"full_name":"Taylor, Verdon","last_name":"Taylor","first_name":"Verdon"},{"full_name":"Schachtrup, Kristina","first_name":"Kristina","last_name":"Schachtrup"},{"full_name":"Uhlenhaut, N Henriette","last_name":"Uhlenhaut","first_name":"N Henriette"},{"last_name":"Schachtrup","first_name":"Christian","full_name":"Schachtrup, Christian"}],"publist_id":"6846","scopus_import":"1","article_processing_charge":"No","external_id":{"isi":["000414025600007"]},"volume":144,"citation":{"ieee":"S. Pfurr et al., “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” Development, vol. 144. Company of Biologists, pp. 3917–3931, 2017.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 2017;144:3917-3931. doi:10.1242/dev.145698","short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931.","chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.145698.","mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:10.1242/dev.145698.","apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. Company of Biologists. https://doi.org/10.1242/dev.145698","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931."},"quality_controlled":"1","intvolume":" 144","date_created":"2018-12-11T11:48:36Z","page":"3917 - 3931","publication":"Development","publication_status":"published","doi":"10.1242/dev.145698","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"date_published":"2017-10-31T00:00:00Z","type":"journal_article","oa_version":"None"},{"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","date_created":"2018-12-11T11:48:36Z","page":"274 - 280","has_accepted_license":"1","department":[{"_id":"E-Lib"}],"language":[{"iso":"eng"}],"type":"journal_article","publist_id":"6843","volume":70,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"popular_science":"1","file":[{"file_size":125065,"relation":"main_file","content_type":"application/pdf","date_created":"2019-01-18T13:39:26Z","date_updated":"2020-07-14T12:48:09Z","file_name":"2017_VOEB_Andrae.pdf","access_level":"open_access","creator":"dernst","checksum":"558c18bcf5580d87dd371ec626d52075","file_id":"5851"}],"author":[{"full_name":"Andrae, Magdalena","last_name":"Andrae","first_name":"Magdalena"},{"full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","last_name":"Villányi"}],"title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"VÖB","doi":"10.31263/voebm.v70i2.1898","publication_status":"published","date_published":"2017-08-01T00:00:00Z","oa_version":"Published Version","ddc":["020"],"file_date_updated":"2020-07-14T12:48:09Z","scopus_import":1,"intvolume":" 70","citation":{"chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280."},"year":"2017","issue":"2","abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"date_updated":"2021-01-12T08:16:45Z","_id":"807","oa":1,"publication_identifier":{"issn":["10222588"]},"status":"public","month":"08"},{"month":"03","oa":1,"publication_identifier":{"issn":["2050-084X"]},"status":"public","_id":"8075","article_number":"e22152","year":"2017","abstract":[{"text":"Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.","lang":"eng"}],"date_updated":"2021-01-12T08:16:46Z","intvolume":" 6","citation":{"chicago":"Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck, Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” ELife. eLife Sciences Publications, Ltd, 2017. https://doi.org/10.7554/elife.22152.","ista":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. 2017. Mapping the function of neuronal ion channels in model and experiment. eLife. 6, e22152.","mla":"Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” ELife, vol. 6, e22152, eLife Sciences Publications, Ltd, 2017, doi:10.7554/elife.22152.","apa":"Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R., & Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model and experiment. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.22152","ieee":"W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,” eLife, vol. 6. eLife Sciences Publications, Ltd, 2017.","ama":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. Mapping the function of neuronal ion channels in model and experiment. eLife. 2017;6. doi:10.7554/elife.22152","short":"W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P. Vogels, ELife 6 (2017)."},"ddc":["570"],"file_date_updated":"2020-07-16T12:08:40Z","date_published":"2017-03-06T00:00:00Z","oa_version":"Published Version","doi":"10.7554/elife.22152","publication_status":"published","title":"Mapping the function of neuronal ion channels in model and experiment","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"eLife Sciences Publications, Ltd","file":[{"content_type":"application/pdf","relation":"main_file","file_size":16034505,"success":1,"file_name":"2017_elife_Podlaski.pdf","date_updated":"2020-07-16T12:08:40Z","date_created":"2020-07-16T12:08:40Z","checksum":"e5c5a33bcb3ac38ad62df1010ab29040","creator":"cziletti","file_id":"8124","access_level":"open_access"}],"author":[{"last_name":"Podlaski","first_name":"William F","full_name":"Podlaski, William F"},{"first_name":"Alexander","last_name":"Seeholzer","full_name":"Seeholzer, Alexander"},{"full_name":"Groschner, Lukas N","last_name":"Groschner","first_name":"Lukas N"},{"full_name":"Miesenböck, Gero","last_name":"Miesenböck","first_name":"Gero"},{"last_name":"Ranjan","first_name":"Rajnish","full_name":"Ranjan, Rajnish"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"}],"extern":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"06","pmid":1,"volume":6,"quality_controlled":"1","external_id":{"pmid":["28267430"]},"article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"type":"journal_article","publication":"eLife","date_created":"2020-06-30T13:32:18Z","has_accepted_license":"1"},{"article_processing_charge":"No","external_id":{"arxiv":["1711.02448"]},"volume":30,"quality_controlled":"1","page":"272-283","date_created":"2020-07-16T19:13:10Z","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"type":"conference","title":"Cortical microcircuits as gated-recurrent neural networks","publisher":"Neural Information Processing Systems Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","extern":"1","author":[{"full_name":"Costa, Rui Ponte","first_name":"Rui Ponte","last_name":"Costa"},{"first_name":"Yannis M.","last_name":"Assael","full_name":"Assael, Yannis M."},{"last_name":"Shillingford","first_name":"Brendan","full_name":"Shillingford, Brendan"},{"last_name":"Freitas","first_name":"Nando de","full_name":"Freitas, Nando de"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.02448"}],"intvolume":" 30","citation":{"chicago":"Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas, and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” In Advances in Neural Information Processing Systems, 30:272–83. Neural Information Processing Systems Foundation, 2017.","apa":"Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels, T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach, CA, United States: Neural Information Processing Systems Foundation.","ista":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical microcircuits as gated-recurrent neural networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.","mla":"Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” Advances in Neural Information Processing Systems, vol. 30, Neural Information Processing Systems Foundation, 2017, pp. 272–83.","ama":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits as gated-recurrent neural networks. In: Advances in Neural Information Processing Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.","ieee":"R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels, “Cortical microcircuits as gated-recurrent neural networks,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017, vol. 30, pp. 272–283.","short":"R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2017, pp. 272–283."},"publication_status":"published","conference":{"end_date":"2017-12-09","location":"Long Beach, CA, United States","start_date":"2017-12-04","name":"NIPS: Neural Information Processing System"},"date_published":"2017-12-01T00:00:00Z","oa_version":"Preprint","publication_identifier":{"issn":["10495258"]},"oa":1,"status":"public","month":"12","year":"2017","date_updated":"2021-01-12T08:17:03Z","arxiv":1,"abstract":[{"text":"Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function.\r\nOverall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.","lang":"eng"}],"_id":"8129"},{"publication":"Journal of Structural Biology","date_created":"2018-12-11T11:48:40Z","page":"187-195","has_accepted_license":"1","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"6832","quality_controlled":"1","volume":199,"extern":"1","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":1310009,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"kschuh","file_id":"6168","checksum":"7f2d4bbac767f9acc254d1a4114d181a","date_created":"2019-03-22T09:29:44Z","date_updated":"2020-07-14T12:48:09Z","file_name":"2017_Elsevier_Turonova.pdf"}],"author":[{"full_name":"Turoňová, Beata","first_name":"Beata","last_name":"Turoňová"},{"full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"title":"Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Academic Press","doi":"10.1016/j.jsb.2017.07.007","publication_status":"published","date_published":"2017-09-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"file_date_updated":"2020-07-14T12:48:09Z","citation":{"ieee":"B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press, pp. 187–195, 2017.","ama":"Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007","short":"B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology 199 (2017) 187–195.","apa":"Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007","ista":"Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 199(3), 187–195.","mla":"Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007.","chicago":"Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007."},"intvolume":" 199","year":"2017","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging."}],"issue":"3","date_updated":"2021-01-12T08:17:16Z","_id":"817","oa":1,"status":"public","month":"09"},{"supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","creator":"dernst","file_id":"6210","checksum":"da3993c5f90f59a8e8623cc31ad501dd","date_created":"2019-04-05T08:48:51Z","file_name":"Thesis_KarinMitosch.docx","date_updated":"2020-07-14T12:48:09Z","file_size":6331071,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"file_size":9289852,"content_type":"application/pdf","relation":"main_file","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","creator":"dernst","file_id":"6211","checksum":"24c3d9e51992f1b721f3df55aa13fcb8"}],"author":[{"full_name":"Mitosch, Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2001"},{"status":"public","relation":"part_of_dissertation","id":"666"}]},"pubrep_id":"862","article_processing_charge":"No","publist_id":"6831","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"type":"dissertation","date_created":"2018-12-11T11:48:40Z","page":"113","has_accepted_license":"1","month":"09","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","_id":"818","year":"2017","abstract":[{"lang":"eng","text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. "}],"date_updated":"2023-09-07T12:00:26Z","citation":{"ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","apa":"Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","mla":"Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862."},"ddc":["571","579"],"file_date_updated":"2020-07-14T12:48:09Z","date_published":"2017-09-27T00:00:00Z","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_862","publication_status":"published"},{"supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Disease defence in garden ants","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":18580400,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T07:53:04Z","file_name":"2017_Thesis_Pull.docx","date_updated":"2020-07-14T12:48:09Z","access_level":"closed","creator":"dernst","file_id":"6199","checksum":"4993cdd5382295758ecc3ecbd2a9aaff"},{"date_created":"2019-04-05T07:53:04Z","date_updated":"2020-07-14T12:48:09Z","file_name":"2017_Thesis_Pull.pdf","access_level":"open_access","checksum":"ee2e3ebb5b53c154c866f5b052b25153","file_id":"6200","creator":"dernst","file_size":14400681,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","related_material":{"record":[{"id":"616","relation":"part_of_dissertation","status":"public"},{"id":"806","relation":"part_of_dissertation","status":"public"},{"id":"734","status":"public","relation":"part_of_dissertation"},{"id":"732","status":"public","relation":"part_of_dissertation"}]},"publist_id":"6830","article_processing_charge":"No","pubrep_id":"861","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"type":"dissertation","page":"122","date_created":"2018-12-11T11:48:40Z","has_accepted_license":"1","month":"09","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","_id":"819","year":"2017","date_updated":"2023-09-28T11:31:32Z","abstract":[{"lang":"eng","text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. "}],"citation":{"ama":"Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","mla":"Pull, Christopher. Disease Defence in Garden Ants. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","apa":"Pull, C. (2017). Disease defence in garden ants. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861."},"ddc":["576","577","578","579","590","592"],"file_date_updated":"2020-07-14T12:48:09Z","date_published":"2017-09-26T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:ISTA:th_861"},{"ddc":["576","577","579"],"file_date_updated":"2020-07-14T12:48:10Z","citation":{"chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.","mla":"Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.","apa":"Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017."},"publication_status":"published","doi":"10.15479/AT:ISTA:th_857","date_published":"2017-08-25T00:00:00Z","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","ec_funded":1,"month":"08","year":"2017","date_updated":"2023-09-07T12:01:21Z","abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"_id":"820","publist_id":"6829","pubrep_id":"857","article_processing_charge":"No","date_created":"2018-12-11T11:48:41Z","page":"87","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JoBo"}],"type":"dissertation","title":"The lac operon in the wild","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"25","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","file":[{"date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","date_created":"2018-12-12T10:17:00Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","file_id":"5252","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":3417773},{"date_created":"2019-04-05T08:51:59Z","file_name":"2017_thesis_Jesse_source.tex","date_updated":"2020-07-14T12:48:10Z","access_level":"closed","file_id":"6212","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","creator":"dernst","file_size":215899,"content_type":"application/x-tex","relation":"source_file"}],"project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Jesse, Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne"}]},{"file_date_updated":"2020-07-14T12:48:10Z","ddc":["000"],"citation":{"ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017."},"publication_status":"published","doi":"10.15479/AT:ISTA:th_854","oa_version":"Published Version","date_published":"2017-08-09T00:00:00Z","status":"public","publication_identifier":{"issn":["2663-337X"]},"oa":1,"month":"08","ec_funded":1,"date_updated":"2023-09-07T12:01:59Z","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"year":"2017","_id":"821","publist_id":"6828","article_processing_charge":"No","pubrep_id":"854","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1071"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"status":"public","relation":"part_of_dissertation","id":"1604"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"id":"1714","status":"public","relation":"part_of_dissertation"}]},"has_accepted_license":"1","page":"418","date_created":"2018-12-11T11:48:41Z","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Algorithmic advances in program analysis and their applications","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"day":"09","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"file":[{"file_size":4103115,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_id":"4900","creator":"system","date_created":"2018-12-12T10:11:44Z","date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf"},{"file_size":14744374,"content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","file_id":"6201","creator":"dernst","date_created":"2019-04-05T07:59:31Z","date_updated":"2020-07-14T12:48:10Z","file_name":"2017_thesis_Pavlogiannis.zip"}]},{"volume":114,"quality_controlled":"1","external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"article_processing_charge":"No","publist_id":"6827","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PNAS","page":"10666 - 10671","date_created":"2018-12-11T11:48:41Z","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"National Academy of Sciences","author":[{"full_name":"De Vos, Marjon","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos"},{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","full_name":"Zagórski, Marcin P"},{"full_name":"Mcnally, Alan","first_name":"Alan","last_name":"Mcnally"},{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"isi":1,"project":[{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"},{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"}],"day":"03","pmid":1,"intvolume":" 114","citation":{"ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}],"scopus_import":"1","date_published":"2017-10-03T00:00:00Z","oa_version":"Submitted Version","doi":"10.1073/pnas.1713372114","publication_status":"published","ec_funded":1,"month":"10","oa":1,"publication_identifier":{"issn":["00278424"]},"status":"public","_id":"822","year":"2017","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"issue":"40","date_updated":"2023-09-26T16:18:48Z"},{"volume":2017,"quality_controlled":"1","external_id":{"isi":["000411842900001"]},"article_processing_charge":"No","publist_id":"6826","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":" Journal of Statistical Mechanics: Theory and Experiment","date_created":"2018-12-11T11:48:41Z","title":"Phase transitions in integer linear problems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"IOPscience","isi":1,"author":[{"last_name":"Colabrese","first_name":"Simona","full_name":"Colabrese, Simona"},{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","orcid":"0000-0002-5214-4706","first_name":"Daniele"},{"last_name":"Leuzzi","first_name":"Luca","full_name":"Leuzzi, Luca"},{"full_name":"Marinari, Enzo","last_name":"Marinari","first_name":"Enzo"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"day":"26","citation":{"chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","apa":"Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3"},"intvolume":" 2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"scopus_import":"1","date_published":"2017-09-26T00:00:00Z","oa_version":"Submitted Version","doi":"10.1088/1742-5468/aa85c3","publication_status":"published","ec_funded":1,"month":"09","oa":1,"publication_identifier":{"issn":["17425468"]},"status":"public","_id":"823","article_number":"093404","year":"2017","issue":"9","abstract":[{"text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.","lang":"eng"}],"date_updated":"2023-09-26T16:18:12Z"},{"author":[{"orcid":"0000-0002-8777-3502","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit"},{"last_name":"Berroterán-Infante","first_name":"Neydher","full_name":"Berroterán-Infante, Neydher"},{"last_name":"Rami-Mark","first_name":"Christina","full_name":"Rami-Mark, Christina"},{"last_name":"Dumanic","first_name":"Monika","full_name":"Dumanic, Monika"},{"full_name":"Matz, Miroslawa","last_name":"Matz","first_name":"Miroslawa"},{"full_name":"Willmann, Michael","first_name":"Michael","last_name":"Willmann"},{"full_name":"Andreae, Fritz","first_name":"Fritz","last_name":"Andreae"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"first_name":"Wolfgang","last_name":"Wadsak","full_name":"Wadsak, Wolfgang"},{"first_name":"Markus","last_name":"Mitterhauser","full_name":"Mitterhauser, Markus"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"_id":"8235","date_updated":"2021-01-12T08:17:39Z","abstract":[{"text":"Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients.","lang":"eng"}],"day":"15","year":"2017","extern":"1","month":"09","publisher":"Impact Journals","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials","publication_identifier":{"issn":["1949-2553"]},"oa":1,"oa_version":"Published Version","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-09-15T00:00:00Z","publication_status":"published","doi":"10.18632/oncotarget.20914","date_created":"2020-08-10T11:53:18Z","page":"83128-83141","publication":"Oncotarget","quality_controlled":"1","intvolume":" 8","citation":{"mla":"Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 83128–41, doi:10.18632/oncotarget.20914.","apa":"Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann, M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20914","ista":"Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M, Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 8, 83128–83141.","chicago":"Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914.","short":"J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann, F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget 8 (2017) 83128–83141.","ama":"Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 2017;8:83128-83141. doi:10.18632/oncotarget.20914","ieee":"J. Singer et al., “Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals, pp. 83128–83141, 2017."},"volume":8,"main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.20914","open_access":"1"}],"article_type":"original","article_processing_charge":"No"}]