[{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaSe"}],"title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","author":[{"full_name":"De Nicola, Stefano","orcid":"0000-0002-4842-6671","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"full_name":"Doyon, B.","first_name":"B.","last_name":"Doyon"},{"full_name":"Bhaseen, M. J.","last_name":"Bhaseen","first_name":"M. J."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2020-04-06T13:15:49Z","date_updated":"2020-07-14T12:48:01Z","file_name":"2020_JournStatisticalMech_DeNicola.pdf","access_level":"open_access","relation":"main_file","checksum":"4030e683c15d30b7b4794ec7dc1b6537","content_type":"application/pdf","file_id":"7648","file_size":3159026,"creator":"dernst"}],"has_accepted_license":"1","publisher":"IOP Publishing","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","_id":"7638","quality_controlled":"1","citation":{"apa":"De Nicola, S., Doyon, B., & Bhaseen, M. J. (2020). Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab6093","mla":"De Nicola, Stefano, et al. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1, 013106, IOP Publishing, 2020, doi:10.1088/1742-5468/ab6093.","ama":"De Nicola S, Doyon B, Bhaseen MJ. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020;2020(1). doi:10.1088/1742-5468/ab6093","short":"S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020).","ista":"De Nicola S, Doyon B, Bhaseen MJ. 2020. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020(1), 013106.","ieee":"S. De Nicola, B. Doyon, and M. J. Bhaseen, “Non-equilibrium quantum spin dynamics from classical stochastic processes,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2020, no. 1. IOP Publishing, 2020.","chicago":"De Nicola, Stefano, B. Doyon, and M. J. Bhaseen. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2020. https://doi.org/10.1088/1742-5468/ab6093."},"publication_identifier":{"eissn":["17425468"]},"arxiv":1,"abstract":[{"lang":"eng","text":"Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development."}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","year":"2020","external_id":{"isi":["000520187500001"],"arxiv":["1909.13142"]},"date_updated":"2023-08-18T10:27:15Z","oa":1,"issue":"1","date_published":"2020-01-22T00:00:00Z","month":"01","intvolume":" 2020","article_number":"013106","oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","doi":"10.1088/1742-5468/ab6093","date_created":"2020-04-05T22:00:50Z","ddc":["530"],"day":"22","status":"public","volume":2020},{"intvolume":" 183","month":"05","date_published":"2020-05-08T00:00:00Z","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","date_updated":"2023-09-07T13:13:04Z","issue":"5","oa":1,"external_id":{"isi":["000536641800018"],"pmid":["32107280"]},"page":"37-40","year":"2020","pmid":1,"volume":183,"date_created":"2020-04-06T10:06:40Z","status":"public","day":"08","doi":"10.1104/pp.20.00212","main_file_link":[{"url":"https://doi.org/10.1104/pp.20.00212","open_access":"1"}],"publication":"Plant Physiology","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8589"}]},"isi":1,"ec_funded":1,"oa_version":"Published Version","publisher":"American Society of Plant Biologists","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","author":[{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"letter_note","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"citation":{"ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212."},"type":"journal_article","scopus_import":"1","_id":"7643","quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"publication_status":"published"},{"pmid":1,"volume":71,"ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-06T10:57:08Z","day":"06","status":"public","doi":"10.1093/jxb/eraa138","publication":"Journal of Experimental Botany","isi":1,"oa_version":"Published Version","month":"07","intvolume":" 71","date_published":"2020-07-06T00:00:00Z","date_updated":"2023-08-18T10:27:52Z","issue":"14","oa":1,"page":"3986–3998","external_id":{"pmid":["32179893"],"isi":["000553125400007"]},"year":"2020","citation":{"short":"E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M. Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A. Rosado, Journal of Experimental Botany 71 (2020) 3986–3998.","ieee":"E. Lee et al., “Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,” Journal of Experimental Botany, vol. 71, no. 14. Oxford University Press, pp. 3986–3998, 2020.","ista":"Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 71(14), 3986–3998.","ama":"Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 2020;71(14):3986–3998. doi:10.1093/jxb/eraa138","chicago":"Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella, J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa138.","apa":"Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa138","mla":"Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal of Experimental Botany, vol. 71, no. 14, Oxford University Press, 2020, pp. 3986–3998, doi:10.1093/jxb/eraa138."},"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"type":"journal_article","file_date_updated":"2020-10-06T07:41:35Z","abstract":[{"lang":"eng","text":"In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM."}],"_id":"7646","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Oxford University Press","file":[{"success":1,"file_name":"2020_JourExperimBotany_Lee.pdf","date_created":"2020-10-06T07:41:35Z","date_updated":"2020-10-06T07:41:35Z","file_id":"8613","content_type":"application/pdf","creator":"dernst","file_size":1916031,"access_level":"open_access","checksum":"b06aaaa93dc41896da805fe4b75cf3a1","relation":"main_file"}],"title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","author":[{"full_name":"Lee, E","last_name":"Lee","first_name":"E"},{"last_name":"Vila Nova Santana","first_name":"B","full_name":"Vila Nova Santana, B"},{"last_name":"Samuels","first_name":"E","full_name":"Samuels, E"},{"full_name":"Benitez-Fuente, F","first_name":"F","last_name":"Benitez-Fuente"},{"last_name":"Corsi","first_name":"E","full_name":"Corsi, E"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"},{"full_name":"Perez-Sancho, J","first_name":"J","last_name":"Perez-Sancho"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Macho, A","last_name":"Macho","first_name":"A"},{"last_name":"Alves Azevedo","first_name":"A","full_name":"Alves Azevedo, A"},{"first_name":"A","last_name":"Rosado","full_name":"Rosado, A"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original"},{"_id":"7650","quality_controlled":"1","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01489-4.","ama":"Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 2020;236(6):1217-1271. doi:10.1007/s00205-020-01489-4","short":"A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271.","ista":"Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271.","ieee":"A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature,” Archive for Rational Mechanics and Analysis, vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020.","mla":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4.","apa":"Deuchert, A., & Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01489-4"},"scopus_import":"1","abstract":[{"lang":"eng","text":"We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution."}],"arxiv":1,"file_date_updated":"2020-11-20T13:17:42Z","type":"journal_article","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_status":"published","author":[{"full_name":"Deuchert, Andreas","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","last_name":"Deuchert"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","file":[{"creator":"dernst","file_size":704633,"content_type":"application/pdf","file_id":"8785","relation":"main_file","checksum":"b645fb64bfe95bbc05b3eea374109a9c","access_level":"open_access","file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","success":1,"date_updated":"2020-11-20T13:17:42Z","date_created":"2020-11-20T13:17:42Z"}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"RoSe"}],"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-08T15:18:03Z","status":"public","day":"09","volume":236,"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Archive for Rational Mechanics and Analysis","doi":"10.1007/s00205-020-01489-4","date_updated":"2023-09-05T14:18:49Z","oa":1,"issue":"6","date_published":"2020-03-09T00:00:00Z","month":"03","intvolume":" 236","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions. Financial support by the European Research Council (ERC) under the European Union’sHorizon 2020 research and innovation programme (Grant Agreement No. 694227) is gratefully acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 836146.","year":"2020","external_id":{"arxiv":["1901.11363"],"isi":["000519415000001"]},"page":"1217-1271"},{"article_processing_charge":"No","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"The Royal Society","author":[{"first_name":"J.","last_name":"Larsson","full_name":"Larsson, J."},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M"},{"last_name":"Bengmark","first_name":"S.","full_name":"Bengmark, S."},{"full_name":"Lundh, T.","first_name":"T.","last_name":"Lundh"},{"full_name":"Butlin, R. K.","first_name":"R. K.","last_name":"Butlin"}],"title":"A developmentally descriptive method for quantifying shape in gastropod shells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2020-04-14T12:31:16Z","date_updated":"2020-07-14T12:48:01Z","file_name":"2020_JournRoyalSociety_Larsson.pdf","checksum":"4eb102304402f5c56432516b84df86d6","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":1556190,"content_type":"application/pdf","file_id":"7660"}],"publication_status":"published","citation":{"ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721."},"publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:48:01Z","_id":"7651","quality_controlled":"1","year":"2020","date_published":"2020-02-01T00:00:00Z","intvolume":" 17","month":"02","article_number":"20190721","date_updated":"2021-01-12T08:14:41Z","oa":1,"issue":"163","publication":"Journal of The Royal Society Interface","doi":"10.1098/rsif.2019.0721","oa_version":"Published Version","volume":17,"date_created":"2020-04-08T15:19:17Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"day":"01","status":"public"},{"publication_status":"published","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"file_date_updated":"2020-10-09T09:56:01Z","type":"journal_article","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"scopus_import":"1","citation":{"chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7"},"publication_identifier":{"issn":["2397-334X"]},"quality_controlled":"1","_id":"7652","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","file":[{"date_created":"2020-10-09T09:56:01Z","date_updated":"2020-10-09T09:56:01Z","file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"ef3bbf42023e30b2c24a6278025d2040","file_size":745242,"creator":"dernst","content_type":"application/pdf","file_id":"8640"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Gene amplification as a form of population-level gene expression regulation","author":[{"first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","last_name":"Tomanek","full_name":"Tomanek, Isabella"},{"full_name":"Grah, Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"full_name":"Lagator, M.","last_name":"Lagator","first_name":"M."},{"full_name":"Andersson, A. M. C.","last_name":"Andersson","first_name":"A. M. C."},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"doi":"10.1038/s41559-020-1132-7","publication":"Nature Ecology & Evolution","isi":1,"oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8155"},{"id":"7383","relation":"research_data","status":"public"},{"id":"7016","status":"public","relation":"research_data"},{"relation":"used_in_publication","status":"public","id":"8653"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage"}]},"volume":4,"status":"public","day":"01","ddc":["570"],"date_created":"2020-04-08T15:20:53Z","page":"612-625","external_id":{"isi":["000519008300005"]},"year":"2020","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","intvolume":" 4","month":"04","date_published":"2020-04-01T00:00:00Z","issue":"4","oa":1,"date_updated":"2024-03-25T23:30:20Z"},{"external_id":{"isi":["000525543200001"],"pmid":["32231528"]},"year":"2020","article_number":"20","date_published":"2020-03-13T00:00:00Z","month":"03","intvolume":" 14","oa":1,"date_updated":"2023-08-18T10:30:11Z","publication":"Frontiers in Computational Neuroscience","doi":"10.3389/fncom.2020.00020","oa_version":"Published Version","isi":1,"volume":14,"pmid":1,"status":"public","day":"13","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-12T22:00:40Z","department":[{"_id":"GaTk"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Frontiers","has_accepted_license":"1","author":[{"full_name":"Berry, Michael J.","first_name":"Michael J.","last_name":"Berry"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Clustering of neural activity: A design principle for population codes","file":[{"relation":"main_file","checksum":"2b1da23823eae9cedbb42d701945b61e","access_level":"open_access","file_id":"7659","content_type":"application/pdf","creator":"dernst","file_size":4082937,"date_created":"2020-04-14T12:20:39Z","date_updated":"2020-07-14T12:48:01Z","file_name":"2020_Frontiers_Berry.pdf"}],"publication_status":"published","scopus_import":"1","abstract":[{"lang":"eng","text":"We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement."}],"file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","publication_identifier":{"eissn":["16625188"]},"citation":{"mla":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.","apa":"Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. Frontiers. https://doi.org/10.3389/fncom.2020.00020","chicago":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience. Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020.","ieee":"M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","short":"M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).","ama":"Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020"},"quality_controlled":"1","_id":"7656"},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaLo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Felhofer, Martin","first_name":"Martin","last_name":"Felhofer"},{"full_name":"Bock, Peter","first_name":"Peter","last_name":"Bock"},{"full_name":"Singh, Adya","first_name":"Adya","last_name":"Singh"},{"first_name":"Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze"},{"full_name":"Zirbs, Ronald","first_name":"Ronald","last_name":"Zirbs"},{"first_name":"Notburga","last_name":"Gierlinger","full_name":"Gierlinger, Notburga"}],"title":"Wood deformation leads to rearrangement of molecules at the nanoscale","file":[{"checksum":"fe46146a9c4c620592a1932a8599069e","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":7108014,"content_type":"application/pdf","file_id":"7667","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T10:43:36Z","file_name":"2020_NanoLetters_Felhofer.pdf"}],"has_accepted_license":"1","publisher":"American Chemical Society","publication_status":"published","_id":"7663","quality_controlled":"1","publication_identifier":{"eissn":["15306992"]},"citation":{"short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","ieee":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” Nano Letters, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020.","ista":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653.","ama":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 2020;20(4):2647-2653. doi:10.1021/acs.nanolett.0c00205","chicago":"Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c00205.","apa":"Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., & Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c00205","mla":"Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:10.1021/acs.nanolett.0c00205."},"scopus_import":"1","abstract":[{"text":"Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","year":"2020","page":"2647-2653","external_id":{"isi":["000526413400055"],"pmid":["32196350"]},"date_updated":"2023-08-21T06:12:09Z","oa":1,"issue":"4","date_published":"2020-04-08T00:00:00Z","month":"04","intvolume":" 20","oa_version":"Published Version","isi":1,"publication":"Nano Letters","doi":"10.1021/acs.nanolett.0c00205","date_created":"2020-04-19T22:00:54Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"day":"08","status":"public","volume":20,"pmid":1},{"has_accepted_license":"1","publisher":"MDPI","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","author":[{"first_name":"Alejandro","last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro"},{"full_name":"Aguado, Carolina","first_name":"Carolina","last_name":"Aguado"},{"first_name":"Rocío","last_name":"Alfaro-Ruíz","full_name":"Alfaro-Ruíz, Rocío"},{"full_name":"Moreno-Martínez, Ana Esther","first_name":"Ana Esther","last_name":"Moreno-Martínez"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"first_name":"José","last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José"},{"full_name":"Buisson, Alain","last_name":"Buisson","first_name":"Alain"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"}],"file":[{"date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T11:43:18Z","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","access_level":"open_access","relation":"main_file","checksum":"b9d2f1657d8c4a74b01a62b474d009b0","content_type":"application/pdf","file_id":"7669","creator":"dernst","file_size":2941197}],"article_processing_charge":"No","department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"mla":"Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences, vol. 21, no. 7, 2459, MDPI, 2020, doi:10.3390/ijms21072459.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21072459","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459.","ieee":"A. Martín-Belmonte et al., “Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” International journal of molecular sciences, vol. 21, no. 7. MDPI, 2020.","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján, International Journal of Molecular Sciences 21 (2020).","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 2020;21(7). doi:10.3390/ijms21072459"},"publication_identifier":{"eissn":["14220067"]},"scopus_import":"1","abstract":[{"text":"Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:01Z","_id":"7664","quality_controlled":"1","publication_status":"published","date_published":"2020-04-02T00:00:00Z","intvolume":" 21","month":"04","article_number":"2459","date_updated":"2023-08-21T06:13:19Z","oa":1,"issue":"7","external_id":{"pmid":["32252271"],"isi":["000535574200201"]},"year":"2020","volume":21,"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-19T22:00:55Z","ddc":["570"],"status":"public","day":"02","publication":"International journal of molecular sciences","doi":"10.3390/ijms21072459","oa_version":"Published Version","isi":1},{"publication_status":"published","project":[{"_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482","call_identifier":"H2020"},{"grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","_id":"7665","abstract":[{"text":"Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.","lang":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","citation":{"mla":"Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience, vol. 14, 63, Frontiers Media, 2020, doi:10.3389/fncel.2020.00063.","apa":"Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., & Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2020.00063","chicago":"Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience. Frontiers Media, 2020. https://doi.org/10.3389/fncel.2020.00063.","ieee":"K. Eguchi et al., “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” Frontiers in Cellular Neuroscience, vol. 14. Frontiers Media, 2020.","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","ista":"Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63.","ama":"Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 2020;14. doi:10.3389/fncel.2020.00063"},"publication_identifier":{"issn":["16625102"]},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"},{"_id":"RySh"}],"article_processing_charge":"Yes (via OA deal)","title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431"},{"full_name":"Hollergschwandtner, Elena","first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","last_name":"Hollergschwandtner"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"file":[{"file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","date_created":"2020-04-20T10:59:49Z","date_updated":"2020-07-14T12:48:01Z","file_size":9227283,"creator":"dernst","content_type":"application/pdf","file_id":"7668","relation":"main_file","access_level":"open_access","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e"}],"publisher":"Frontiers Media","has_accepted_license":"1","ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"Frontiers in Cellular Neuroscience","doi":"10.3389/fncel.2020.00063","status":"public","day":"19","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-04-19T22:00:55Z","volume":14,"year":"2020","external_id":{"isi":["000525582200001"]},"oa":1,"date_updated":"2023-08-21T06:12:48Z","article_number":"63","date_published":"2020-03-19T00:00:00Z","month":"03","intvolume":" 14"},{"_id":"7666","quality_controlled":"1","citation":{"ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775.","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775, 2020.","chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00188-x.","apa":"Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00188-x","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x."},"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"file_date_updated":"2020-11-20T13:22:21Z","type":"journal_article","abstract":[{"lang":"eng","text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups."}],"scopus_import":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35"}],"publication_status":"published","file":[{"checksum":"f8cc96e497f00c38340b5dafe0cb91d7","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8786","creator":"dernst","file_size":701673,"date_created":"2020-11-20T13:22:21Z","date_updated":"2020-11-20T13:22:21Z","success":1,"file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf"}],"title":"Tri-partitions and bases of an ordered complex","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Ölsböck","orcid":"0000-0002-4672-8297","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina"}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"HeEd"}],"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-19T22:00:56Z","day":"20","status":"public","volume":64,"isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1007/s00454-020-00188-x","publication":"Discrete and Computational Geometry","date_updated":"2023-08-21T06:13:48Z","oa":1,"month":"03","intvolume":" 64","date_published":"2020-03-20T00:00:00Z","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","external_id":{"isi":["000520918800001"]},"page":"759-775"},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["540"],"date_created":"2020-04-20T19:29:31Z","status":"public","day":"01","volume":362,"oa_version":"Published Version","isi":1,"publication":"Electrochimica Acta","doi":"10.1016/j.electacta.2020.137175","date_updated":"2023-08-21T06:14:21Z","oa":1,"issue":"12","date_published":"2020-12-01T00:00:00Z","intvolume":" 362","month":"12","article_number":"137175","acknowledgement":"S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell.","year":"2020","external_id":{"isi":["000582869700060"]},"_id":"7672","quality_controlled":"1","citation":{"apa":"Samojlov, A., Schuster, D., Kahr, J., & Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2020.137175","mla":"Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta, vol. 362, no. 12, 137175, Elsevier, 2020, doi:10.1016/j.electacta.2020.137175.","ama":"Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 2020;362(12). doi:10.1016/j.electacta.2020.137175","ista":"Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175.","ieee":"A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” Electrochimica Acta, vol. 362, no. 12. Elsevier, 2020.","short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020).","chicago":"Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta. Elsevier, 2020. https://doi.org/10.1016/j.electacta.2020.137175."},"abstract":[{"text":"Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-10-01T13:20:45Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Samojlov","first_name":"Aleksej","full_name":"Samojlov, Aleksej"},{"full_name":"Schuster, David","first_name":"David","last_name":"Schuster"},{"last_name":"Kahr","first_name":"Jürgen","full_name":"Kahr, Jürgen"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","file":[{"date_created":"2020-10-01T13:20:45Z","date_updated":"2020-10-01T13:20:45Z","success":1,"file_name":"2020_ElectrochimicaActa_Samojlov.pdf","checksum":"1ab1aa2024d431e2a089ea336bc08298","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8593","file_size":1404030,"creator":"dernst"}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"StFr"}]},{"article_processing_charge":"No","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"year":"2020","month":"04","date_published":"2020-04-18T00:00:00Z","publisher":"Cold Spring Harbor Laboratory","date_updated":"2024-03-25T23:30:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"title":"A minimal biophysical model of combined antibiotic action","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"publication_status":"published","doi":"10.1101/2020.04.18.047886","publication":"bioRxiv","related_material":{"record":[{"status":"public","relation":"later_version","id":"8997"},{"id":"8657","relation":"dissertation_contains","status":"public"}]},"oa_version":"Preprint","citation":{"ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886."},"type":"preprint","abstract":[{"lang":"eng","text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions."}],"_id":"7673","date_created":"2020-04-22T08:27:56Z","status":"public","day":"18"},{"abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology."}],"type":"preprint","citation":{"ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405."},"day":"09","status":"public","date_created":"2020-04-23T10:12:51Z","_id":"7675","publication":"bioRxiv","doi":"10.1101/2020.04.08.029405","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"project":[{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","related_material":{"record":[{"id":"8155","relation":"dissertation_contains","status":"public"}]},"publisher":"Cold Spring Harbor Laboratory","date_published":"2020-04-09T00:00:00Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Normative models of enhancer function","author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"date_updated":"2023-09-07T13:13:26Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","year":"2020","language":[{"iso":"eng"}]},{"ddc":["570"],"date_created":"2020-04-24T16:00:51Z","day":"24","status":"public","supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7680","related_material":{"record":[{"id":"1028","relation":"dissertation_contains","status":"public"}]},"oa_version":"None","date_published":"2020-04-24T00:00:00Z","alternative_title":["ISTA Thesis"],"month":"04","date_updated":"2023-09-22T09:20:10Z","oa":1,"page":"98","year":"2020","publication_identifier":{"eissn":["2663-337X"]},"citation":{"apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680."},"abstract":[{"text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.","lang":"eng"}],"file_date_updated":"2021-10-31T23:30:05Z","type":"dissertation","_id":"7680","publication_status":"published","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath"}],"file":[{"embargo":"2021-10-30","relation":"main_file","access_level":"open_access","checksum":"fb9a4468eb27be92690728e35c823796","content_type":"application/pdf","file_id":"7692","file_size":3268017,"creator":"stgingl","date_created":"2020-04-28T11:19:21Z","date_updated":"2021-10-31T23:30:05Z","file_name":"Thesis_without-signatures_PDFA.pdf"},{"file_name":"Thesis_without signatures.docx","date_created":"2020-04-28T11:19:24Z","date_updated":"2021-10-31T23:30:05Z","file_id":"7693","content_type":"application/octet-stream","creator":"stgingl","file_size":5167703,"embargo_to":"open_access","relation":"source_file","access_level":"closed","checksum":"f6c80ca97104a631a328cb79a2c53493"}],"article_processing_charge":"No","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}]},{"year":"2020","external_id":{"isi":["000526036400001"],"arxiv":["1801.01429"]},"issue":"2","oa":1,"date_updated":"2023-08-21T06:14:58Z","article_number":"30","month":"04","intvolume":" 26","date_published":"2020-04-15T00:00:00Z","isi":1,"oa_version":"Published Version","doi":"10.1007/s00029-020-00553-x","publication":"Selecta Mathematica, New Series","day":"15","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-04-26T22:00:44Z","ddc":["510"],"volume":26,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2020_SelectaMathematica_Minets.pdf","date_updated":"2020-07-14T12:48:02Z","date_created":"2020-04-28T10:57:58Z","file_id":"7690","content_type":"application/pdf","creator":"dernst","file_size":792469,"relation":"main_file","access_level":"open_access","checksum":"2368c4662629b4759295eb365323b2ad"}],"author":[{"first_name":"Sasha","id":"3E7C5304-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3883-1806","last_name":"Minets","full_name":"Minets, Sasha"}],"title":"Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","has_accepted_license":"1","publication_status":"published","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","_id":"7683","file_date_updated":"2020-07-14T12:48:02Z","type":"journal_article","scopus_import":"1","abstract":[{"text":"For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.","lang":"eng"}],"arxiv":1,"citation":{"ama":"Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 2020;26(2). doi:10.1007/s00029-020-00553-x","short":"S. Minets, Selecta Mathematica, New Series 26 (2020).","ieee":"S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” Selecta Mathematica, New Series, vol. 26, no. 2. Springer Nature, 2020.","ista":"Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30.","chicago":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series. Springer Nature, 2020. https://doi.org/10.1007/s00029-020-00553-x.","apa":"Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. Springer Nature. https://doi.org/10.1007/s00029-020-00553-x","mla":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series, vol. 26, no. 2, 30, Springer Nature, 2020, doi:10.1007/s00029-020-00553-x."},"publication_identifier":{"eissn":["14209020"],"issn":["10221824"]}},{"pmid":1,"volume":106,"date_created":"2020-04-26T22:00:45Z","day":"22","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.021"}],"doi":"10.1016/j.neuron.2020.01.021","publication":"Neuron","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/librarian-of-memory/"}]},"isi":1,"ec_funded":1,"oa_version":"Published Version","intvolume":" 106","month":"04","date_published":"2020-04-22T00:00:00Z","date_updated":"2023-08-21T06:15:31Z","issue":"2","oa":1,"page":"291-300.e6","external_id":{"pmid":["32070475"],"isi":["000528268200013"]},"year":"2020","citation":{"ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Assembly-specific disruption of hippocampal replay leads to selective memory deficit,” Neuron, vol. 106, no. 2. Elsevier, p. 291–300.e6, 2020.","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 106(2), 291–300.e6.","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, Neuron 106 (2020) 291–300.e6.","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 2020;106(2):291-300.e6. doi:10.1016/j.neuron.2020.01.021","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.021.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.021","mla":"Gridchyn, Igor, et al. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron, vol. 106, no. 2, Elsevier, 2020, p. 291–300.e6, doi:10.1016/j.neuron.2020.01.021."},"publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"type":"journal_article","scopus_import":"1","_id":"7684","quality_controlled":"1","project":[{"grant_number":"281511","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Elsevier","author":[{"full_name":"Gridchyn, Igor","last_name":"Gridchyn","orcid":"0000-0002-1807-1929","first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Schönenberger","full_name":"Schönenberger, Philipp"},{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"title":"Assembly-specific disruption of hippocampal replay leads to selective memory deficit","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"article_type":"original"},{"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"(Core Trust) Seal your repository!","author":[{"full_name":"Ernst, Doris","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","first_name":"Doris","orcid":"0000-0002-2354-0195","last_name":"Ernst"},{"full_name":"Novotny, Gertraud","first_name":"Gertraud","last_name":"Novotny"},{"last_name":"Schönher","first_name":"Eva Maria","full_name":"Schönher, Eva Maria"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","file_size":579291,"creator":"dernst","content_type":"application/pdf","file_id":"7970","date_created":"2020-06-17T10:50:13Z","date_updated":"2023-04-03T09:17:25Z","file_name":"2020_VOEB_Ernst.pdf"}],"department":[{"_id":"E-Lib"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"ger"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested."},{"text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich.","lang":"ger"}],"file_date_updated":"2023-04-03T09:17:25Z","type":"journal_article","citation":{"mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491.","apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491.","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491"},"publication_identifier":{"issn":["1022-2588"]},"_id":"7687","publication_status":"published","popular_science":"1","date_published":"2020-04-28T00:00:00Z","intvolume":" 73","month":"04","oa":1,"issue":"1","date_updated":"2024-02-27T13:41:03Z","page":"46-59","year":"2020","volume":73,"status":"public","day":"28","date_created":"2020-04-28T08:37:38Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["020"],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","doi":"10.31263/voebm.v73i1.3491","oa_version":"Published Version"},{"license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"GeKa"}],"article_processing_charge":"No","year":"2020","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"05","date_published":"2020-05-01T00:00:00Z","file":[{"relation":"main_file","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","access_level":"open_access","creator":"gkatsaro","file_size":5514403,"file_id":"7786","content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:48:02Z","date_created":"2020-05-01T15:13:28Z","file_name":"DOI_ZeroFieldSplitting.zip"}],"title":"Supplementary data for \"Zero field splitting of heavy-hole states in quantum dots\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"oa":1,"date_updated":"2024-02-21T12:44:02Z","doi":"10.15479/AT:ISTA:7689","project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020"},{"grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"id":"8203","relation":"used_in_publication","status":"public"}]},"contributor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","contributor_type":"contact_person"}],"file_date_updated":"2020-07-14T12:48:02Z","type":"research_data","abstract":[{"lang":"eng","text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n"}],"citation":{"ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689","short":"G. Katsaros, (2020).","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689.","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","mla":"Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689."},"status":"public","day":"01","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2020-05-01T15:14:46Z","_id":"7689","ddc":["530"]},{"year":"2020","page":"986-997","external_id":{"isi":["000550682000018"],"pmid":["32321842"]},"date_updated":"2023-09-05T12:20:02Z","oa":1,"issue":"3","date_published":"2020-07-01T00:00:00Z","month":"07","intvolume":" 183","oa_version":"Preprint","isi":1,"publication":"Plant Physiology","doi":"10.1104/pp.20.00178","main_file_link":[{"url":"https://doi.org/10.1101/2020.02.13.948109","open_access":"1"}],"date_created":"2020-04-29T15:23:00Z","day":"01","status":"public","volume":183,"pmid":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JiFr"}],"author":[{"full_name":"Wang, J","first_name":"J","last_name":"Wang"},{"last_name":"Mylle","first_name":"E","full_name":"Mylle, E"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Besbrugge, N","first_name":"N","last_name":"Besbrugge"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Pleskot, R","last_name":"Pleskot","first_name":"R"},{"full_name":"van Damme, D","first_name":"D","last_name":"van Damme"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","publisher":"American Society of Plant Biologists","project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"7695","quality_controlled":"1","citation":{"mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:10.1104/pp.20.00178.","apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00178","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00178.","ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 2020;183(3):986-997. doi:10.1104/pp.20.00178","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997.","ieee":"J. Wang et al., “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” Plant Physiology, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020."},"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"scopus_import":"1","abstract":[{"text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex.","lang":"eng"}],"type":"journal_article"}]