[{"article_processing_charge":"No","day":"05","scopus_import":"1","date_published":"2021-01-05T00:00:00Z","article_type":"original","citation":{"ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 2021;118(1). doi:10.1073/pnas.2010054118","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2010054118.","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118.","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021)."},"publication":"PNAS","issue":"1","abstract":[{"text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 118","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","status":"public","_id":"8988","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"01","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1073/pnas.2010054118","project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["33443153"],"isi":["000607270100018"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2010054118"}],"article_number":"e2010054118","volume":118,"date_updated":"2023-08-04T11:20:46Z","date_created":"2021-01-03T23:01:23Z","author":[{"full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F"},{"full_name":"Auer, Albert","last_name":"Auer","first_name":"Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","first_name":"Nikola","last_name":"Canigova","full_name":"Canigova, Nikola"},{"first_name":"Katrin","last_name":"Loibl","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2429-7668","full_name":"Loibl, Katrin"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. "},{"scopus_import":"1","article_processing_charge":"No","day":"05","citation":{"chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:10.1073/pnas.2020857118.","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118","ieee":"L. Abas et al., “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118"},"publication":"PNAS","article_type":"original","date_published":"2021-01-05T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8993","intvolume":" 118","status":"public","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","oa_version":"Published Version","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"01","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"oa":1,"external_id":{"pmid":["33443187"],"isi":["000607270100073"]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.2020857118","language":[{"iso":"eng"}],"article_number":"e2020857118","ec_funded":1,"pmid":1,"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","year":"2021","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"publisher":"National Academy of Sciences","publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2102232118","relation":"erratum"}]},"author":[{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"first_name":"Johannes","last_name":"Stadlmann","full_name":"Stadlmann, Johannes"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"full_name":"Lukic, Kristina","last_name":"Lukic","first_name":"Kristina","orcid":"0000-0003-1581-881X","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwechheimer, Claus","last_name":"Schwechheimer","first_name":"Claus"},{"first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"},{"full_name":"Mach, Lukas","last_name":"Mach","first_name":"Lukas"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Hammes, Ulrich Z.","last_name":"Hammes","first_name":"Ulrich Z."}],"volume":118,"date_created":"2021-01-03T23:01:23Z","date_updated":"2023-08-07T13:29:23Z"},{"file_date_updated":"2020-10-27T14:57:50Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"first_name":"Ori","last_name":"Maoz","full_name":"Maoz, Ori"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"last_name":"Esteki","first_name":"Mohamad Saleh","full_name":"Esteki, Mohamad Saleh"},{"last_name":"Kiani","first_name":"Roozbeh","full_name":"Kiani, Roozbeh"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"volume":117,"date_updated":"2023-08-22T12:11:23Z","date_created":"2020-10-25T23:01:16Z","pmid":1,"acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","year":"2020","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"10","doi":"10.1073/pnas.1912804117","language":[{"iso":"eng"}],"external_id":{"isi":["000579045200012"],"pmid":["32948691"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","issue":"40","abstract":[{"lang":"eng","text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","checksum":"c6a24fdecf3f28faf447078e7a274a88","success":1,"relation":"main_file","file_id":"8713","content_type":"application/pdf","file_size":1755359,"creator":"cziletti","file_name":"2020_PNAS_Maoz.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8698","intvolume":" 117","ddc":["570"],"title":"Learning probabilistic neural representations with randomly connected circuits","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2020-10-06T00:00:00Z","citation":{"apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"25066-25073","article_type":"original"},{"month":"10","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"doi":"10.1073/pnas.2012043117","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2009.12262"],"isi":["000579059100029"],"pmid":["32958669"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"file_date_updated":"2020-10-28T11:53:12Z","ec_funded":1,"author":[{"first_name":"Eugenio","last_name":"Paris","full_name":"Paris, Eugenio"},{"full_name":"Tseng, Yi","first_name":"Yi","last_name":"Tseng"},{"full_name":"Paerschke, Ekaterina","first_name":"Ekaterina","last_name":"Paerschke","id":"8275014E-6063-11E9-9B7F-6338E6697425","orcid":"0000-0003-0853-8182"},{"last_name":"Zhang","first_name":"Wenliang","full_name":"Zhang, Wenliang"},{"last_name":"Upton","first_name":"Mary H","full_name":"Upton, Mary H"},{"first_name":"Anna","last_name":"Efimenko","full_name":"Efimenko, Anna"},{"last_name":"Rolfs","first_name":"Katharina","full_name":"Rolfs, Katharina"},{"first_name":"Daniel E","last_name":"McNally","full_name":"McNally, Daniel E"},{"last_name":"Maurel","first_name":"Laura","full_name":"Maurel, Laura"},{"last_name":"Naamneh","first_name":"Muntaser","full_name":"Naamneh, Muntaser"},{"last_name":"Caputo","first_name":"Marco","full_name":"Caputo, Marco"},{"full_name":"Strocov, Vladimir N","last_name":"Strocov","first_name":"Vladimir N"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"full_name":"Casa, Diego","last_name":"Casa","first_name":"Diego"},{"full_name":"Schneider, Christof W","first_name":"Christof W","last_name":"Schneider"},{"full_name":"Pomjakushina, Ekaterina","first_name":"Ekaterina","last_name":"Pomjakushina"},{"first_name":"Krzysztof","last_name":"Wohlfeld","full_name":"Wohlfeld, Krzysztof"},{"first_name":"Milan","last_name":"Radovic","full_name":"Radovic, Milan"},{"full_name":"Schmitt, Thorsten","first_name":"Thorsten","last_name":"Schmitt"}],"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T12:11:52Z","volume":117,"year":"2020","acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","pmid":1,"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-06T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770.","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117"},"article_type":"original","page":"24764-24770","abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}],"issue":"40","type":"journal_article","file":[{"date_updated":"2020-10-28T11:53:12Z","date_created":"2020-10-28T11:53:12Z","checksum":"1638fa36b442e2868576c6dd7d6dc505","success":1,"relation":"main_file","file_id":"8715","content_type":"application/pdf","file_size":1176522,"creator":"cziletti","file_name":"2020_PNAS_Paris.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"8699","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","intvolume":" 117"},{"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"31614-31622","publication":"PNAS","citation":{"mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.","short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020."},"date_published":"2020-12-15T00:00:00Z","type":"journal_article","abstract":[{"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 biophysical 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 nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium 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 nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}],"issue":"50","title":"Nonequilibrium models of optimal enhancer function","ddc":["570"],"status":"public","intvolume":" 117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9000","file":[{"file_name":"2020_PNAS_Grah.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1199247,"creator":"dernst","relation":"main_file","file_id":"9004","date_updated":"2021-01-11T08:37:31Z","date_created":"2021-01-11T08:37:31Z","checksum":"69039cd402a571983aa6cb4815ffa863","success":1}],"oa_version":"Published Version","month":"12","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"quality_controlled":"1","isi":1,"project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2006731117","file_date_updated":"2021-01-11T08:37:31Z","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","year":"2020","pmid":1,"date_updated":"2023-08-24T11:10:22Z","date_created":"2021-01-10T23:01:17Z","volume":117,"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/","relation":"press_release","description":"News on IST Homepage"}]}},{"type":"journal_article","issue":"21","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"intvolume":" 117","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","status":"public","_id":"7932","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"26","page":"11233-11239","article_type":"original","citation":{"ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2020-05-26T00:00:00Z","ec_funded":1,"publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2020","volume":117,"date_created":"2020-06-07T22:00:51Z","date_updated":"2023-11-30T10:55:13Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"id":"14530","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/"}]},"author":[{"full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Duo"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0179-9737","first_name":"Xingyu","last_name":"Ma","full_name":"Ma, Xingyu"},{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang"},{"first_name":"Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"05","project":[{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2005.11190","open_access":"1"}],"oa":1,"external_id":{"isi":["000536797100014"],"arxiv":["2005.11190"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1913716117"},{"date_published":"2019-03-19T00:00:00Z","page":"5344-5349","citation":{"chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","file":[{"date_created":"2019-04-03T14:10:30Z","date_updated":"2020-07-14T12:47:23Z","checksum":"8b67eee0ea8e5db61583e4d485215258","file_id":"6193","relation":"main_file","creator":"dernst","file_size":3456045,"content_type":"application/pdf","file_name":"2019_PNAS_Recho.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 116","status":"public","title":"Theory of mechanochemical patterning in biphasic biological tissues","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6191","issue":"12","abstract":[{"text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1813255116","project":[{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000461679000027"],"pmid":["30819884"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"03","volume":116,"date_updated":"2023-08-25T08:57:30Z","date_created":"2019-03-31T21:59:13Z","related_material":{"link":[{"url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental","relation":"supplementary_material"}]},"author":[{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"full_name":"Hallou, Adrien","last_name":"Hallou","first_name":"Adrien"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"department":[{"_id":"EdHa"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2019","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:23Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-12-11T00:00:00Z","page":"12728-12732","citation":{"ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"50","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"type":"journal_article","file":[{"file_name":"2018_PNAS_Kotlobay.pdf","access_level":"open_access","creator":"dernst","file_size":1271988,"content_type":"application/pdf","file_id":"5926","relation":"main_file","date_created":"2019-02-05T15:21:40Z","date_updated":"2020-07-14T12:47:11Z","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf"}],"oa_version":"Published Version","intvolume":" 115","ddc":["580"],"title":"Genetically encodable bioluminescent system from fungi","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5780","publication_identifier":{"issn":["00278424"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1803615115","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000452866000068"]},"oa":1,"file_date_updated":"2020-07-14T12:47:11Z","volume":115,"date_updated":"2023-09-11T14:04:05Z","date_created":"2018-12-23T22:59:18Z","author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","last_name":"Sarkisyan","first_name":"Karen"},{"last_name":"Mokrushina","first_name":"Yuliana A.","full_name":"Mokrushina, Yuliana A."},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"first_name":"Ekaterina O.","last_name":"Serebrovskaya","full_name":"Serebrovskaya, Ekaterina O."},{"full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M.","last_name":"Markina"},{"orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa"},{"first_name":"Andrey Y.","last_name":"Gorokhovatsky","full_name":"Gorokhovatsky, Andrey Y."},{"first_name":"Andrey","last_name":"Vvedensky","full_name":"Vvedensky, Andrey"},{"full_name":"Purtov, Konstantin V.","first_name":"Konstantin V.","last_name":"Purtov"},{"last_name":"Petushkov","first_name":"Valentin N.","full_name":"Petushkov, Valentin N."},{"full_name":"Rodionova, Natalja S.","first_name":"Natalja S.","last_name":"Rodionova"},{"full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh","first_name":"Tatiana V."},{"first_name":"Liliia","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia"},{"full_name":"Guglya, Elena B.","first_name":"Elena B.","last_name":"Guglya"},{"full_name":"Ziganshin, Rustam","first_name":"Rustam","last_name":"Ziganshin"},{"full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S.","last_name":"Tsarkova"},{"full_name":"Kaskova, Zinaida M.","first_name":"Zinaida M.","last_name":"Kaskova"},{"last_name":"Shender","first_name":"Victoria","full_name":"Shender, Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"last_name":"Abakumova","first_name":"Tatiana O.","full_name":"Abakumova, Tatiana O."},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Eroshkin, Fedor M.","first_name":"Fedor M.","last_name":"Eroshkin"},{"full_name":"Zaraisky, Andrey G.","last_name":"Zaraisky","first_name":"Andrey G."},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"last_name":"Mitiouchkina","first_name":"Tatiana Y.","full_name":"Mitiouchkina, Tatiana Y."},{"last_name":"Kopantzev","first_name":"Eugene P.","full_name":"Kopantzev, Eugene P."},{"full_name":"Waldenmaier, Hans E.","first_name":"Hans E.","last_name":"Waldenmaier"},{"last_name":"Oliveira","first_name":"Anderson G.","full_name":"Oliveira, Anderson G."},{"last_name":"Oba","first_name":"Yuichi","full_name":"Oba, Yuichi"},{"full_name":"Barsova, Ekaterina","first_name":"Ekaterina","last_name":"Barsova"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"full_name":"Gabaldón, Toni","last_name":"Gabaldón","first_name":"Toni"},{"last_name":"Stevani","first_name":"Cassius V.","full_name":"Stevani, Cassius V."},{"full_name":"Lukyanov, Sergey","first_name":"Sergey","last_name":"Lukyanov"},{"last_name":"Smirnov","first_name":"Ivan V.","full_name":"Smirnov, Ivan V."},{"first_name":"Josef I.","last_name":"Gitelson","full_name":"Gitelson, Josef I."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"department":[{"_id":"FyKo"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2018"},{"intvolume":" 115","status":"public","ddc":["570"],"title":"Selection and gene flow shape genomic islands that control floral guides","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","file":[{"creator":"dernst","file_size":1911302,"content_type":"application/pdf","access_level":"open_access","file_name":"11006.full.pdf","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","file_id":"5683","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"43","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"page":"11006 - 11011","citation":{"ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115."},"publication":"PNAS","date_published":"2018-10-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"23","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2018","acknowledgement":" ERC Grant 201252 (to N.H.B.)","volume":115,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Desmond","last_name":"Bradley","full_name":"Bradley, Desmond"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"full_name":"Elleouet, Joane","last_name":"Elleouet","first_name":"Joane"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"publist_id":"8017","file_date_updated":"2020-07-14T12:46:16Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","publication_identifier":{"issn":["00278424"]},"month":"10"},{"status":"public","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"64","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"issue":"35","article_type":"original","page":"E8135 - E8142","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","citation":{"short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142."},"date_published":"2018-08-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"year":"2018","date_updated":"2023-09-18T08:41:16Z","date_created":"2018-12-11T11:44:26Z","volume":115,"author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"full_name":"Guzmán Sáenz, Aldo","last_name":"Guzmán Sáenz","first_name":"Aldo"},{"last_name":"Prieto","first_name":"Y","full_name":"Prieto, Y"},{"last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail"},{"first_name":"V","last_name":"Kalinina","full_name":"Kalinina, V"},{"first_name":"Ernesto","last_name":"Lupercio","full_name":"Lupercio, Ernesto"}],"ec_funded":1,"publist_id":"7990","quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1805847115","month":"08","publication_identifier":{"issn":["00278424"]}},{"month":"12","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"oa":1,"external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1811580115","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"FlSc"}],"year":"2018","pmid":1,"date_updated":"2023-09-19T09:57:45Z","date_created":"2018-12-20T21:09:37Z","volume":115,"author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"first_name":"Bärbel","last_name":"Glass","full_name":"Glass, Bärbel"},{"first_name":"Michal","last_name":"Doležal","full_name":"Doležal, Michal"},{"full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian"},{"first_name":"Brice","last_name":"Murciano","full_name":"Murciano, Brice"},{"last_name":"Rein","first_name":"Alan","full_name":"Rein, Alan"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"full_name":"Ruml, Tomáš","first_name":"Tomáš","last_name":"Ruml"},{"full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg","last_name":"Kräusslich"},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."}],"scopus_import":"1","day":"11","article_processing_charge":"No","page":"E11751-E11760","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115."},"date_published":"2018-12-11T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry."}],"issue":"50","title":"Structure and architecture of immature and mature murine leukemia virus capsids","status":"public","intvolume":" 115","_id":"5770","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version"},{"pmid":1,"year":"2017","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"last_name":"Ten Hove","first_name":"Colette","full_name":"Ten Hove, Colette"},{"full_name":"Xiang, Daoquan","first_name":"Daoquan","last_name":"Xiang"},{"full_name":"Williams, Nerys","first_name":"Nerys","last_name":"Williams"},{"full_name":"López, Lorena","first_name":"Lorena","last_name":"López"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko","full_name":"Yoshida, Saiko"},{"first_name":"Margot","last_name":"Smit","full_name":"Smit, Margot"},{"full_name":"Datla, Raju","first_name":"Raju","last_name":"Datla"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"volume":114,"date_created":"2018-12-11T11:47:45Z","date_updated":"2021-01-12T08:08:02Z","publist_id":"7076","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"oa":1,"external_id":{"pmid":["28265057"]},"quality_controlled":"1","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"657","intvolume":" 114","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator."}],"citation":{"ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114."},"publication":"PNAS","page":"E2533 - E2539","date_published":"2017-03-21T00:00:00Z","scopus_import":1,"day":"21"},{"day":"28","scopus_import":1,"date_published":"2017-03-28T00:00:00Z","citation":{"chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114"},"publication":"PNAS","page":"3427 - 3432","issue":"13","abstract":[{"text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"660","intvolume":" 114","status":"public","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","publication_identifier":{"issn":["00278424"]},"month":"03","doi":"10.1073/pnas.1620274114","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"external_id":{"pmid":["28280102"]},"oa":1,"quality_controlled":"1","publist_id":"7073","author":[{"full_name":"Rickman, Jamie","first_name":"Jamie","last_name":"Rickman"},{"full_name":"Düllberg, Christian F","first_name":"Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748"},{"full_name":"Cade, Nicholas","first_name":"Nicholas","last_name":"Cade"},{"full_name":"Griffin, Lewis","last_name":"Griffin","first_name":"Lewis"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"volume":114,"date_updated":"2021-01-12T08:08:09Z","date_created":"2018-12-11T11:47:46Z","pmid":1,"year":"2017","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","publisher":"National Academy of Sciences","department":[{"_id":"MaLo"}],"publication_status":"published"},{"day":"02","article_processing_charge":"Yes (in subscription journal)","scopus_import":1,"date_published":"2017-05-02T00:00:00Z","page":"4715 - 4720","publication":"PNAS","citation":{"chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114"},"abstract":[{"lang":"eng","text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation."}],"issue":"18","type":"journal_article","oa_version":"Published Version","status":"public","title":"Memory-n strategies of direct reciprocity","intvolume":" 114","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"671","month":"05","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1621239114","quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["28420786"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/"}],"oa":1,"ec_funded":1,"publist_id":"7053","date_created":"2018-12-11T11:47:50Z","date_updated":"2021-01-12T08:08:37Z","volume":114,"author":[{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Martinez, Vaquero","first_name":"Vaquero","last_name":"Martinez"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1},{"file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7013","publication_status":"published","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"date_updated":"2023-02-23T12:54:57Z","date_created":"2018-12-11T11:47:57Z","volume":114,"author":[{"full_name":"Miki, Takafumi","first_name":"Takafumi","last_name":"Miki"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Alain","last_name":"Marty","full_name":"Marty, Alain"}],"month":"06","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","external_id":{"pmid":["28607047"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1704470114","type":"journal_article","abstract":[{"lang":"eng","text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. "}],"issue":"26","status":"public","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","ddc":["570"],"intvolume":" 114","_id":"693","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":2721544,"file_name":"2017_PNAS_Miki.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z","checksum":"2ab75d554f3df4a34d20fa8040589b7e","file_id":"7223","relation":"main_file"}],"oa_version":"Published Version","scopus_import":1,"day":"27","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","page":"E5246 - E5255","publication":"PNAS","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114"},"date_published":"2017-06-27T00:00:00Z"},{"publist_id":"7002","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"date_updated":"2021-01-12T08:11:21Z","date_created":"2018-12-11T11:48:00Z","volume":114,"author":[{"first_name":"Carl","last_name":"Veller","full_name":"Veller, Carl"},{"full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"}],"month":"07","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/"}],"oa":1,"external_id":{"pmid":["28630336"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1702020114","type":"journal_article","abstract":[{"lang":"eng","text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. "}],"issue":"27","status":"public","title":"The red queen and king in finite populations","intvolume":" 114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"699","oa_version":"Submitted Version","scopus_import":1,"day":"03","page":"E5396 - E5405","publication":"PNAS","citation":{"ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114."},"date_published":"2017-07-03T00:00:00Z"},{"citation":{"short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154."},"publication":"PNAS","page":"10149 - 10154","date_published":"2017-09-19T00:00:00Z","scopus_import":1,"day":"19","_id":"725","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","title":"Discrete modes of social information processing predict individual behavior of fish in a group","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"38","abstract":[{"lang":"eng","text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species."}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28874581"]},"quality_controlled":"1","doi":"10.1073/pnas.1703817114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"09","pmid":1,"year":"2017","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"}],"volume":114,"date_created":"2018-12-11T11:48:10Z","date_updated":"2021-01-12T08:12:36Z","publist_id":"6953"},{"scopus_import":"1","day":"03","article_processing_charge":"No","page":"10666 - 10671","publication":"PNAS","citation":{"chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114.","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114"},"date_published":"2017-10-03T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"issue":"40","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","status":"public","intvolume":" 114","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"822","oa_version":"Submitted Version","month":"10","publication_identifier":{"issn":["00278424"]},"isi":1,"quality_controlled":"1","project":[{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}],"external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1713372114","publist_id":"6827","ec_funded":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"ToBo"}],"year":"2017","pmid":1,"date_created":"2018-12-11T11:48:41Z","date_updated":"2023-09-26T16:18:48Z","volume":114,"author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","first_name":"Marjon","full_name":"De Vos, Marjon"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P"},{"full_name":"Mcnally, Alan","first_name":"Alan","last_name":"Mcnally"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}]}]