[{"date_updated":"2026-04-16T10:07:32Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","date_created":"2018-12-11T11:49:25Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"735"},{"status":"public","id":"1100","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1537"},{"status":"public","id":"1912","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"3246","status":"public"},{"id":"2926","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"676","status":"public"}]},"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"242f88c87f2cf267bf05049fa26a687b","creator":"dernst","file_name":"2017_Barone_thesis_final.docx","file_size":14497822,"file_id":"6205","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","access_level":"closed"},{"content_type":"application/pdf","relation":"main_file","checksum":"ba5b0613ed8bade73a409acdd880fb8a","creator":"dernst","file_name":"2017_Barone_thesis_.pdf","file_size":14995941,"date_created":"2019-04-05T08:36:52Z","file_id":"6206","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z"}],"abstract":[{"text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.","lang":"eng"}],"OA_place":"publisher","author":[{"last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","status":"public","publication_status":"published","date_published":"2017-03-01T00:00:00Z","year":"2017","corr_author":"1","citation":{"short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825.","apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825."},"alternative_title":["ISTA Thesis"],"file_date_updated":"2020-07-14T12:48:16Z","language":[{"iso":"eng"}],"pubrep_id":"825","oa_version":"Published Version","month":"03","type":"dissertation","article_processing_charge":"No","ddc":["570","590"],"page":"109","department":[{"_id":"CaHe"}],"publist_id":"6444","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"_id":"961","publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_825","day":"01"},{"issue":"3","intvolume":" 13","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"}],"has_accepted_license":"1","publication_status":"published","status":"public","date_published":"2017-09-13T00:00:00Z","year":"2017","citation":{"mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017)."},"corr_author":"1","file_date_updated":"2020-07-14T12:46:33Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000419163000005"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-04-29T06:14:48Z","date_created":"2018-12-11T11:46:37Z","publication":"Logical Methods in Computer Science","related_material":{"record":[{"status":"public","id":"5438","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"1610"}]},"title":"Edit distance for pushdown automata","ec_funded":1,"publisher":"International Federation of Computational Logic","oa":1,"file":[{"date_created":"2018-12-12T10:14:37Z","file_id":"5090","access_level":"open_access","date_updated":"2020-07-14T12:46:33Z","content_type":"application/pdf","relation":"main_file","checksum":"08041379ba408d40664f449eb5907a8f","creator":"system","file_name":"IST-2015-321-v1+1_main.pdf","file_size":279071},{"file_id":"5091","date_created":"2018-12-12T10:14:38Z","access_level":"open_access","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","relation":"main_file","content_type":"application/pdf","file_size":279071,"file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","creator":"system"}],"abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"publist_id":"7356","volume":13,"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"_id":"465","publication_identifier":{"issn":["1860-5974"]},"day":"13","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"doi":"10.23638/LMCS-13(3:23)2017","pubrep_id":"955","oa_version":"Published Version","month":"09","type":"journal_article","article_processing_charge":"No","isi":1,"ddc":["004"],"scopus_import":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["1610.09350"]},"quality_controlled":"1","citation":{"ama":"Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 2017;96(23). doi:10.1103/PhysRevB.96.235141","ieee":"Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, and N. Gedik, “Origin of the exciton mass in the frustrated Mott insulator Na2IrO3,” Physical Review B, vol. 96, no. 23. American Physical Society, 2017.","apa":"Alpichshev, Z., Sie, E., Mahmood, F., Cao, G., & Gedik, N. (2017). Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.235141","ista":"Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. 2017. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 96(23), 235141.","mla":"Alpichshev, Zhanybek, et al. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B, vol. 96, no. 23, 235141, American Physical Society, 2017, doi:10.1103/PhysRevB.96.235141.","short":"Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, N. Gedik, Physical Review B 96 (2017).","chicago":"Alpichshev, Zhanybek, Edbert Sie, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.235141."},"OA_type":"green","status":"public","extern":"1","publication_status":"published","year":"2017","date_published":"2017-12-26T00:00:00Z","author":[{"full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","last_name":"Alpichshev"},{"last_name":"Sie","first_name":"Edbert","full_name":"Sie, Edbert"},{"last_name":"Mahmood","first_name":"Fahad","full_name":"Mahmood, Fahad"},{"last_name":"Cao","full_name":"Cao, Gang","first_name":"Gang"},{"last_name":"Gedik","first_name":"Nuh","full_name":"Gedik, Nuh"}],"issue":"23","intvolume":" 96","abstract":[{"lang":"eng","text":"We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. "}],"OA_place":"repository","oa":1,"publisher":"American Physical Society","publication":"Physical Review B","title":"Origin of the exciton mass in the frustrated Mott insulator Na2IrO3","acknowledgement":"Z.A. gratefully acknowledges discussions with P. A. Lee and A. Kemper. A conversation with J. Zaanen was instrumental in clarifying the physical picture described in this paper. We would also like to thank A. Kogar for thoroughly reading the manuscript and making valuable comments. This work was supported by Army Research Office Grant No. W911NF-15-1-0128 and Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4540 (time resolved optical spectroscopy), Skoltech, as part of the Skoltech NGP program (theory) and National Science Foundation Grant No. DMR-1265162 (material growth).","date_created":"2018-12-11T11:46:13Z","main_file_link":[{"open_access":"1","url":"http://dspace.mit.edu/handle/1721.1/114259"}],"date_updated":"2026-04-29T06:27:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"doi":"10.1103/PhysRevB.96.235141","day":"26","volume":96,"_id":"393","article_type":"original","publist_id":"7436","article_number":"235141 ","article_processing_charge":"No","month":"12","type":"journal_article","oa_version":"Submitted Version"},{"OA_type":"green","citation":{"chicago":"Massuda, Aviram, Charles Roques-Carmes, Yujia Yang, Steven E. Kooi, Yi Yang, Chitraang Murdia, Karl K. Berggren, Ido Kaminer, and Marin Soljačić. “Smith-Purcell Radiation from Low-Energy Electrons.” In Conference on Lasers and Electro-Optics. Optica Publishing Group, 2017. https://doi.org/10.1364/cleo_qels.2017.fm3h.6.","short":"A. Massuda, C. Roques-Carmes, Y. Yang, S.E. Kooi, Y. Yang, C. Murdia, K.K. Berggren, I. Kaminer, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2017.","mla":"Massuda, Aviram, et al. “Smith-Purcell Radiation from Low-Energy Electrons.” Conference on Lasers and Electro-Optics, FM3H.6, Optica Publishing Group, 2017, doi:10.1364/cleo_qels.2017.fm3h.6.","apa":"Massuda, A., Roques-Carmes, C., Yang, Y., Kooi, S. E., Yang, Y., Murdia, C., … Soljačić, M. (2017). Smith-Purcell radiation from low-energy electrons. In Conference on Lasers and Electro-Optics. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_qels.2017.fm3h.6","ama":"Massuda A, Roques-Carmes C, Yang Y, et al. Smith-Purcell radiation from low-energy electrons. In: Conference on Lasers and Electro-Optics. Optica Publishing Group; 2017. doi:10.1364/cleo_qels.2017.fm3h.6","ieee":"A. Massuda et al., “Smith-Purcell radiation from low-energy electrons,” in Conference on Lasers and Electro-Optics, San Jose, CA, United States, 2017.","ista":"Massuda A, Roques-Carmes C, Yang Y, Kooi SE, Yang Y, Murdia C, Berggren KK, Kaminer I, Soljačić M. 2017. Smith-Purcell radiation from low-energy electrons. Conference on Lasers and Electro-Optics. CLEO: Fundamental Science, FM3H.6."},"publication_status":"published","extern":"1","status":"public","date_published":"2017-05-01T00:00:00Z","year":"2017","language":[{"iso":"eng"}],"external_id":{"arxiv":["1710.05358"]},"quality_controlled":"1","author":[{"last_name":"Massuda","first_name":"Aviram","full_name":"Massuda, Aviram"},{"full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","first_name":"Charles","last_name":"Roques-Carmes"},{"full_name":"Yang, Yujia","first_name":"Yujia","last_name":"Yang"},{"last_name":"Kooi","full_name":"Kooi, Steven E.","first_name":"Steven E."},{"full_name":"Yang, Yi","first_name":"Yi","last_name":"Yang"},{"last_name":"Murdia","full_name":"Murdia, Chitraang","first_name":"Chitraang"},{"full_name":"Berggren, Karl K.","first_name":"Karl K.","last_name":"Berggren"},{"last_name":"Kaminer","full_name":"Kaminer, Ido","first_name":"Ido"},{"last_name":"Soljačić","first_name":"Marin","full_name":"Soljačić, Marin"}],"publisher":"Optica Publishing Group","abstract":[{"lang":"eng","text":"Focused electron beams can induce electromagnetic radiation from periodic surfaces. We have used low-energy electrons (1.5-6kV) to induce visible light emission from nanoscale gratings (50nm and 60nm). Our results coincide well with numerical simulations."}],"OA_place":"repository","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1710.05358","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2026-05-05T06:46:39Z","publication":"Conference on Lasers and Electro-Optics","title":"Smith-Purcell radiation from low-energy electrons","date_created":"2026-03-30T12:22:48Z","conference":{"start_date":"2017-05-14","location":"San Jose, CA, United States","end_date":"2017-05-19","name":"CLEO: Fundamental Science"},"_id":"21615","doi":"10.1364/cleo_qels.2017.fm3h.6","day":"01","publication_identifier":{"eisbn":["9781943580279"]},"article_number":"FM3H.6","article_processing_charge":"No","scopus_import":"1","month":"05","type":"conference","oa_version":"Preprint"},{"type":"conference","title":"High-order Smith-Purcell radiation in silicon nanowires","publication":"Conference on Lasers and Electro-Optics","month":"06","oa_version":"None","date_created":"2026-03-30T12:22:48Z","date_updated":"2026-05-05T06:43:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present experimental results demonstrating multiple order Smith-Purcell radiation in high aspect ratio Silicon Nanowires structures using low-energy electrons (2.5-10keV). These produce emission spanning the visible, paving the way to a fully tunable ultraviolet source."}],"scopus_import":"1","publisher":"Optica Publishing Group","article_processing_charge":"No","author":[{"last_name":"Massuda","full_name":"Massuda, Aviram","first_name":"Aviram"},{"full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","first_name":"Charles","last_name":"Roques-Carmes"},{"full_name":"Solanki, Amit","first_name":"Amit","last_name":"Solanki"},{"full_name":"Yang, Yi","first_name":"Yi","last_name":"Yang"},{"full_name":"Kooi, Steven E.","first_name":"Steven E.","last_name":"Kooi"},{"last_name":"Habbal","full_name":"Habbal, Fawwaz","first_name":"Fawwaz"},{"full_name":"Kaminer, Ido","first_name":"Ido","last_name":"Kaminer"},{"first_name":"Marin","full_name":"Soljačić, Marin","last_name":"Soljačić"}],"article_number":"JTh5B.8","day":"01","doi":"10.1364/cleo_at.2017.jth5b.8","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eisbn":["9781943580279"],"issnl":["2162-2701"]},"conference":{"name":"CLEO: Applications and Technology","end_date":"2017-05-19","location":"San Jose, CA, United States","start_date":"2017-05-14"},"citation":{"mla":"Massuda, Aviram, et al. “High-Order Smith-Purcell Radiation in Silicon Nanowires.” Conference on Lasers and Electro-Optics, JTh5B.8, Optica Publishing Group, 2017, doi:10.1364/cleo_at.2017.jth5b.8.","ieee":"A. Massuda et al., “High-order Smith-Purcell radiation in silicon nanowires,” in Conference on Lasers and Electro-Optics, San Jose, CA, United States, 2017.","ama":"Massuda A, Roques-Carmes C, Solanki A, et al. High-order Smith-Purcell radiation in silicon nanowires. In: Conference on Lasers and Electro-Optics. Optica Publishing Group; 2017. doi:10.1364/cleo_at.2017.jth5b.8","apa":"Massuda, A., Roques-Carmes, C., Solanki, A., Yang, Y., Kooi, S. E., Habbal, F., … Soljačić, M. (2017). High-order Smith-Purcell radiation in silicon nanowires. In Conference on Lasers and Electro-Optics. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2017.jth5b.8","ista":"Massuda A, Roques-Carmes C, Solanki A, Yang Y, Kooi SE, Habbal F, Kaminer I, Soljačić M. 2017. High-order Smith-Purcell radiation in silicon nanowires. Conference on Lasers and Electro-Optics. CLEO: Applications and Technology, JTh5B.8.","chicago":"Massuda, Aviram, Charles Roques-Carmes, Amit Solanki, Yi Yang, Steven E. Kooi, Fawwaz Habbal, Ido Kaminer, and Marin Soljačić. “High-Order Smith-Purcell Radiation in Silicon Nanowires.” In Conference on Lasers and Electro-Optics. Optica Publishing Group, 2017. https://doi.org/10.1364/cleo_at.2017.jth5b.8.","short":"A. Massuda, C. Roques-Carmes, A. Solanki, Y. Yang, S.E. Kooi, F. Habbal, I. Kaminer, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2017."},"OA_type":"closed access","year":"2017","_id":"21588","date_published":"2017-06-01T00:00:00Z","publication_status":"published","extern":"1","status":"public"},{"author":[{"first_name":"Mohammadreza","full_name":"Khorasaninejad, Mohammadreza","last_name":"Khorasaninejad"},{"last_name":"Chen","full_name":"Chen, Wei Ting","first_name":"Wei Ting"},{"last_name":"Zhu","full_name":"Zhu, Alexander Y.","first_name":"Alexander Y."},{"full_name":"Oh, Jaewon","first_name":"Jaewon","last_name":"Oh"},{"last_name":"Devlin","first_name":"Robert C.","full_name":"Devlin, Robert C."},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"last_name":"Mishra","full_name":"Mishra, Ishan","first_name":"Ishan"},{"last_name":"Capasso","full_name":"Capasso, Federico","first_name":"Federico"}],"article_number":"101130G ","intvolume":" 10113","citation":{"mla":"Khorasaninejad, Mohammadreza, et al. “Planar Optics at Visible Wavelengths Based on Titanium Dioxide .” High Contrast Metastructures VI, vol. 10113, 101130G, 2017, doi:10.1117/12.2255916.","ieee":"M. Khorasaninejad et al., “Planar optics at visible wavelengths based on titanium dioxide ,” in High Contrast Metastructures VI, San Francisco, CA, United States, 2017, vol. 10113.","ama":"Khorasaninejad M, Chen WT, Zhu AY, et al. Planar optics at visible wavelengths based on titanium dioxide . In: High Contrast Metastructures VI. Vol 10113. ; 2017. doi:10.1117/12.2255916","apa":"Khorasaninejad, M., Chen, W. T., Zhu, A. Y., Oh, J., Devlin, R. C., Roques-Carmes, C., … Capasso, F. (2017). Planar optics at visible wavelengths based on titanium dioxide . In High Contrast Metastructures VI (Vol. 10113). San Francisco, CA, United States. https://doi.org/10.1117/12.2255916","ista":"Khorasaninejad M, Chen WT, Zhu AY, Oh J, Devlin RC, Roques-Carmes C, Mishra I, Capasso F. 2017. Planar optics at visible wavelengths based on titanium dioxide . High Contrast Metastructures VI. SPIE OPTO vol. 10113, 101130G.","chicago":"Khorasaninejad, Mohammadreza, Wei Ting Chen, Alexander Y. Zhu, Jaewon Oh, Robert C. Devlin, Charles Roques-Carmes, Ishan Mishra, and Federico Capasso. “Planar Optics at Visible Wavelengths Based on Titanium Dioxide .” In High Contrast Metastructures VI, Vol. 10113, 2017. https://doi.org/10.1117/12.2255916.","short":"M. Khorasaninejad, W.T. Chen, A.Y. Zhu, J. Oh, R.C. Devlin, C. Roques-Carmes, I. Mishra, F. Capasso, in:, High Contrast Metastructures VI, 2017."},"OA_type":"closed access","conference":{"start_date":"2017-01-28","end_date":"2017-02-02","name":"SPIE OPTO","location":"San Francisco, CA, United States"},"publication_status":"published","status":"public","volume":10113,"extern":"1","date_published":"2017-04-28T00:00:00Z","_id":"21573","year":"2017","language":[{"iso":"eng"}],"day":"28","doi":"10.1117/12.2255916","quality_controlled":"1","date_updated":"2026-05-05T09:41:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publication":"High Contrast Metastructures VI","type":"conference","title":"Planar optics at visible wavelengths based on titanium dioxide ","oa_version":"None","date_created":"2026-03-30T12:22:47Z","article_processing_charge":"No","abstract":[{"text":"We present a new platform that realizes high performance metasurfaces in the visible spectrum. This platform is based on atomic layer deposition of titanium dioxide and allows molding incident light wavefront to desired shapes including holographic images, optical vortices, and Bessel beams. The focus of this work will be on the design and demonstration of planar metalenses. We report on our recent experimental realization of high numerical aperture metalenses with efficiency as high as 86%. These metalenses can focus light into a diffraction-limited spot and can be employed for imaging purposes to provide sub-wavelength imaging resolution. In addition, by the judicious design of metalens building blocks, one can achieve a multispectral chiral metalens (MCML) within a single metasurface layer. The MCML can simultaneously resolve chiral and spectral information of an object without the requirement of additional optical components such as polarizers, wave-plates, or even gratings. Using this MCML, we map the chiroptical properties of a macroscopic chiral biological specimen across the visible range. Finally, since many applications require polarization insensitive planar lenses, we discuss the experimental realization of such metalenses with numerical apertures as high as NA=0.85. These metalenses can focus incident light to a spot as small as ~0.6lambda with efficiencies up to 70%. The straightforward and CMOS-compatible fabrication process of this platform is promising for a wide range of optics-based applications in multidisciplinary science and technology. ","lang":"eng"}]},{"publisher":"American Physical Society","OA_place":"repository","abstract":[{"text":"We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static.","lang":"eng"}],"oa":1,"date_updated":"2026-05-06T06:56:15Z","main_file_link":[{"url":"http://dspace.mit.edu/handle/1721.1/109835","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ","publication":"Physical Review B","date_created":"2018-12-11T11:46:13Z","acknowledgement":"Optical pump-probe work was supported by the Gordon and Betty Moore Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization was supported by AFOSR FA95501410332 and NSF DMR1410665.","OA_type":"green","citation":{"chicago":"Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins, and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125.","short":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical Review B 95 (2017).","mla":"Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B, vol. 95, no. 11, 115125, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125.","ista":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 95(11), 115125.","apa":"Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene, R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.95.115125","ieee":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene, “Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American Physical Society, 2017.","ama":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125"},"year":"2017","date_published":"2017-03-13T00:00:00Z","status":"public","publication_status":"published","extern":"1","external_id":{"arxiv":["1601.06694"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"first_name":"Inna","full_name":"Vishik, Inna","last_name":"Vishik"},{"last_name":"Mahmood","first_name":"Fahad","full_name":"Mahmood, Fahad"},{"last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek"},{"last_name":"Gedik","full_name":"Gedik, Nuh","first_name":"Nuh"},{"full_name":"Higgins, Joshu","first_name":"Joshu","last_name":"Higgins"},{"full_name":"Greene, Richard","first_name":"Richard","last_name":"Greene"}],"intvolume":" 95","issue":"11","article_processing_charge":"No","scopus_import":"1","type":"journal_article","month":"03","oa_version":"Preprint","_id":"392","volume":95,"day":"13","doi":"10.1103/PhysRevB.95.115125","publication_identifier":{"eissn":["2469-9969"],"issnl":["2469-9950"]},"publist_id":"7437","article_number":"115125","article_type":"original"},{"department":[{"_id":"ToBo"}],"isi":1,"ddc":["570"],"scopus_import":"1","article_processing_charge":"Yes","month":"03","type":"journal_article","oa_version":"Published Version","pubrep_id":"800","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1371/journal.pone.0174066","day":"16","publication_identifier":{"issn":["1932-6203"]},"volume":12,"_id":"1029","publist_id":"6361","article_number":"e0174066","file":[{"file_size":3429381,"file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","creator":"system","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:09:47Z","date_created":"2018-12-12T10:09:47Z","file_id":"4772"}],"abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}],"oa":1,"publisher":"Public Library of Science","related_material":{"record":[{"id":"5556","relation":"popular_science","status":"public"},{"status":"public","id":"6392","relation":"dissertation_contains"}]},"publication":"PLoS One","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","date_created":"2018-12-11T11:49:46Z","date_updated":"2026-06-14T22:30:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"external_id":{"isi":["000396318300121"]},"quality_controlled":"1","citation":{"chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066."},"file_date_updated":"2018-12-12T10:09:47Z","status":"public","publication_status":"published","date_published":"2017-03-16T00:00:00Z","year":"2017","has_accepted_license":"1","author":[{"orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Lukacisin"},{"first_name":"Matthieu","full_name":"Landon, Matthieu","last_name":"Landon"},{"full_name":"Jajoo, Rishi","first_name":"Rishi","last_name":"Jajoo"}],"issue":"3","intvolume":" 12"},{"date_updated":"2026-06-14T22:30:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","publication":"Developmental Cell","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"relation":"dissertation_contains","id":"8350","status":"public"}]},"date_created":"2018-12-11T11:48:13Z","publisher":"Cell Press","ec_funded":1,"abstract":[{"text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.","lang":"eng"}],"author":[{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone"},{"first_name":"Moritz","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang"},{"last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Pradhan","full_name":"Pradhan, Saurabh","first_name":"Saurabh"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"last_name":"Sako","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"intvolume":" 43","issue":"2","corr_author":"1","citation":{"mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014","ieee":"V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.014","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211."},"date_published":"2017-10-23T00:00:00Z","year":"2017","status":"public","publication_status":"published","external_id":{"isi":["000413443700011"]},"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","month":"10","oa_version":"None","article_processing_charge":"No","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"page":"198 - 211","scopus_import":"1","isi":1,"publist_id":"6934","_id":"735","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","name":"Cell segregation in gastrulation: the role of cell fate specification","grant_number":"I2058"}],"volume":43,"doi":"10.1016/j.devcel.2017.09.014","day":"23","publication_identifier":{"issn":["1534-5807"]}},{"article_processing_charge":"No","ddc":["540"],"isi":1,"scopus_import":"1","page":"4608-4611","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"oa_version":"Published Version","month":"03","type":"journal_article","volume":56,"project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"1028","publication_identifier":{"issn":["1433-7851"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1002/anie.201611998","day":"20","publist_id":"6362","ec_funded":1,"publisher":"Wiley-Blackwell","oa":1,"file":[{"creator":"dernst","file_size":2614942,"file_name":"2017_communications_Kainrath.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2019-01-18T09:39:55Z","access_level":"open_access","file_id":"5845","date_created":"2019-01-18T09:39:55Z","success":1}],"abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"date_updated":"2026-06-14T22:30:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by a grant from the European Union􏰝s Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","date_created":"2018-12-11T11:49:46Z","related_material":{"record":[{"id":"418","relation":"dissertation_contains","status":"public"},{"relation":"part_of_dissertation","id":"7680","status":"public"}]},"publication":"Angewandte Chemie - International Edition","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","publication_status":"published","status":"public","year":"2017","date_published":"2017-03-20T00:00:00Z","file_date_updated":"2019-01-18T09:39:55Z","citation":{"mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611."},"corr_author":"1","quality_controlled":"1","external_id":{"isi":["000398154000038"]},"language":[{"iso":"eng"}],"issue":"16","intvolume":" 56","author":[{"last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie","orcid":"0000-0002-6709-2195"},{"first_name":"Manuela","full_name":"Stadler, Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Gschaider-Reichhart"},{"first_name":"Martin","full_name":"Distel, Martin","last_name":"Distel"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"has_accepted_license":"1"},{"has_accepted_license":"1","author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen"},{"last_name":"Düllberg","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","first_name":"Christian F"},{"last_name":"Mieck","first_name":"Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","full_name":"Mieck, Christine","orcid":"0000-0003-1919-7416"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"intvolume":" 11","language":[{"iso":"eng"}],"external_id":{"isi":["000404486700001"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:16Z","citation":{"mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017)."},"date_published":"2017-06-28T00:00:00Z","year":"2017","publication_status":"published","status":"public","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","related_material":{"record":[{"relation":"dissertation_contains","id":"9962","status":"public"}]},"publication":"Frontiers in Cellular Neuroscience","date_created":"2018-12-11T11:49:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-14T22:30:44Z","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"dc1f5a475b918d09a0f9f587400b1626","creator":"system","file_size":2153858,"file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","file_id":"4764","date_created":"2018-12-12T10:09:40Z","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access"}],"abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"oa":1,"publisher":"Frontiers Research Foundation","ec_funded":1,"publist_id":"6445","article_number":"176","doi":"10.3389/fncel.2017.00176","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"28","publication_identifier":{"issn":["1662-5102"]},"_id":"960","project":[{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"T00817-B21","name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":11,"type":"journal_article","month":"06","oa_version":"Published Version","pubrep_id":"830","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"scopus_import":"1","isi":1,"ddc":["570"],"article_processing_charge":"Yes"},{"quality_controlled":"1","external_id":{"isi":["000399451100002"]},"language":[{"iso":"eng"}],"status":"public","publication_status":"published","date_published":"2017-04-18T00:00:00Z","year":"2017","citation":{"short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006."},"corr_author":"1","issue":"4","intvolume":" 46","author":[{"first_name":"Frank P","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"publisher":"Cell Press","date_created":"2018-12-11T11:47:47Z","publication":"Immunity","related_material":{"record":[{"status":"public","id":"6947","relation":"dissertation_contains"}]},"title":"The dynamic cytokine niche","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-14T22:30:52Z","publication_identifier":{"issn":["1074-7613"]},"doi":"10.1016/j.immuni.2017.04.006","day":"18","volume":46,"_id":"664","publist_id":"7065","isi":1,"scopus_import":"1","page":"519 - 520","department":[{"_id":"MiSi"}],"article_processing_charge":"No","oa_version":"None","month":"04","type":"journal_article"},{"ec_funded":1,"publisher":"Public Library of Science","oa":1,"file":[{"date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","date_created":"2018-12-12T10:15:01Z","file_id":"5117","file_size":3775716,"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","creator":"system","checksum":"9143c290fa6458ed2563bff4b295554a","relation":"main_file","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"date_updated":"2026-06-14T22:30:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:47:58Z","related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"status":"public","id":"9852","relation":"research_data"},{"status":"public","id":"6263","relation":"dissertation_contains"}]},"publication":"PLoS Computational Biology","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","publication_status":"published","status":"public","date_published":"2017-07-18T00:00:00Z","year":"2017","file_date_updated":"2020-07-14T12:47:46Z","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609."},"corr_author":"1","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000406619800014"]},"issue":"7","intvolume":" 13","author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao"}],"has_accepted_license":"1","article_processing_charge":"No","isi":1,"ddc":["576"],"scopus_import":"1","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"pubrep_id":"894","oa_version":"Published Version","month":"07","type":"journal_article","volume":13,"_id":"696","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_identifier":{"issn":["1553-734X"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"18","doi":"10.1371/journal.pcbi.1005609","article_number":"e1005609","publist_id":"7004","article_type":"original"},{"publication_identifier":{"issn":["1932-6203"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1371/journal.pone.0179377","day":"01","volume":12,"_id":"682","article_type":"original","article_number":"e0179377","publist_id":"7034","ddc":["571"],"isi":1,"scopus_import":"1","department":[{"_id":"RySh"}],"article_processing_charge":"No","oa_version":"Published Version","month":"06","type":"journal_article","pubrep_id":"897","quality_controlled":"1","external_id":{"isi":["000402923200125"]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2017-06-01T00:00:00Z","year":"2017","file_date_updated":"2020-07-14T12:47:40Z","citation":{"mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017)."},"has_accepted_license":"1","issue":"6","intvolume":" 12","author":[{"last_name":"Ukai","full_name":"Ukai, Hikari","first_name":"Hikari"},{"first_name":"Aiko","full_name":"Kawahara, Aiko","last_name":"Kawahara"},{"last_name":"Hirayama","full_name":"Hirayama, Keiko","first_name":"Keiko"},{"first_name":"Matthew J","full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case"},{"full_name":"Aino, Shotaro","first_name":"Shotaro","last_name":"Aino"},{"last_name":"Miyabe","full_name":"Miyabe, Masahiro","first_name":"Masahiro"},{"last_name":"Wakita","first_name":"Ken","full_name":"Wakita, Ken"},{"full_name":"Oogi, Ryohei","first_name":"Ryohei","last_name":"Oogi"},{"full_name":"Kasayuki, Michiyo","first_name":"Michiyo","last_name":"Kasayuki"},{"last_name":"Kawashima","first_name":"Shihomi","full_name":"Kawashima, Shihomi"},{"first_name":"Shunichi","full_name":"Sugimoto, Shunichi","last_name":"Sugimoto"},{"last_name":"Chikamatsu","full_name":"Chikamatsu, Kanako","first_name":"Kanako"},{"last_name":"Nitta","first_name":"Noritaka","full_name":"Nitta, Noritaka"},{"last_name":"Koga","first_name":"Tsuneyuki","full_name":"Koga, Tsuneyuki"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Takai, Toshiyuki","first_name":"Toshiyuki","last_name":"Takai"},{"full_name":"Ito, Isao","first_name":"Isao","last_name":"Ito"}],"oa":1,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:12:16Z","file_id":"4934","creator":"system","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","file_size":5798454,"relation":"main_file","content_type":"application/pdf","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8"}],"abstract":[{"lang":"eng","text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry."}],"publisher":"Public Library of Science","date_created":"2018-12-11T11:47:54Z","publication":"PLoS One","related_material":{"record":[{"id":"51","relation":"dissertation_contains","status":"public"}]},"title":"PirB regulates asymmetries in hippocampal circuitry","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-14T22:30:55Z"},{"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"ToBo"}],"page":"90 - 97","scopus_import":"1","ddc":["570"],"isi":1,"pubrep_id":"801","type":"journal_article","month":"08","oa_version":"Published Version","_id":"1027","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"volume":46,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"01","doi":"10.1016/j.copbio.2017.02.013","publist_id":"6364","article_type":"original","publisher":"Elsevier","ec_funded":1,"abstract":[{"text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.","lang":"eng"}],"file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":858338,"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","date_created":"2019-01-18T09:57:57Z","file_id":"5846","success":1,"access_level":"open_access","date_updated":"2019-01-18T09:57:57Z"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2026-06-14T22:30:54Z","title":"Toward a quantitative understanding of antibiotic resistance evolution","related_material":{"record":[{"relation":"dissertation_contains","id":"6263","status":"public"}]},"publication":"Current Opinion in Biotechnology","date_created":"2018-12-11T11:49:45Z","citation":{"ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013."},"corr_author":"1","file_date_updated":"2019-01-18T09:57:57Z","year":"2017","date_published":"2017-08-01T00:00:00Z","status":"public","publication_status":"published","external_id":{"isi":["000408077400015"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"}],"intvolume":" 46","has_accepted_license":"1"},{"scopus_import":"1","isi":1,"ddc":["576"],"department":[{"_id":"CaGu"}],"article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","month":"07","pubrep_id":"890","publication_identifier":{"issn":["2050-084X"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.7554/eLife.25100","day":"25","_id":"704","volume":6,"article_number":"e25100","publist_id":"6990","oa":1,"file":[{"creator":"system","file_size":2092088,"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","relation":"main_file","content_type":"application/pdf","checksum":"6b908b5db9f61f6820ebd7f8fa815571","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:54Z","file_id":"4975"},{"creator":"system","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","file_size":3428681,"relation":"main_file","content_type":"application/pdf","checksum":"ca21530389b720243552678125fdba35","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","file_id":"4976","date_created":"2018-12-12T10:12:55Z"}],"abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"publisher":"eLife Sciences Publications","date_created":"2018-12-11T11:48:01Z","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","related_material":{"record":[{"status":"public","id":"5564","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"publication":"eLife","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-14T22:30:58Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000406183700001"]},"date_published":"2017-07-25T00:00:00Z","year":"2017","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:47:48Z","citation":{"chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100."},"corr_author":"1","has_accepted_license":"1","intvolume":" 6","author":[{"last_name":"Steinrück","first_name":"Magdalena","orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"}]},{"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","date_published":"2017-03-17T00:00:00Z","year":"2017","citation":{"short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1."},"file_date_updated":"2019-10-15T07:47:05Z","corr_author":"1","alternative_title":["Methods in Molecular Biology"],"has_accepted_license":"1","intvolume":" 1569","author":[{"orcid":"0000-0003-3638-1426","full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej","last_name":"Hurny"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"}],"oa":1,"file":[{"date_created":"2018-12-12T10:14:18Z","file_id":"5068","date_updated":"2019-10-15T07:47:05Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"system","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","file_size":840646}],"abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"publisher":"Springer","date_created":"2018-12-11T11:49:45Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"539"}]},"publication":"Auxins and Cytokinins in Plant Biology","title":"Methodological advances in auxin and cytokinin biology","date_updated":"2026-06-14T22:30:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1064-3745"]},"doi":"10.1007/978-1-4939-6831-2_1","day":"17","volume":1569,"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}],"_id":"1024","publist_id":"6369","ddc":["575"],"scopus_import":"1","page":"1 - 29","department":[{"_id":"EvBe"}],"article_processing_charge":"No","oa_version":"Submitted Version","month":"03","type":"journal_article","pubrep_id":"1019"},{"date_updated":"2026-06-14T22:30:59Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","publication":"The Journal of Clinical Investigation","related_material":{"record":[{"status":"public","id":"12401","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:47:53Z","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","publisher":"American Society for Clinical Investigation","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"oa":1,"author":[{"full_name":"Ebner, Florian","first_name":"Florian","last_name":"Ebner"},{"last_name":"Sedlyarov","full_name":"Sedlyarov, Vitaly","first_name":"Vitaly"},{"last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ivin, Masa","first_name":"Masa","last_name":"Ivin"},{"full_name":"Kratochvill, Franz","first_name":"Franz","last_name":"Kratochvill"},{"last_name":"Gratz","full_name":"Gratz, Nina","first_name":"Nina"},{"last_name":"Kenner","full_name":"Kenner, Lukas","first_name":"Lukas"},{"last_name":"Villunger","first_name":"Andreas","full_name":"Villunger, Andreas"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Kovarik, Pavel","first_name":"Pavel","last_name":"Kovarik"}],"intvolume":" 127","issue":"6","citation":{"ieee":"F. Ebner et al., “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” The Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:10.1172/JCI80631.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631."},"date_published":"2017-06-01T00:00:00Z","year":"2017","publication_status":"published","status":"public","external_id":{"pmid":["28504646"],"isi":["000402620800008"]},"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","month":"06","oa_version":"Submitted Version","article_processing_charge":"No","department":[{"_id":"MiSi"}],"page":"2051 - 2065","scopus_import":"1","isi":1,"publist_id":"7038","project":[{"name":"The biochemical basis of PAR polarization","grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"679","volume":127,"doi":"10.1172/JCI80631","day":"01","publication_identifier":{"issn":["0021-9738"]}},{"month":"05","type":"journal_article","oa_version":"Published Version","page":"1798 - 1806","department":[{"_id":"Bio"},{"_id":"CaHe"}],"isi":1,"ddc":["570"],"scopus_import":"1","article_processing_charge":"No","article_type":"original","publist_id":"7047","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1242/dev.144964","day":"15","publication_identifier":{"issn":["0950-1991"]},"volume":144,"_id":"676","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"publication":"Development","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","date_created":"2018-12-11T11:47:52Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-06-14T22:31:03Z","pmid":1,"file":[{"creator":"dernst","file_size":8194516,"file_name":"2017_Development_Krens.pdf","relation":"main_file","content_type":"application/pdf","checksum":"bc25125fb664706cdf180e061429f91d","access_level":"open_access","date_updated":"2020-07-14T12:47:39Z","file_id":"6905","date_created":"2019-09-24T06:56:22Z"}],"abstract":[{"text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.","lang":"eng"}],"oa":1,"publisher":"Company of Biologists","has_accepted_license":"1","author":[{"last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Jim","full_name":"Veldhuis, Jim","last_name":"Veldhuis"},{"last_name":"Barone","first_name":"Vanessa","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Capek"},{"last_name":"Maître","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"},{"first_name":"Wayne","full_name":"Brodland, Wayne","last_name":"Brodland"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"issue":"10","intvolume":" 144","external_id":{"isi":["000402275900007"],"pmid":["28512197"]},"language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","citation":{"chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964"},"file_date_updated":"2020-07-14T12:47:39Z","status":"public","publication_status":"published","date_published":"2017-05-15T00:00:00Z","year":"2017"},{"month":"03","type":"journal_article","oa_version":"Submitted Version","page":"306 - 317","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"isi":1,"scopus_import":"1","article_processing_charge":"No","publist_id":"7074","day":"27","doi":"10.1038/ncb3492","publication_identifier":{"issn":["1465-7392"]},"volume":19,"project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"661","publication":"Nature Cell Biology","related_material":{"record":[{"id":"8350","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"title":"Friction forces position the neural anlage","date_created":"2018-12-11T11:47:46Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-14T22:31:03Z","main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"pmid":1,"abstract":[{"text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.","lang":"eng"}],"oa":1,"publisher":"Nature Publishing Group","ec_funded":1,"author":[{"orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny"},{"full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa","last_name":"Ákos"},{"first_name":"Silvia","full_name":"Grigolon, Silvia","last_name":"Grigolon"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"last_name":"Ruprecht","full_name":"Ruprecht, Verena","first_name":"Verena"},{"last_name":"Capek","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin","last_name":"Behrndt"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","last_name":"Papusheva"},{"last_name":"Tada","first_name":"Masazumi","full_name":"Tada, Masazumi"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"},{"last_name":"Vicsek","full_name":"Vicsek, Tamás","first_name":"Tamás"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"intvolume":" 19","external_id":{"pmid":["28346437"],"isi":["000397917000009"]},"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","citation":{"chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492","ieee":"M. Smutny et al., “Friction forces position the neural anlage,” Nature Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017."},"publication_status":"published","status":"public","year":"2017","date_published":"2017-03-27T00:00:00Z"}]