[{"citation":{"chicago":"Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>.","apa":"Schmied, V. (2025). <i>Human microglia impact neuronal development in retinal organoids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>","mla":"Schmied, Verena. <i>Human Microglia Impact Neuronal Development in Retinal Organoids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>.","short":"V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025.","ieee":"V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025.","ista":"Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria.","ama":"Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>"},"project":[{"grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"alternative_title":["ISTA Thesis"],"status":"public","day":"24","file_date_updated":"2025-07-30T09:29:09Z","oa":1,"date_published":"2025-07-24T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2026-08-12T08:45:16Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","type":"dissertation","_id":"20074","corr_author":"1","file":[{"checksum":"d09f9984002353ad7442358394919bf3","relation":"source_file","access_level":"closed","date_updated":"2025-07-30T08:47:53Z","file_size":43566093,"file_id":"20086","creator":"vhuebsch","date_created":"2025-07-30T08:47:53Z","file_name":"PhD_Thesis_Schmied.zip","content_type":"application/x-zip-compressed"},{"creator":"vhuebsch","file_name":"PhD_Thesis_Schmied.pdf","content_type":"application/pdf","date_created":"2025-07-30T08:47:46Z","file_size":13120922,"date_updated":"2025-07-30T09:29:09Z","access_level":"open_access","checksum":"4833690d7283c587f518ba98eeb2c946","relation":"main_file","file_id":"20087"}],"has_accepted_license":"1","ddc":["570"],"date_created":"2025-07-24T12:37:22Z","year":"2025","doi":"10.15479/AT-ISTA-20074","publication_identifier":{"isbn":["978-3-99078-060-2"],"issn":["2663-337X"]},"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","page":"151","publication_status":"published","abstract":[{"lang":"eng","text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development."}],"supervisor":[{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"doi_confirm":"1","title":"Human microglia impact neuronal development in retinal organoids","degree_awarded":"PhD","author":[{"full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","last_name":"Hübschmann"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11478"},{"status":"public","relation":"part_of_dissertation","id":"19593"}]}},{"corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.16373","open_access":"1"}],"date_created":"2025-03-09T23:01:28Z","year":"2025","doi":"10.2140/pmp.2025.6.281","publication_identifier":{"eissn":["2690-1005"],"issn":["2690-0998"]},"issue":"1","publication":"Probability and Mathematical Physics","article_processing_charge":"No","page":"281-325","external_id":{"arxiv":["2306.16373"]},"publication_status":"published","abstract":[{"text":"We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.","lang":"eng"}],"title":"Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Brooks","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas"}],"OA_place":"repository","volume":6,"citation":{"mla":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>.","apa":"Brooks, M., &#38; Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>","chicago":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2025. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>.","ista":"Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325.","ama":"Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. 2025;6(1):281-325. doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>","ieee":"M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.","short":"M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325."},"OA_type":"green","status":"public","day":"23","oa":1,"date_published":"2025-02-23T00:00:00Z","language":[{"iso":"eng"}],"month":"02","date_updated":"2026-08-12T08:44:53Z","publisher":"Mathematical Sciences Publishers","department":[{"_id":"RoSe"}],"arxiv":1,"intvolume":"         6","oa_version":"Preprint","article_type":"original","acknowledgement":"M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478.","type":"journal_article","scopus_import":"1","_id":"19372"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"13221"},{"id":"20147","relation":"dissertation_contains","status":"public"}]},"OA_place":"publisher","volume":21,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E"}],"title":"Safety and liveness of quantitative properties and automata","external_id":{"isi":["001468887900001"],"arxiv":["2307.06016"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata."}],"article_processing_charge":"Yes","publication":"Logical Methods in Computer Science","doi":"10.46298/lmcs-21(2:2)2025","publication_identifier":{"eissn":["1860-5974"]},"issue":"2","article_number":"13149","date_created":"2025-09-11T12:17:52Z","year":"2025","ddc":["000"],"has_accepted_license":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2307.06016.pdf","date_created":"2025-09-11T12:17:12Z","success":1,"creator":"esarac","file_id":"20343","file_size":709584,"date_updated":"2025-09-11T12:17:12Z","access_level":"open_access","relation":"main_file","checksum":"0b4d477bd981379724c35a4de2c176e5"}],"corr_author":"1","scopus_import":"1","_id":"20342","type":"journal_article","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","oa_version":"Published Version","intvolume":"        21","article_type":"original","date_updated":"2026-08-12T08:46:05Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"arxiv":1,"publisher":"EPI Sciences","date_published":"2025-04-08T00:00:00Z","month":"04","language":[{"iso":"eng"}],"file_date_updated":"2025-09-11T12:17:12Z","DOAJ_listed":"1","oa":1,"isi":1,"status":"public","day":"08","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","ec_funded":1,"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"citation":{"mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>.","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2025. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>.","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. 2025;21(2). doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2. EPI Sciences, 2025.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025)."},"PlanS_conform":"1"},{"date_created":"2025-08-07T15:57:57Z","year":"2025","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-20147","corr_author":"1","file":[{"file_id":"20200","relation":"source_file","checksum":"0f3015f1db36576a23d8d669afb60b41","access_level":"closed","date_updated":"2025-09-10T08:19:51Z","file_size":8884801,"date_created":"2025-08-21T09:40:28Z","content_type":"application/x-zip-compressed","file_name":"2025_Sarac_NaciEge_Thesis.zip","creator":"esarac"},{"access_level":"open_access","checksum":"332ed2fe61f580641664ec3f05d30f14","relation":"main_file","date_updated":"2025-08-21T09:40:34Z","file_size":2955584,"file_id":"20201","success":1,"creator":"esarac","date_created":"2025-08-21T09:40:34Z","content_type":"application/pdf","file_name":"2025_Sarac_NaciEge_Thesis.pdf"}],"has_accepted_license":"1","ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","first_name":"Naci E"}],"OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","id":"11775","status":"public"},{"relation":"part_of_dissertation","id":"13140","status":"deleted"},{"status":"public","relation":"part_of_dissertation","id":"19741"},{"status":"deleted","id":"19643","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17634","status":"public"},{"id":"13221","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"9356","status":"public"},{"status":"public","id":"20342","relation":"part_of_dissertation"}]},"article_processing_charge":"No","page":"149","publication_status":"published","abstract":[{"lang":"eng","text":"Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n\r\n"}],"supervisor":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"doi_confirm":"1","degree_awarded":"PhD","title":"A monitoring-oriented theory and classification of quantitative specifications","publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink.  If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"alternative_title":["ISTA Thesis"],"status":"public","day":"07","citation":{"apa":"Sarac, N. E. (2025). <i>A monitoring-oriented theory and classification of quantitative specifications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>","chicago":"Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>.","mla":"Sarac, Naci E. <i>A Monitoring-Oriented Theory and Classification of Quantitative Specifications</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>.","short":"N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025.","ieee":"N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025.","ista":"Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria.","ama":"Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>"},"project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"oa_version":"Published Version","type":"dissertation","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n","_id":"20147","file_date_updated":"2025-09-10T08:19:51Z","oa":1,"date_published":"2025-08-07T00:00:00Z","month":"08","language":[{"iso":"eng"}],"date_updated":"2026-08-12T08:46:04Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ToHe"}]},{"corr_author":"1","file":[{"file_id":"19710","access_level":"open_access","relation":"main_file","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","file_size":317925,"date_updated":"2025-05-19T07:55:51Z","date_created":"2025-05-19T07:55:51Z","content_type":"application/pdf","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","success":1,"creator":"dernst"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"],"date_created":"2025-05-18T22:02:50Z","year":"2025","doi":"10.1146/annurev-biophys-060524-102720","publication_identifier":{"eissn":["1936-1238"]},"publication":"Annual Review of Biophysics","article_processing_charge":"Yes (in subscription journal)","page":"249-274","external_id":{"isi":["001488641500013"],"pmid":["39929539"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components."}],"title":"Information processing in biochemical networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"},{"last_name":"Wolde","first_name":"Pieter Rein Ten","full_name":"Wolde, Pieter Rein Ten"}],"volume":54,"OA_place":"publisher","pmid":1,"citation":{"mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>.","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274.","short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual Review of Biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025."},"project":[{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"},{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","day":"01","status":"public","isi":1,"file_date_updated":"2025-05-19T07:55:51Z","oa":1,"date_published":"2025-05-01T00:00:00Z","language":[{"iso":"eng"}],"month":"05","date_updated":"2026-08-12T09:25:42Z","publisher":"Annual Reviews","department":[{"_id":"GaTk"}],"intvolume":"        54","oa_version":"Published Version","article_type":"original","acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","type":"journal_article","scopus_import":"1","_id":"19701"},{"ddc":["570"],"has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"808d8aa28df79d23fb661838d1fdc1be","relation":"main_file","file_size":25935563,"date_updated":"2025-07-23T08:43:01Z","file_id":"20070","success":1,"creator":"dernst","date_created":"2025-07-23T08:43:01Z","file_name":"2025_Development_Moriyama.pdf","content_type":"application/pdf"}],"quality_controlled":"1","corr_author":"1","publication":"Development","issue":"12","doi":"10.1242/dev.204261","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_number":"dev204261","year":"2025","date_created":"2025-07-21T08:10:32Z","title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","abstract":[{"text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001525252300001"],"pmid":["40576478"]},"article_processing_charge":"Yes (via OA deal)","pmid":1,"OA_place":"publisher","volume":152,"author":[{"first_name":"Yuuta","last_name":"Moriyama","id":"addc9b8c-67a0-11f0-b374-a2e094825470","orcid":"0000-0002-2853-8051","full_name":"Moriyama, Yuuta"},{"last_name":"Mitsui","first_name":"Toshiyuki","full_name":"Mitsui, Toshiyuki"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","citation":{"mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>.","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>.","apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. Company of Biologists, 2025."},"status":"public","day":"27","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Company of Biologists","department":[{"_id":"CaHe"}],"date_updated":"2026-08-12T10:01:31Z","month":"06","language":[{"iso":"eng"}],"date_published":"2025-06-27T00:00:00Z","oa":1,"file_date_updated":"2025-07-23T08:43:01Z","isi":1,"_id":"20048","scopus_import":"1","type":"journal_article","acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","article_type":"original","intvolume":"       152","oa_version":"Published Version"},{"intvolume":"        12","oa_version":"Published Version","article_type":"original","acknowledgement":"While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278).","type":"journal_article","scopus_import":"1","_id":"21343","file_date_updated":"2026-02-24T07:56:34Z","DOAJ_listed":"1","oa":1,"date_published":"2025-10-21T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2026-08-12T11:17:50Z","department":[{"_id":"TiBr"}],"arxiv":1,"publisher":"Ecole Polytechnique","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","status":"public","day":"21","citation":{"short":"T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691.","ieee":"T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025.","ama":"Browning TD, Chan S. Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2025;12:1677-1691. doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>","ista":"Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.","chicago":"Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2025. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>.","apa":"Browning, T. D., &#38; Chan, S. (2025). Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>","mla":"Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>."},"PlanS_conform":"1","project":[{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"full_name":"Chan, Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","orcid":"0000-0001-8467-4106","last_name":"Chan","first_name":"Yik Tung"}],"OA_place":"publisher","volume":12,"article_processing_charge":"Yes","page":"1677-1691","external_id":{"arxiv":["2411.09264"]},"publication_status":"published","abstract":[{"lang":"eng","text":"The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given"},{"lang":"fre","text":" Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques."}],"title":"Solubility of a resultant equation and applications","date_created":"2026-02-22T23:01:36Z","year":"2025","researchdata_availability":"no","publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"doi":"10.5802/jep.320","das_tickbox":"0","publication":"Journal de l'Ecole Polytechnique - Mathematiques","supplementarymaterial":"no","corr_author":"1","quality_controlled":"1","file":[{"access_level":"open_access","relation":"main_file","checksum":"828577ea48ac6109d3e9dd1aeddd45c4","date_updated":"2026-02-24T07:56:34Z","file_size":1003689,"file_id":"21356","success":1,"creator":"dernst","date_created":"2026-02-24T07:56:34Z","file_name":"2025_JEP_Browning.pdf","content_type":"application/pdf"}],"has_accepted_license":"1","ddc":["510"]},{"project":[{"grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","name":"New frontiers of the Manin conjecture","call_identifier":"FWF"},{"_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278","name":"Rational curves via function field analytic number theory"}],"citation":{"apa":"Browning, T. D., &#38; Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>","chicago":"Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>.","mla":"Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4, 81, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>.","ieee":"T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4. Springer Nature, 2025.","short":"T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).","ama":"Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. 2025;31(4). doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>","ista":"Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81."},"PlanS_conform":"1","day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","date_updated":"2026-08-12T12:15:32Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"TiBr"}],"date_published":"2025-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"file_date_updated":"2025-09-03T06:44:44Z","oa":1,"isi":1,"scopus_import":"1","_id":"20249","acknowledgement":"The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","type":"journal_article","intvolume":"        31","oa_version":"Published Version","article_type":"original","ddc":["500"],"has_accepted_license":"1","file":[{"content_type":"application/pdf","file_name":"2025_SelectaMathematica_Browning.pdf","date_created":"2025-09-03T06:44:44Z","success":1,"creator":"dernst","file_id":"20281","date_updated":"2025-09-03T06:44:44Z","file_size":2484757,"access_level":"open_access","checksum":"89352f1f7e8d2b367ae5f4e9bf9eb1f5","relation":"main_file"}],"quality_controlled":"1","supplementarymaterial":"yes","corr_author":"1","das_tickbox":"1","publication":"Selecta Mathematica New Series","doi":"10.1007/s00029-025-01074-1","dataavailabilitystatement":"The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page.","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"issue":"4","article_number":"81","researchdata_availability":"yes","date_created":"2025-08-31T22:01:31Z","year":"2025","title":"Integral points on cubic surfaces: heuristics and numerics","publication_status":"published","external_id":{"arxiv":["2407.16315"],"isi":["001552779800001"]},"abstract":[{"text":"We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","related_material":{"link":[{"url":"https://github.com/fwilsch/cubicpts","relation":"software"}],"record":[{"relation":"research_data","id":"22234","status":"public"}]},"volume":31,"OA_place":"publisher","author":[{"first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"last_name":"Wilsch","first_name":"Florian Alexander","full_name":"Wilsch, Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","orcid":"0000-0001-7302-8256"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Journal of Physics: Condensed Matter","doi":"10.1088/1361-648X/adebd3","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"issue":"33","article_number":"333501","date_created":"2025-08-24T22:01:30Z","year":"2025","ddc":["530"],"has_accepted_license":"1","quality_controlled":"1","file":[{"access_level":"open_access","checksum":"7309274f78bed785b158bd290337f456","relation":"main_file","file_size":8997829,"date_updated":"2025-09-02T07:22:48Z","file_id":"20271","success":1,"creator":"dernst","date_created":"2025-09-02T07:22:48Z","content_type":"application/pdf","file_name":"2025_CondensedMatter_Volpe.pdf"}],"volume":37,"OA_place":"publisher","author":[{"last_name":"Volpe","first_name":"Giorgio","full_name":"Volpe, Giorgio"},{"full_name":"Araújo, Nuno A.M.","first_name":"Nuno A.M.","last_name":"Araújo"},{"last_name":"Guix","first_name":"Maria","full_name":"Guix, Maria"},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"first_name":"Nicolas","last_name":"Martin","full_name":"Martin, Nicolas"},{"full_name":"Alvarez, Laura","last_name":"Alvarez","first_name":"Laura"},{"first_name":"Juliane","last_name":"Simmchen","full_name":"Simmchen, Juliane"},{"full_name":"Leonardo, Roberto Di","last_name":"Leonardo","first_name":"Roberto Di"},{"full_name":"Pellicciotta, Nicola","last_name":"Pellicciotta","first_name":"Nicola"},{"full_name":"Martinet, Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","orcid":"0000-0002-2916-6632","last_name":"Martinet","first_name":"Quentin"},{"first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Ng, Wai Kit","last_name":"Ng","first_name":"Wai Kit"},{"first_name":"Dhruv","last_name":"Saxena","full_name":"Saxena, Dhruv"},{"full_name":"Sapienza, Riccardo","first_name":"Riccardo","last_name":"Sapienza"},{"last_name":"Nadine","first_name":"Sara","full_name":"Nadine, Sara"},{"first_name":"João F.","last_name":"Mano","full_name":"Mano, João F."},{"full_name":"Mahdavi, Reza","last_name":"Mahdavi","first_name":"Reza"},{"last_name":"Beck Adiels","first_name":"Caroline","full_name":"Beck Adiels, Caroline"},{"first_name":"Joe","last_name":"Forth","full_name":"Forth, Joe"},{"full_name":"Santangelo, Christian","last_name":"Santangelo","first_name":"Christian"},{"last_name":"Palagi","first_name":"Stefano","full_name":"Palagi, Stefano"},{"full_name":"Seok, Ji Min","first_name":"Ji Min","last_name":"Seok"},{"full_name":"Webster-Wood, Victoria A.","first_name":"Victoria A.","last_name":"Webster-Wood"},{"first_name":"Shuhong","last_name":"Wang","full_name":"Wang, Shuhong"},{"full_name":"Yao, Lining","first_name":"Lining","last_name":"Yao"},{"full_name":"Aghakhani, Amirreza","first_name":"Amirreza","last_name":"Aghakhani"},{"first_name":"Thomas","last_name":"Barois","full_name":"Barois, Thomas"},{"full_name":"Kellay, Hamid","first_name":"Hamid","last_name":"Kellay"},{"full_name":"Coulais, Corentin","last_name":"Coulais","first_name":"Corentin"},{"last_name":"Van Hecke","first_name":"Martin","full_name":"Van Hecke, Martin"},{"first_name":"Christopher J.","last_name":"Pierce","full_name":"Pierce, Christopher J."},{"first_name":"Tianyu","last_name":"Wang","full_name":"Wang, Tianyu"},{"last_name":"Chong","first_name":"Baxi","full_name":"Chong, Baxi"},{"last_name":"Goldman","first_name":"Daniel I.","full_name":"Goldman, Daniel I."},{"last_name":"Reina","first_name":"Andreagiovanni","full_name":"Reina, Andreagiovanni"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"full_name":"Volpe, Giovanni","last_name":"Volpe","first_name":"Giovanni"},{"full_name":"Beckett, Richard","first_name":"Richard","last_name":"Beckett"},{"full_name":"Nair, Sean P.","last_name":"Nair","first_name":"Sean P."},{"last_name":"Armstrong","first_name":"Rachel","full_name":"Armstrong, Rachel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Roadmap for animate matter","publication_status":"published","external_id":{"arxiv":["2407.10623"],"isi":["001550090200001"]},"abstract":[{"lang":"eng","text":"Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner."}],"article_processing_charge":"Yes (in subscription journal)","status":"public","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","citation":{"ieee":"G. Volpe <i>et al.</i>, “Roadmap for animate matter,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33. IOP Publishing, 2025.","short":"G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J. Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng, D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth, C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani, T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong, D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong, Journal of Physics: Condensed Matter 37 (2025).","ama":"Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. 2025;37(33). doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>","ista":"Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J, Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal of Physics: Condensed Matter. 37(33), 333501.","apa":"Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>","chicago":"Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>.","mla":"Volpe, Giorgio, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>."},"PlanS_conform":"1","scopus_import":"1","_id":"20218","type":"journal_article","acknowledgement":"Living Architecture is Funded by the EU Horizon 2020 Future Emerging Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6 collaborating institutions—Newcastle University, University of Trento, University of the West of England, Spanish National Research Council, Explora Biotech and Liquifer Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE) project is funded by an EU Innovation Award for the development of a bio-digital ‘brick’ prototype, a collaboration between Newcastle University, Translating Nature, and the University of the West of England (2019–2021) under EU Grant Agreement No. 851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy) is Funded by the European Union under Grant Agreement Number 101114746, which is a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton (UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish National Research Council (Spain), and Associated Partners, the University of the West of England (UK) and University of Southampton (UK). Mi-Hy is also supported through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL).","oa_version":"Published Version","intvolume":"        37","article_type":"original","date_updated":"2026-08-12T14:00:12Z","department":[{"_id":"JePa"}],"arxiv":1,"publisher":"IOP Publishing","date_published":"2025-08-18T00:00:00Z","month":"08","language":[{"iso":"eng"}],"file_date_updated":"2025-09-02T07:22:48Z","oa":1,"isi":1},{"title":"Non-linear magnetotropic susceptibility in FePS3","article_processing_charge":"Yes (via OA deal)","publication_status":"published","external_id":{"isi":["001585824100001"],"pmid":["40967257"]},"abstract":[{"lang":"eng","text":"Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work."}],"pmid":1,"author":[{"first_name":"Hamza","last_name":"Farooq","full_name":"Farooq, Hamza"},{"full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","orcid":"0000-0002-2111-4846","first_name":"Muhammad","last_name":"Nauman"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":37,"OA_place":"publisher","has_accepted_license":"1","ddc":["530"],"corr_author":"1","file":[{"file_id":"20458","date_updated":"2025-10-13T06:34:15Z","file_size":1709516,"checksum":"b182856a5a655496e149afa49ec464f3","relation":"main_file","access_level":"open_access","file_name":"2025_JourPhysicsCondMatter_Farooq.pdf","content_type":"application/pdf","date_created":"2025-10-13T06:34:15Z","creator":"dernst","success":1}],"quality_controlled":"1","doi":"10.1088/1361-648X/ae0913","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"issue":"40","publication":"Journal of Physics: Condensed Matter","date_created":"2025-10-12T22:01:26Z","year":"2025","article_number":"405801","date_published":"2025-10-06T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2026-08-12T14:00:34Z","publisher":"IOP Publishing","department":[{"_id":"KiMo"}],"isi":1,"file_date_updated":"2025-10-13T06:34:15Z","oa":1,"scopus_import":"1","_id":"20453","oa_version":"Published Version","intvolume":"        37","article_type":"original","acknowledgement":"We thank Kimberly A. Modic for her support and discussions regarding the technique in the context of a project indirectly related to, but distinct from, the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific discussions not directly related to this study, but whose insights proved helpful. We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain for informal discussions on various aspects of the technique, and to Naoya Iwahara for his thoughtful and constructive feedback. The experimental curve shown in figures 3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for granting access to the laboratory facilities. Je Geun Park provided the crystal used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge. Institutional support from the Institute of Science and Technology Austria (ISTA) is also gratefully acknowledged.","type":"journal_article","citation":{"ieee":"H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40. IOP Publishing, 2025.","short":"H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).","ama":"Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. 2025;37(40). doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>","ista":"Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. 37(40), 405801.","chicago":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>.","apa":"Farooq, H., &#38; Nauman, M. (2025). Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>","mla":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40, 405801, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>."},"PlanS_conform":"1","status":"public","day":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid"},{"citation":{"ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.","ama":"Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. 2025;22(229). doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>","ieee":"O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229. Royal Society, 2025.","short":"O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).","mla":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229, 20250202, Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>.","apa":"Ayalon, O., &#38; Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>","chicago":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>."},"day":"13","status":"public","OA_type":"closed access","publisher":"Royal Society","department":[{"_id":"SyCr"}],"date_updated":"2026-08-12T14:09:20Z","month":"08","language":[{"iso":"eng"}],"date_published":"2025-08-13T00:00:00Z","isi":1,"_id":"20219","scopus_import":"1","type":"journal_article","acknowledgement":"We acknowledge Prof. Uri Alon for introducing us to the topic of systems biology during the graduate course at the Weizmann Institute of Science, whose insights and teachings have greatly inspired this work.","article_type":"original","intvolume":"        22","oa_version":"None","quality_controlled":"1","corr_author":"1","publication":"Journal of the Royal Society Interface","issue":"229","publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"doi":"10.1098/rsif.2025.0202","article_number":"20250202","year":"2025","date_created":"2025-08-24T22:01:30Z","title":"Interplay of asexual and sexual reproduction in bifunctional insects","abstract":[{"text":"Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.","lang":"eng"}],"external_id":{"isi":["001548084900001"],"pmid":["40799050"]},"publication_status":"published","article_processing_charge":"No","pmid":1,"volume":22,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ayalon, Oran","first_name":"Oran","last_name":"Ayalon"},{"first_name":"Harikrishnan","last_name":"Rajendran","full_name":"Rajendran, Harikrishnan","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416"}]},{"citation":{"mla":"Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","chicago":"Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>.","apa":"Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton, L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>","ama":"Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>","ista":"Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","ieee":"A. Cárdenas <i>et al.</i>, “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” <i>bioRxiv</i>. .","short":"A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton, V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv (n.d.)."},"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"day":"23","status":"public","OA_type":"green","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"month":"05","language":[{"iso":"eng"}],"date_published":"2025-05-23T00:00:00Z","department":[{"_id":"SiHi"}],"date_updated":"2026-08-13T07:18:38Z","oa":1,"_id":"19762","oa_version":"Preprint","type":"preprint","acknowledgement":"We thank A. Iñigo for assistance with imaging, and members of the Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency (AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1) to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship (JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012) to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council (101118729) to V.B., who also acknowledges financial support from AEI through the “Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S).","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.22.655488","open_access":"1"}],"doi":"10.1101/2025.05.22.655488","publication":"bioRxiv","year":"2025","date_created":"2025-05-29T10:45:55Z","title":"Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_processing_charge":"No","abstract":[{"text":"The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process.","lang":"eng"}],"external_id":{"biorxivid":["10.1101/2025.05.22.655488"]},"publication_status":"submitted","biorxivid":1,"author":[{"last_name":"Cárdenas","first_name":"Adrián","full_name":"Cárdenas, Adrián"},{"full_name":"Çelik, Irem","last_name":"Çelik","first_name":"Irem"},{"full_name":"Espinós, Alexandre","first_name":"Alexandre","last_name":"Espinós"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lara","last_name":"López-González","full_name":"López-González, Lara"},{"first_name":"Lucia","last_name":"del-Valle-Anton","full_name":"del-Valle-Anton, Lucia"},{"full_name":"Fernández, Virginia","last_name":"Fernández","first_name":"Virginia"},{"full_name":"Amin, Salma","last_name":"Amin","first_name":"Salma"},{"full_name":"Negri, Enrico","last_name":"Negri","first_name":"Enrico"},{"first_name":"Eduardo Fernández","last_name":"Ortuño","full_name":"Ortuño, Eduardo Fernández"},{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Borrell, Víctor","last_name":"Borrell","first_name":"Víctor"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository"},{"OA_type":"green","year":"2025","date_created":"2025-05-20T10:19:29Z","day":"07","publication":"bioRxiv","status":"public","doi":"10.1101/2025.05.07.652665","citation":{"mla":"Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","chicago":"Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>.","apa":"Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., &#38; Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>","ista":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","ama":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>","short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.).","ieee":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” <i>bioRxiv</i>. ."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.07.652665"}],"acknowledgement":"We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n","type":"preprint","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","author":[{"last_name":"Varela-Martínez","first_name":"I","full_name":"Varela-Martínez, I"},{"id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","last_name":"Villalba Requena","first_name":"Ana"},{"full_name":"Garcia-Marqués, J.","last_name":"Garcia-Marqués","first_name":"J."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Nieto, M.","first_name":"M.","last_name":"Nieto"}],"_id":"19717","abstract":[{"text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.","lang":"eng"}],"oa":1,"publication_status":"submitted","article_processing_charge":"No","department":[{"_id":"SiHi"}],"date_updated":"2026-08-13T07:16:48Z","month":"05","title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","language":[{"iso":"eng"}],"date_published":"2025-05-07T00:00:00Z"},{"citation":{"mla":"Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, 2411.00246, doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>.","chicago":"Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>.","apa":"Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., &#38; Locatello, F. (n.d.). ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>","ista":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246.","ama":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>","ieee":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual transformer alignment with spectral decomposition,” <i>arXiv</i>. .","short":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.)."},"day":"14","status":"public","OA_type":"green","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"FrLo"}],"arxiv":1,"date_updated":"2026-08-13T07:33:41Z","month":"04","language":[{"iso":"eng"}],"date_published":"2025-04-14T00:00:00Z","oa":1,"_id":"19674","type":"preprint","acknowledgement":"The authors gratefully acknowledge Volkan Cevher for an insightful discussion about sparse recovery algorithms, Alex Smola for valuable feedback on the experiments, and Marco Baroni for an engaging conversation on the phenomenon of head specialization in NLP.\r\n","oa_version":"Preprint","ddc":["000"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.00246","open_access":"1"}],"has_accepted_license":"1","publication":"arXiv","doi":"10.48550/arXiv.2411.00246","article_number":"2411.00246","year":"2025","date_created":"2025-05-11T22:02:41Z","title":"ResiDual transformer alignment with spectral decomposition","abstract":[{"lang":"eng","text":"When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets)."}],"publication_status":"submitted","external_id":{"arxiv":["2411.00246"]},"article_processing_charge":"No","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Basile, Lorenzo","first_name":"Lorenzo","last_name":"Basile"},{"first_name":"Valentino","last_name":"Maiorca","full_name":"Maiorca, Valentino"},{"first_name":"Luca","last_name":"Bortolussi","full_name":"Bortolussi, Luca"},{"first_name":"Emanuele","last_name":"Rodolà","full_name":"Rodolà, Emanuele"},{"first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}]},{"_id":"20167","oa_version":"Published Version","type":"dissertation","acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","language":[{"iso":"eng"}],"month":"08","date_published":"2025-08-13T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-08-13T13:05:37Z","file_date_updated":"2026-08-13T13:05:36Z","alternative_title":["ISTA Thesis"],"status":"public","day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria.","ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>","apa":"Schön, H. (2025). <i>The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>","chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>.","mla":"Schön, Hanna. <i>The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>."},"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"grant_number":"ALTF 302-2019","_id":"23813290-32DE-11EA-91FC-C7463DDC885E","name":"Control of gene expression at the endoplasmic reticulum"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","full_name":"Schön, Hanna","first_name":"Hanna","last_name":"Schön"}],"OA_place":"publisher","degree_awarded":"PhD","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","supervisor":[{"first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"}],"doi_confirm":"1","page":"171","article_processing_charge":"No","publication_status":"published","doi":"10.15479/AT-ISTA-20167","publication_identifier":{"isbn":["978-3-99078-061-9"],"issn":["2663-337X"]},"year":"2025","date_created":"2025-08-13T11:13:13Z","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"file_id":"20311","access_level":"closed","relation":"source_file","checksum":"b40c74404b8d9593802dabf57bfdf10f","date_updated":"2025-09-09T08:57:04Z","file_size":78812587,"date_created":"2025-09-08T14:33:50Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_Schoen_Hanna_Thesis.docx","creator":"hschoen"},{"access_level":"closed","relation":"main_file","checksum":"16abc3ff66396ce2457fe07ffa8bed90","embargo_to":"open_access","file_size":9667057,"date_updated":"2026-08-13T13:05:36Z","embargo":"2027-03-15","file_id":"20347","creator":"hschoen","date_created":"2025-09-11T14:20:59Z","content_type":"application/pdf","file_name":"2025_Schoen_Hanna_Thesis.pdf"}]},{"article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins."}],"external_id":{"pmid":["41016549"]},"publication_status":"published","title":"A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Knödlstorfer, Sonja","last_name":"Knödlstorfer","first_name":"Sonja"},{"id":"334a5e40-8747-11f0-b671-ba1f5154b4b4","full_name":"Toscano, Giorgia","last_name":"Toscano","first_name":"Giorgia"},{"first_name":"Aleksandra L.","last_name":"Ptaszek","full_name":"Ptaszek, Aleksandra L."},{"first_name":"Georg","last_name":"Kontaxis","full_name":"Kontaxis, Georg"},{"full_name":"Napoli, Federico","orcid":"0000-0002-9043-136X","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","first_name":"Federico","last_name":"Napoli"},{"last_name":"Schneider","first_name":"Jakob","id":"64368429-eb97-11eb-a6c2-c980b1f44415","full_name":"Schneider, Jakob"},{"last_name":"Maier","first_name":"Katharina","full_name":"Maier, Katharina"},{"full_name":"Kapitonova, Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","first_name":"Anna"},{"last_name":"Lichtenecker","first_name":"Roman J.","full_name":"Lichtenecker, Roman J."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"},{"full_name":"Konrat, Robert","last_name":"Konrat","first_name":"Robert"}],"OA_place":"publisher","volume":437,"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"pmid":1,"quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-12-30T10:29:08Z","content_type":"application/pdf","file_name":"2025_JourMolecularBiology_Knoedlstorfer.pdf","access_level":"open_access","checksum":"feb92f9c79032c261165f4ca573f444a","relation":"main_file","file_size":3076611,"date_updated":"2025-12-30T10:29:08Z","file_id":"20915"}],"has_accepted_license":"1","ddc":["540"],"year":"2025","date_created":"2025-10-26T23:01:35Z","article_number":"169465","issue":"23","publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"doi":"10.1016/j.jmb.2025.169465","publication":"Journal of Molecular Biology","oa":1,"file_date_updated":"2025-12-30T10:29:08Z","month":"12","language":[{"iso":"eng"}],"date_published":"2025-12-01T00:00:00Z","publisher":"Elsevier","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"date_updated":"2026-08-13T14:19:02Z","article_type":"original","intvolume":"       437","oa_version":"Published Version","type":"journal_article","acknowledgement":"A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70.","_id":"20538","scopus_import":"1","PlanS_conform":"1","citation":{"ama":"Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>","ista":"Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465.","ieee":"S. Knödlstorfer <i>et al.</i>, “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.","short":"S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025).","mla":"Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169465, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>.","apa":"Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>","chicago":"Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>."},"project":[{"_id":"bdb9578d-d553-11ed-ba76-ed5d39fce6f0","grant_number":"I06223","name":"Structure and mechanism of the mitochondrial MIM insertase"},{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"}],"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01"},{"PlanS_conform":"1","citation":{"ieee":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P. Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.","short":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda, Journal of Molecular Biology 437 (2025).","ama":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>","ista":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 437(23), 169379.","chicago":"Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>.","apa":"Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., &#38; Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>","mla":"Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169379, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>."},"project":[{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"}],"day":"01","status":"public","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"12","date_published":"2025-12-01T00:00:00Z","publisher":"Elsevier","department":[{"_id":"PaSc"}],"date_updated":"2026-08-13T14:19:01Z","isi":1,"oa":1,"file_date_updated":"2025-12-29T14:51:40Z","_id":"20258","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":"       437","acknowledgement":"This work was supported financially by the Austrian Science Fund (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent support of the NMR facility.","type":"journal_article","has_accepted_license":"1","ddc":["540"],"corr_author":"1","quality_controlled":"1","file":[{"file_size":2270555,"date_updated":"2025-12-29T14:51:40Z","access_level":"open_access","checksum":"90d50594d8ea9860ac5da41297992847","relation":"main_file","file_id":"20876","success":1,"creator":"dernst","file_name":"2025_JourMolecularBiology_Rohden.pdf","content_type":"application/pdf","date_created":"2025-12-29T14:51:40Z"}],"issue":"23","doi":"10.1016/j.jmb.2025.169379","publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"publication":"Journal of Molecular Biology","year":"2025","date_created":"2025-08-31T22:01:33Z","article_number":"169379","title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR."}],"publication_status":"published","external_id":{"isi":["001618289100020"]},"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"19956"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Darja","last_name":"Rohden","id":"81dc668a-19fa-11f0-bf31-d56534059ef3","full_name":"Rohden, Darja"},{"id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","orcid":"0000-0002-9043-136X","full_name":"Napoli, Federico","first_name":"Federico","last_name":"Napoli"},{"last_name":"Kapitonova","first_name":"Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","full_name":"Kapitonova, Anna"},{"last_name":"Tatman","first_name":"Benjamin","full_name":"Tatman, Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"},{"full_name":"Lichtenecker, Roman J.","last_name":"Lichtenecker","first_name":"Roman J."},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"OA_place":"publisher","volume":437},{"related_material":{"record":[{"relation":"used_in_publication","id":"20258","status":"public"}]},"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"author":[{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","title":"Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme","abstract":[{"lang":"eng","text":"The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_processing_charge":"No","doi":"10.15479/AT-ISTA-19956","contributor":[{"first_name":"Darja","contributor_type":"researcher","last_name":"Rohden"},{"last_name":"Napoli","contributor_type":"researcher","first_name":"Federico"},{"contributor_type":"researcher","last_name":"Tatman","first_name":"Ben"},{"first_name":"Paul","contributor_type":"researcher","last_name":"Schanda"}],"year":"2025","date_created":"2025-07-03T04:21:37Z","ddc":["572"],"has_accepted_license":"1","file":[{"file_id":"19960","date_updated":"2025-07-03T10:30:14Z","file_size":1160,"relation":"main_file","checksum":"a2ef61aa9fb5313c7d426913eb0482c0","access_level":"open_access","file_name":"README","content_type":"application/octet-stream","date_created":"2025-07-03T10:30:14Z","creator":"pschanda","success":1},{"file_id":"19961","access_level":"open_access","relation":"main_file","checksum":"8fb77b96d0fcc95c9903005652207a8c","date_updated":"2025-07-03T10:30:55Z","file_size":128597184,"date_created":"2025-07-03T10:30:55Z","content_type":"application/zip","file_name":"data_Arg_MASNMR_Rohden.zip","success":1,"creator":"pschanda"},{"file_id":"20172","checksum":"a60cc16d20b089c4bef94040a99cfba5","relation":"main_file","access_level":"open_access","file_size":4766564,"date_updated":"2025-08-14T07:06:58Z","date_created":"2025-08-14T07:06:58Z","file_name":"20240903_ubi_DN_Argd1C13_2D_spectra.tar.xz","content_type":"application/x-xz","creator":"pschanda","success":1}],"corr_author":"1","_id":"19956","type":"research_data","oa_version":"Published Version","department":[{"_id":"PaSc"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-08-13T14:19:01Z","month":"07","date_published":"2025-07-03T00:00:00Z","oa":1,"file_date_updated":"2025-08-14T07:06:58Z","day":"03","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"}],"citation":{"ieee":"P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025.","short":"P. Schanda, (2025).","ista":"Schanda P. 2025. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>.","ama":"Schanda P. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>","chicago":"Schanda, Paul. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">https://doi.org/10.15479/AT-ISTA-19956</a>.","apa":"Schanda, P. (2025). Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">https://doi.org/10.15479/AT-ISTA-19956</a>","mla":"Schanda, Paul. <i>Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>."}},{"citation":{"apa":"Monzer, A. (2025). <i>Cell-surface auxin signaling: Linking molecular pathways to plant development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>","chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>.","mla":"Monzer, Aline. <i>Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>.","ieee":"A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.","ista":"Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","ama":"Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>"},"alternative_title":["ISTA Thesis"],"day":"13","status":"public","date_published":"2025-03-13T00:00:00Z","month":"03","language":[{"iso":"eng"}],"date_updated":"2026-08-14T09:33:46Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2025-04-01T07:55:27Z","oa":1,"_id":"19395","oa_version":"Published Version","type":"dissertation","acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research.","has_accepted_license":"1","ddc":["580"],"corr_author":"1","file":[{"creator":"amonzer","success":1,"date_created":"2025-03-12T14:14:49Z","content_type":"application/pdf","file_name":"Final Thesis Aline Monzer.pdf","checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7","relation":"main_file","access_level":"open_access","file_size":13119670,"date_updated":"2025-03-12T14:14:49Z","file_id":"19396"},{"creator":"amonzer","file_name":"Thesis Aline.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-03-12T14:15:19Z","file_size":13774837,"date_updated":"2025-04-01T07:55:27Z","checksum":"a353ce1ee2eabce37bca35499e76dbf1","relation":"source_file","access_level":"closed","file_id":"19397"}],"doi":"10.15479/AT-ISTA-19395","publication_identifier":{"eisbn":["978-3-99078-054-1"],"eissn":["2663-337X"]},"date_created":"2025-03-12T14:25:42Z","year":"2025","doi_confirm":"1","supervisor":[{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"title":"Cell-surface auxin signaling: Linking molecular pathways to plant development","degree_awarded":"PhD","article_processing_charge":"No","page":"160","publication_status":"published","abstract":[{"lang":"eng","text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12291"},{"status":"public","id":"14826","relation":"part_of_dissertation"},{"status":"public","id":"19399","relation":"part_of_dissertation"},{"id":"19398","relation":"part_of_dissertation","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"}],"OA_place":"publisher"},{"oa":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2025-02-20T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"date_updated":"2026-08-14T09:33:45Z","oa_version":"Published Version","acknowledgement":"We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).","type":"preprint","_id":"19399","citation":{"ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. .","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.).","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>.","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>."},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Cell surface receptor complexes for auxin signaling in plants","grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"OA_type":"green","status":"public","day":"20","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena."}],"publication_status":"draft","title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","author":[{"last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"last_name":"Vladimirtsev","first_name":"Dmitrii","full_name":"Vladimirtsev, Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek"},{"full_name":"Yu, Yongfan","first_name":"Yongfan","last_name":"Yu"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","last_name":"Gelová"},{"last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny"},{"first_name":"Meng","last_name":"Chen","full_name":"Chen, Meng"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li"},{"full_name":"Marques-Bueno, Maria Mar","last_name":"Marques-Bueno","first_name":"Maria Mar"},{"full_name":"Quddoos, Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","last_name":"Quddoos","first_name":"Zainab"},{"last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","first_name":"Ivan"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"status":"public","id":"20656","relation":"later_version"},{"relation":"dissertation_contains","id":"20364","status":"public"},{"relation":"dissertation_contains","id":"19395","status":"public"}]},"corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"ddc":["580"],"year":"2025","date_created":"2025-03-13T08:36:48Z","doi":"10.1101/2022.11.30.518503","publication":"bioRxiv","das_tickbox":"1"}]