[{"month":"08","external_id":{"isi":["001559806100033"],"pmid":["40864718"]},"quality_controlled":"1","date_updated":"2025-09-30T14:40:27Z","title":"Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned","PlanS_conform":"1","isi":1,"acknowledgement":"We thank A.-M. Lawrence-Dörner and B. Berkenfeld for technical assistance and the members of the Kümmel Lab for constructive feedback. We are grateful to C. Ungermann and L. Langemeyer for insightful discussions and to F. Barr for providing plasmids encoding Fuzzy, Inturned, Rab23, and Rsg1. The template clone Flag-ciBAR1 was a gift from K.-I. Takemaru (Addgene, plasmid #200440). We thank the Bloomington Drosophila Stock center (BDSC) and DSHB for providing fly stocks and antibodies. This work was supported by the German Research Foundation (DFG) through the grants SFB1557-P10 (D.K.), SFB1557-P11 (A.M.), and SFB1577-P6, PA517/12-2, PA517/14-1, PA517/15-1, and PA517/16-1 (A.P.). Cryo-EM data were collected at the infrastructure of the University of Osnabrück, funded by the DFG (project number 455249646). J.-H.S. was supported by the Friedrich-Ebert Foundation. M.L. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement number 101045340).","article_processing_charge":"Yes","date_published":"2025-08-29T00:00:00Z","volume":11,"publication_identifier":{"eissn":["2375-2548"]},"type":"journal_article","status":"public","OA_type":"gold","publisher":"AAAS","oa_version":"Published Version","abstract":[{"text":"Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies and functional characterization in flies reveal an essential function of RMC1/Bulli as mediator of GEF complex membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.","lang":"eng"}],"scopus_import":"1","citation":{"chicago":"Wilmes, Stephan, Jesse Tönjes, Maik Drechsler, Anita Ruf, Jan Hannes Schäfer, Anna Lürick, Dovile Januliene, et al. “Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adx2893.","apa":"Wilmes, S., Tönjes, J., Drechsler, M., Ruf, A., Schäfer, J. H., Lürick, A., … Kümmel, D. (2025). Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adx2893","short":"S. Wilmes, J. Tönjes, M. Drechsler, A. Ruf, J.H. Schäfer, A. Lürick, D. Januliene, S. Apelt, D. Di Iorio, S.V. Wegner, M. Loose, A. Moeller, A. Paululat, D. Kümmel, Science Advances 11 (2025) eadx2893.","ista":"Wilmes S, Tönjes J, Drechsler M, Ruf A, Schäfer JH, Lürick A, Januliene D, Apelt S, Di Iorio D, Wegner SV, Loose M, Moeller A, Paululat A, Kümmel D. 2025. Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned. Science Advances. 11(35), eadx2893.","mla":"Wilmes, Stephan, et al. “Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.” Science Advances, vol. 11, no. 35, AAAS, 2025, p. eadx2893, doi:10.1126/sciadv.adx2893.","ieee":"S. Wilmes et al., “Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned,” Science Advances, vol. 11, no. 35. AAAS, p. eadx2893, 2025.","ama":"Wilmes S, Tönjes J, Drechsler M, et al. Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned. Science Advances. 2025;11(35):eadx2893. doi:10.1126/sciadv.adx2893"},"file":[{"relation":"main_file","date_updated":"2025-09-15T07:23:12Z","content_type":"application/pdf","file_size":3434827,"access_level":"open_access","file_name":"2025_ScienceAdvance_Wilmes.pdf","creator":"dernst","checksum":"a3de801f3c6c1deadd7099d965db799a","file_id":"20355","success":1,"date_created":"2025-09-15T07:23:12Z"}],"doi":"10.1126/sciadv.adx2893","project":[{"name":"Synthetic and structural biology of Rab GTPase networks","_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","grant_number":"101045340"}],"publication_status":"published","oa":1,"intvolume":" 11","file_date_updated":"2025-09-15T07:23:12Z","author":[{"last_name":"Wilmes","first_name":"Stephan","full_name":"Wilmes, Stephan"},{"full_name":"Tönjes, Jesse","last_name":"Tönjes","first_name":"Jesse"},{"full_name":"Drechsler, Maik","first_name":"Maik","last_name":"Drechsler"},{"first_name":"Anita","last_name":"Ruf","full_name":"Ruf, Anita"},{"first_name":"Jan Hannes","last_name":"Schäfer","full_name":"Schäfer, Jan Hannes"},{"full_name":"Lürick, Anna","first_name":"Anna","last_name":"Lürick"},{"full_name":"Januliene, Dovile","first_name":"Dovile","last_name":"Januliene"},{"full_name":"Apelt, Steven","last_name":"Apelt","first_name":"Steven"},{"first_name":"Daniele","last_name":"Di Iorio","full_name":"Di Iorio, Daniele"},{"last_name":"Wegner","first_name":"Seraphine V.","full_name":"Wegner, Seraphine V."},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Moeller","first_name":"Arne","full_name":"Moeller, Arne"},{"last_name":"Paululat","first_name":"Achim","full_name":"Paululat, Achim"},{"full_name":"Kümmel, Daniel","first_name":"Daniel","last_name":"Kümmel"}],"ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2025-09-14T22:01:32Z","article_type":"original","year":"2025","DOAJ_listed":"1","OA_place":"publisher","publication":"Science Advances","day":"29","page":"eadx2893","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"MaLo"}],"issue":"35","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"20351","pmid":1},{"date_created":"2025-09-14T22:01:32Z","article_type":"original","year":"2025","doi":"10.1038/s41550-025-02610-x","publication_status":"published","oa":1,"intvolume":" 9","author":[{"first_name":"H.","last_name":"Sana","full_name":"Sana, H."},{"first_name":"T.","last_name":"Shenar","full_name":"Shenar, T."},{"last_name":"Bodensteiner","first_name":"J.","full_name":"Bodensteiner, J."},{"last_name":"Britavskiy","first_name":"N.","full_name":"Britavskiy, N."},{"full_name":"Langer, N.","last_name":"Langer","first_name":"N."},{"full_name":"Lennon, D. 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A."},{"full_name":"Crowther, P. A.","last_name":"Crowther","first_name":"P. A."},{"full_name":"Deshmukh, K.","last_name":"Deshmukh","first_name":"K."},{"last_name":"Evans","first_name":"C. J.","full_name":"Evans, C. J."},{"full_name":"Fabry, M.","last_name":"Fabry","first_name":"M."},{"first_name":"M.","last_name":"Gieles","full_name":"Gieles, M."},{"full_name":"Gilkis, A.","first_name":"A.","last_name":"Gilkis"},{"full_name":"González-Torà, G.","first_name":"G.","last_name":"González-Torà"},{"full_name":"Gräfener, G.","last_name":"Gräfener","first_name":"G."},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911"},{"first_name":"C.","last_name":"Hawcroft","full_name":"Hawcroft, C."},{"full_name":"Hénault-Brunet, V.","last_name":"Hénault-Brunet","first_name":"V."},{"full_name":"Herrero, A.","last_name":"Herrero","first_name":"A."},{"last_name":"Holgado","first_name":"G.","full_name":"Holgado, G."},{"full_name":"Izzard, R. G.","first_name":"R. G.","last_name":"Izzard"},{"full_name":"De Koter, A.","first_name":"A.","last_name":"De Koter"},{"last_name":"Janssens","first_name":"S.","full_name":"Janssens, S."},{"full_name":"Johnston, C.","first_name":"C.","last_name":"Johnston"},{"last_name":"Josiek","first_name":"J.","full_name":"Josiek, J."},{"last_name":"Justham","first_name":"S.","full_name":"Justham, S."},{"full_name":"Kalari, V. M.","first_name":"V. M.","last_name":"Kalari"},{"last_name":"Klencki","first_name":"J.","full_name":"Klencki, J."},{"full_name":"Kubát, J.","first_name":"J.","last_name":"Kubát"},{"first_name":"B.","last_name":"Kubátová","full_name":"Kubátová, B."},{"full_name":"Lefever, R. R.","last_name":"Lefever","first_name":"R. R."},{"full_name":"Van Loon, J. Th","first_name":"J. Th","last_name":"Van Loon"},{"full_name":"Ludwig, B.","first_name":"B.","last_name":"Ludwig"},{"last_name":"Mackey","first_name":"J.","full_name":"Mackey, J."},{"full_name":"Maíz Apellániz, J.","last_name":"Maíz Apellániz","first_name":"J."},{"full_name":"Maravelias, G.","last_name":"Maravelias","first_name":"G."},{"first_name":"P.","last_name":"Marchant","full_name":"Marchant, P."},{"full_name":"Mazeh, T.","last_name":"Mazeh","first_name":"T."},{"full_name":"Menon, A.","last_name":"Menon","first_name":"A."},{"last_name":"Moe","first_name":"M.","full_name":"Moe, M."},{"full_name":"Najarro, F.","last_name":"Najarro","first_name":"F."},{"last_name":"Oskinova","first_name":"L. M.","full_name":"Oskinova, L. M."},{"last_name":"Ovadia","first_name":"R.","full_name":"Ovadia, R."},{"full_name":"Pauli, D.","first_name":"D.","last_name":"Pauli"},{"first_name":"M.","last_name":"Pawlak","full_name":"Pawlak, M."},{"full_name":"Ramachandran, V.","last_name":"Ramachandran","first_name":"V."},{"full_name":"Renzo, M.","last_name":"Renzo","first_name":"M."},{"last_name":"Rocha","first_name":"D. F.","full_name":"Rocha, D. F."},{"first_name":"A. A.C.","last_name":"Sander","full_name":"Sander, A. A.C."},{"first_name":"F. R.N.","last_name":"Schneider","full_name":"Schneider, F. R.N."},{"first_name":"A.","last_name":"Schootemeijer","full_name":"Schootemeijer, A."},{"full_name":"Schösser, E. C.","first_name":"E. C.","last_name":"Schösser"},{"full_name":"Schürmann, C.","first_name":"C.","last_name":"Schürmann"},{"full_name":"Sen, K.","last_name":"Sen","first_name":"K."},{"first_name":"S.","last_name":"Shahaf","full_name":"Shahaf, S."},{"last_name":"Simón-Díaz","first_name":"S.","full_name":"Simón-Díaz, S."},{"full_name":"Van Son, L. A.C.","last_name":"Van Son","first_name":"L. A.C."},{"first_name":"M.","last_name":"Stoop","full_name":"Stoop, M."},{"last_name":"Toonen","first_name":"S.","full_name":"Toonen, S."},{"full_name":"Tramper, F.","last_name":"Tramper","first_name":"F."},{"first_name":"R.","last_name":"Valli","full_name":"Valli, R."},{"last_name":"Vigna-Gómez","first_name":"A.","full_name":"Vigna-Gómez, A."},{"last_name":"Vink","first_name":"J. S.","full_name":"Vink, J. S."},{"full_name":"Wang, C.","last_name":"Wang","first_name":"C."},{"last_name":"Willcox","first_name":"R.","full_name":"Willcox, R."}],"language":[{"iso":"eng"}],"page":"1337-1346","department":[{"_id":"YlGo"}],"_id":"20352","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","publication":"Nature Astronomy","day":"02","title":"A high fraction of close massive binary stars at low metallicity","acknowledgement":"Based on data collected at the European Southern Observatory (ESO) under programme ID 112.25R7. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 and Horizon Europe research and innovation programme (grant agreement numbers 772225: MULTIPLES, 772086: ASSESS and 945806: TEL-STARS, ADG101054731: Stellar-BHs-SDSS-V, and 101164755: METAL). This research was supported by the Israel Science Foundation (ISF) under grant number 0603225041. We acknowledge support from the Science and Technology Facilities Council (research grant ST/V000853/1 and ST/V000233/1), UK Research and Innovation (UKRI) and the UK government’s ERC Horizon Europe funding guarantee (grant number EP/Y031059/1), a Royal Society University Research Fellowship (grant number URF\\R1\\231631), a Royal Society–Science Foundation Ireland University Research Fellowship, the German Deutsche Forschungsgemeinschaft (Project-ID 496854903, 445674056 and 443790621, Germany’s Excellence Strategy EXC 2181/1-390900948), the Klaus Tschira Foundation, the JSPS Kakenhi Grant-in-Aid for Scientific Research (23K19071) and international fellowships (at the Graduate school of Science, Tokyo University), the Australian Research Council (ARC) Centre of Excellence for Gravitational Wave Discovery (OzGrav; project number CE230100016), the Deutsches Zentrum für Luft und Raumfahrt (DLR) grants FKZ 50OR2005 and 50OR2306, Agencia Española de Investigación (AEI) of the Spanish Ministerio de Ciencia Innovación y Universidades (MICIU) and the European Regional Development Fund, FEDER and Severo Ochoa Programme (grants PID2021-122397NB-C21 and CEX2019-000920-S), the NextGeneration EU/PRTR and MIU (UNI/551/2021) trough grant Margarita Salas-UL, the CAPES-Br and FAPERJ/DSC-10 (SEI-260003/001630/2023), MCIN/AEI/10.13039/501100011033 by ‘ERDF A way of making Europe’ (grants PID2019-105552RB-C41 and PID2022-137779OB-C41, PID2021-125485NB-C22, CEX2019-000918-M) funded by MCIN/AEI/10.13039/501100011033 (State Agency for Research of the Spanish Ministry of Science and Innovation) and SGR-2021-01069 (AGAUR), the Spanish Government Ministerio de Ciencia e Innovación and Agencia Estatal de Investigación (10.13 039/501 100 011 033; grant PID2022-136 640 NB-C22), the Consejo Superior de Investigaciones Científicas (CSIC; grant 2022-AEP 005), the Polish National Agency for Academic Exchange (BEKKER fellowship BPN/BEK/2022/1/00106) and National Science Center (NCN, Poland; grant number OPUS 2021/41/B/ST9/00757), the ‘La Caixa’ Foundation (ID 100010434) under the fellowship code LCF/BQ/PI23/11970035, the Research foundation Flanders (FWO) PhD fellowship under project 11E1721N and senior postdoctoral fellowship under number 12ZY523N, and the Netherlands Research Council NWO (VIDI 203.061 grant).","isi":1,"date_published":"2025-09-02T00:00:00Z","arxiv":1,"article_processing_charge":"No","volume":9,"month":"09","external_id":{"isi":["001568077900001"],"arxiv":["2509.12488"]},"quality_controlled":"1","date_updated":"2025-12-30T10:27:05Z","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2509.12488","open_access":"1"}],"oa_version":"Preprint","citation":{"ama":"Sana H, Shenar T, Bodensteiner J, et al. A high fraction of close massive binary stars at low metallicity. Nature Astronomy. 2025;9:1337-1346. doi:10.1038/s41550-025-02610-x","ieee":"H. Sana et al., “A high fraction of close massive binary stars at low metallicity,” Nature Astronomy, vol. 9. Springer Nature, pp. 1337–1346, 2025.","short":"H. Sana, T. Shenar, J. Bodensteiner, N. Britavskiy, N. Langer, D.J. Lennon, L. Mahy, I. Mandel, S.E. De Mink, L.R. Patrick, J.I. Villaseñor, M. Dirickx, M. Abdul-Masih, L.A. Almeida, F. Backs, S.R. Berlanas, M. Bernini-Peron, D.M. Bowman, V.A. Bronner, P.A. Crowther, K. Deshmukh, C.J. Evans, M. Fabry, M. Gieles, A. Gilkis, G. González-Torà, G. Gräfener, Y.L.L. Götberg, C. Hawcroft, V. Hénault-Brunet, A. Herrero, G. Holgado, R.G. Izzard, A. De Koter, S. Janssens, C. Johnston, J. Josiek, S. Justham, V.M. Kalari, J. Klencki, J. Kubát, B. Kubátová, R.R. Lefever, J.T. Van Loon, B. Ludwig, J. Mackey, J. Maíz Apellániz, G. Maravelias, P. Marchant, T. Mazeh, A. Menon, M. Moe, F. Najarro, L.M. Oskinova, R. Ovadia, D. Pauli, M. Pawlak, V. Ramachandran, M. Renzo, D.F. Rocha, A.A.C. Sander, F.R.N. Schneider, A. Schootemeijer, E.C. Schösser, C. Schürmann, K. Sen, S. Shahaf, S. Simón-Díaz, L.A.C. Van Son, M. Stoop, S. Toonen, F. Tramper, R. Valli, A. Vigna-Gómez, J.S. Vink, C. Wang, R. Willcox, Nature Astronomy 9 (2025) 1337–1346.","ista":"Sana H, Shenar T, Bodensteiner J, Britavskiy N, Langer N, Lennon DJ, Mahy L, Mandel I, De Mink SE, Patrick LR, Villaseñor JI, Dirickx M, Abdul-Masih M, Almeida LA, Backs F, Berlanas SR, Bernini-Peron M, Bowman DM, Bronner VA, Crowther PA, Deshmukh K, Evans CJ, Fabry M, Gieles M, Gilkis A, González-Torà G, Gräfener G, Götberg YLL, Hawcroft C, Hénault-Brunet V, Herrero A, Holgado G, Izzard RG, De Koter A, Janssens S, Johnston C, Josiek J, Justham S, Kalari VM, Klencki J, Kubát J, Kubátová B, Lefever RR, Van Loon JT, Ludwig B, Mackey J, Maíz Apellániz J, Maravelias G, Marchant P, Mazeh T, Menon A, Moe M, Najarro F, Oskinova LM, Ovadia R, Pauli D, Pawlak M, Ramachandran V, Renzo M, Rocha DF, Sander AAC, Schneider FRN, Schootemeijer A, Schösser EC, Schürmann C, Sen K, Shahaf S, Simón-Díaz S, Van Son LAC, Stoop M, Toonen S, Tramper F, Valli R, Vigna-Gómez A, Vink JS, Wang C, Willcox R. 2025. A high fraction of close massive binary stars at low metallicity. Nature Astronomy. 9, 1337–1346.","mla":"Sana, H., et al. “A High Fraction of Close Massive Binary Stars at Low Metallicity.” Nature Astronomy, vol. 9, Springer Nature, 2025, pp. 1337–46, doi:10.1038/s41550-025-02610-x.","chicago":"Sana, H., T. Shenar, J. Bodensteiner, N. Britavskiy, N. Langer, D. J. Lennon, L. Mahy, et al. “A High Fraction of Close Massive Binary Stars at Low Metallicity.” Nature Astronomy. Springer Nature, 2025. https://doi.org/10.1038/s41550-025-02610-x.","apa":"Sana, H., Shenar, T., Bodensteiner, J., Britavskiy, N., Langer, N., Lennon, D. J., … Willcox, R. (2025). A high fraction of close massive binary stars at low metallicity. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-025-02610-x"},"abstract":[{"lang":"eng","text":"At high metallicity, a majority of massive stars have at least one close stellar companion. The evolution of such binaries is subject to strong interaction processes, which heavily impact the characteristics of their life-ending supernova and compact remnants. For the low-metallicity environments of high-redshift galaxies, constraints on the multiplicity properties of massive stars over the separation range leading to binary interaction are crucially missing. Here we show that the presence of massive stars in close binaries is ubiquitous, even at low metallicity. Using the Very Large Telescope, we obtained multi-epoch radial velocity measurements of a representative sample of 139 massive O-type stars across the Small Magellanic Cloud, which has a metal content of about one-fifth of the solar value. We find that 45% of them show radial velocity variations that demonstrate that they are members of close binary systems, and predominantly have orbital periods shorter than 1 year. Correcting for observational biases indicates that at least 70+11−6 % of the O stars in our sample are in close binaries, and that at least 68+7\r\n−8% of all O stars interact with a companion star during their lifetime. We found no evidence supporting a statistically significant trend of the multiplicity properties with metallicity. Our results indicate that multiplicity and binary interactions govern the evolution of massive stars and determine their cosmic feedback and explosive fates."}],"scopus_import":"1","publication_identifier":{"eissn":["2397-3366"]},"type":"journal_article","status":"public","OA_type":"green"},{"year":"2025","date_created":"2025-09-17T13:28:01Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","file_date_updated":"2025-09-26T07:29:11Z","author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","first_name":"David"}],"ddc":["580"],"language":[{"iso":"eng"}],"file":[{"checksum":"5ecf274281a54a41e0288bc79edf7492","creator":"dbabic","access_level":"closed","file_name":"2025_David_Babic_Thesis.pdf","embargo_to":"open_access","date_created":"2025-09-24T13:43:14Z","file_id":"20388","embargo":"2026-09-25","file_size":7501548,"date_updated":"2025-09-26T07:29:11Z","relation":"main_file","content_type":"application/pdf"},{"checksum":"2703e548390de0a1af7a707137e8ab3b","creator":"dbabic","access_level":"closed","file_name":"Thesis_Babic_draft.docx","date_created":"2025-09-24T13:43:14Z","file_id":"20389","file_size":23206052,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-26T07:29:11Z","relation":"source_file"}],"doi":"10.15479/AT-ISTA-20362","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"20362","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"116","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"18","corr_author":"1","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","article_processing_charge":"No","date_published":"2025-09-18T00:00:00Z","date_updated":"2026-04-07T11:52:02Z","month":"09","oa_version":"Published Version","citation":{"ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:10.15479/AT-ISTA-20362","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","mla":"Babic, David. Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20362.","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20362.","apa":"Babic, D. (2025). Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20362"},"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"20187","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","status":"public"},{"publisher":"AAAS","citation":{"ama":"Carpentier R, Kim J, Capizzi M, et al. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. Science Advances. 2025;11(38). doi:10.1126/sciadv.adw4124","ieee":"R. Carpentier et al., “Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization,” Science Advances, vol. 11, no. 38. AAAS, 2025.","ista":"Carpentier R, Kim J, Capizzi M, Kim H, Fäßler F, Hansen J, Kim MJ, Denarier E, Blot B, Degennaro M, Labou S, Arnal I, Marcaida MJ, Peraro MD, Kim D, Schur FK, Song J-J, Humbert S. 2025. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. Science Advances. 11(38), eadw4124.","short":"R. Carpentier, J. Kim, M. Capizzi, H. Kim, F. Fäßler, J. Hansen, M.J. Kim, E. Denarier, B. Blot, M. Degennaro, S. Labou, I. Arnal, M.J. Marcaida, M.D. Peraro, D. Kim, F.K. Schur, J.-J. Song, S. Humbert, Science Advances 11 (2025).","mla":"Carpentier, Rémi, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” Science Advances, vol. 11, no. 38, eadw4124, AAAS, 2025, doi:10.1126/sciadv.adw4124.","chicago":"Carpentier, Rémi, Jaesung Kim, Mariacristina Capizzi, Hyeongju Kim, Florian Fäßler, Jesse Hansen, Min Jeong Kim, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adw4124.","apa":"Carpentier, R., Kim, J., Capizzi, M., Kim, H., Fäßler, F., Hansen, J., … Humbert, S. (2025). Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adw4124"},"article_number":"eadw4124","abstract":[{"text":"The Huntingtin protein (HTT), named for its role in Huntington’s disease, has been best understood as a scaffolding protein that promotes vesicle transport by molecular motors along microtubules. Here, we show that HTT also interacts with the actin cytoskeleton, and its loss of function disturbs the morphology and function of the axonal growth cone. We demonstrate that HTT organizes F-actin into bundles. Cryo–electron tomography (cryo-ET) and subtomogram averaging (STA) structural analyses reveal that HTT’s N-terminal HEAT and Bridge domains wrap around F-actin, while the C-terminal HEAT domain is displaced; furthermore, HTT dimerizes via the N-HEAT domain to bridge parallel actin filaments separated by ~20 nanometers. Our study provides the structural basis for understanding how HTT interacts with and organizes the actin cytoskeleton.","lang":"eng"}],"scopus_import":"1","oa_version":"Published Version","type":"journal_article","publication_identifier":{"issn":["2375-2548"]},"status":"public","OA_type":"gold","title":"Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization","PlanS_conform":"1","article_processing_charge":"Yes","date_published":"2025-09-19T00:00:00Z","isi":1,"acknowledgement":"We thank C. Cuveillier, J. Delaroche, T. Ferraro, and A. Zanchi for help with TIRF experiments, electron microscopy preparation, data analysis, and cell cultures, respectively; A. Antkowiak, C. Bosc, C. Fassier, A. Fourest-Lieuvin, and V. Brandt for helpful discussions. We acknowledge the contribution of the Photonic Imaging Center of Grenoble Institute Neuroscience which is part of the ISdV core facility and certified by the IBiSA label and ICM.Quant (RRID:SCR_026393) core facility of the Paris Brain Institute (ICM); the AniRA lentivector production facility from the CELPHEDIA Infrastructure and SFR Biosciences (UAR3444/CNRS, US8/Inserm, ENS de Lyon, UCBL); the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp, A. Schloegl and S. Elefante); and the Electron Microscopy Facility (EMF, V.V. Hodirnau). The software programs used for the processing were supported by SBGrid (www.sbgrid.org). This work was supported by the Agence Nationale pour la Recherche (AXYON: ANR-18-CE16-0009-01, S.H.), Austrian Science Fund (FWF) grants (P33367, F.K.M.S.; E435, J.M.H.), ChanZuckerberg Initiative (CZI) grant (DAF2021-234754, F.K.M.S.), Hereditary Disease Foundation Research Grant (HDF 990846, M.C.), European Union (ERC: ActinID 101076260, F.K.M.S.), Fondation pour la Recherche Médicale (FRM: équipe labellisée DEQ202203014675, S.H.; PhD fellowship, FDT202001010865, R.C.), Korea Health Industry Development Institute (KHIDI) (Korea-Switzerland global research support grant: RS-2023-00266300, J.-J.S.), National Research Foundation (NRF) of Korea (Korea-Austria collaborative grant NRF-2019K1A3A1A181160, J.-J.S. and F.K.M.S.; NRF-2020R1A2B5B03001517 and RS-2024-00333346 and RS-2024-00436173, J.-J.S.; 2021R1C1C1006700, D.K.).","volume":11,"month":"09","external_id":{"isi":["001575751700013"],"pmid":["40971423"]},"date_updated":"2026-05-20T08:20:27Z","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20370","department":[{"_id":"FlSc"}],"issue":"38","pmid":1,"OA_place":"publisher","corr_author":"1","publication":"Science Advances","day":"19","date_created":"2025-09-22T08:00:52Z","article_type":"original","year":"2025","DOAJ_listed":"1","oa":1,"publication_status":"published","file":[{"file_size":3599137,"date_updated":"2025-09-23T07:57:51Z","content_type":"application/pdf","relation":"main_file","checksum":"4e2407bdabf8d53f399eb8a20d86218e","creator":"dernst","file_name":"2025_ScienceAdvance_Carpentier.pdf","access_level":"open_access","date_created":"2025-09-23T07:57:51Z","success":1,"file_id":"20372"}],"doi":"10.1126/sciadv.adw4124","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","grant_number":"101076260"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"intvolume":" 11","APC_amount":"1395,61 EUR","file_date_updated":"2025-09-23T07:57:51Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Carpentier, Rémi","last_name":"Carpentier","first_name":"Rémi"},{"last_name":"Kim","first_name":"Jaesung","full_name":"Kim, Jaesung"},{"full_name":"Capizzi, Mariacristina","last_name":"Capizzi","first_name":"Mariacristina"},{"first_name":"Hyeongju","last_name":"Kim","full_name":"Kim, Hyeongju"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","orcid":"0000-0001-7967-2085","first_name":"Jesse","last_name":"Hansen"},{"last_name":"Kim","first_name":"Min Jeong","full_name":"Kim, Min Jeong"},{"full_name":"Denarier, Eric","first_name":"Eric","last_name":"Denarier"},{"full_name":"Blot, Béatrice","first_name":"Béatrice","last_name":"Blot"},{"first_name":"Marine","last_name":"Degennaro","full_name":"Degennaro, Marine"},{"full_name":"Labou, Sophia","first_name":"Sophia","last_name":"Labou"},{"full_name":"Arnal, Isabelle","first_name":"Isabelle","last_name":"Arnal"},{"full_name":"Marcaida, Maria J.","last_name":"Marcaida","first_name":"Maria J."},{"last_name":"Peraro","first_name":"Matteo Dal","full_name":"Peraro, Matteo Dal"},{"last_name":"Kim","first_name":"Doory","full_name":"Kim, Doory"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078"},{"last_name":"Song","first_name":"Ji-Joon","full_name":"Song, Ji-Joon"},{"full_name":"Humbert, Sandrine","last_name":"Humbert","first_name":"Sandrine"}]},{"volume":85,"acknowledgement":"We thank M. Schütz for laboratory management, organization, and assistance with manuscript editing. We are grateful to all Thomä and Schübeler lab members. We thank Ulrich Hassiepen from Novartis for his support and insightful discussions on the kinetic analysis. This work was supported by funding from the European Research Council (ERC), under the European Union’s H2020 research program (NucEM, grant no. 884331); the Swiss National Science Foundation (SNF, grant no. 310030_301206 and 310030_214852); Krebsforschung (KFS, grant no. KFS-5933-08-2023); Novartis Research Foundation (to N.H.T.); the Novartis Freenovation (grant no. FN23-0000000514 to C.R.S.); the National Health and Medical Research Council CJ Martin Fellowship (APP1148380); the EU Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant (grant no. 748760); the South Australian immunoGENomics Cancer Institute grant funding from the Australian Government; and the Sylvia and Charles Viertel Charitable Foundation Senior Medical Research Fellowship (to L.I.).","article_processing_charge":"Yes (in subscription journal)","date_published":"2025-08-07T00:00:00Z","title":"Nucleosomes specify co-factor access to p53","PlanS_conform":"1","quality_controlled":"1","date_updated":"2025-09-24T08:21:55Z","month":"08","oa_version":"Published Version","citation":{"mla":"Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.” Molecular Cell, vol. 85, no. 15, Elsevier, 2025, p. 2919–2936.e12, doi:10.1016/j.molcel.2025.06.027.","short":"D. Chakraborty, C.R. Sandate, L. Isbel, G. Kempf, J. Weiss, S. Cavadini, L. Kater, J. Seebacher, Z. Kozicka, L. Stoos, R.S. Grand, D. Schübeler, A.K. Michael, N.H. Thomä, Molecular Cell 85 (2025) 2919–2936.e12.","ista":"Chakraborty D, Sandate CR, Isbel L, Kempf G, Weiss J, Cavadini S, Kater L, Seebacher J, Kozicka Z, Stoos L, Grand RS, Schübeler D, Michael AK, Thomä NH. 2025. Nucleosomes specify co-factor access to p53. Molecular Cell. 85(15), 2919–2936.e12.","apa":"Chakraborty, D., Sandate, C. R., Isbel, L., Kempf, G., Weiss, J., Cavadini, S., … Thomä, N. H. (2025). Nucleosomes specify co-factor access to p53. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.06.027","chicago":"Chakraborty, Deyasini, Colby R. Sandate, Luke Isbel, Georg Kempf, Joscha Weiss, Simone Cavadini, Lukas Kater, et al. “Nucleosomes Specify Co-Factor Access to P53.” Molecular Cell. Elsevier, 2025. https://doi.org/10.1016/j.molcel.2025.06.027.","ama":"Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access to p53. Molecular Cell. 2025;85(15):2919-2936.e12. doi:10.1016/j.molcel.2025.06.027","ieee":"D. Chakraborty et al., “Nucleosomes specify co-factor access to p53,” Molecular Cell, vol. 85, no. 15. Elsevier, p. 2919–2936.e12, 2025."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However, it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors. In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring inaccessible chromatin. We examined the interaction of chromatin-bound p53 with co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct motif locations on the nucleosome (super-helical location [SHL]−5.7 and SHL+5.9), the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered interaction domains of co-factors and TFs govern compatibility between co-factors, TFs, and chromatin."}],"publisher":"Elsevier","OA_type":"hybrid","status":"public","publication_identifier":{"issn":["1097-2765"]},"type":"journal_article","year":"2025","article_type":"original","date_created":"2025-09-23T08:56:13Z","author":[{"first_name":"Deyasini","last_name":"Chakraborty","full_name":"Chakraborty, Deyasini"},{"first_name":"Colby R.","last_name":"Sandate","full_name":"Sandate, Colby R."},{"full_name":"Isbel, Luke","last_name":"Isbel","first_name":"Luke"},{"last_name":"Kempf","first_name":"Georg","full_name":"Kempf, Georg"},{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"first_name":"Simone","last_name":"Cavadini","full_name":"Cavadini, Simone"},{"first_name":"Lukas","last_name":"Kater","full_name":"Kater, Lukas"},{"full_name":"Seebacher, Jan","first_name":"Jan","last_name":"Seebacher"},{"first_name":"Zuzanna","last_name":"Kozicka","full_name":"Kozicka, Zuzanna"},{"last_name":"Stoos","first_name":"Lisa","full_name":"Stoos, Lisa"},{"full_name":"Grand, Ralph S.","last_name":"Grand","first_name":"Ralph S."},{"first_name":"Dirk","last_name":"Schübeler","full_name":"Schübeler, Dirk"},{"orcid":"0000-0002-6080-839X","last_name":"Michael","first_name":"Alicia","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"last_name":"Thomä","first_name":"Nicolas H.","full_name":"Thomä, Nicolas H."}],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2025-09-24T07:54:03Z","intvolume":" 85","file":[{"file_size":41813494,"date_updated":"2025-09-24T07:54:03Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"e60390ca629b350af3221d4718ca6534","access_level":"open_access","file_name":"2025_MolecularCell_Chakraborty.pdf","date_created":"2025-09-24T07:54:03Z","file_id":"20386","success":1}],"doi":"10.1016/j.molcel.2025.06.027","oa":1,"publication_status":"published","issue":"15","department":[{"_id":"AlMi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20374","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"2919-2936.e12","day":"07","publication":"Molecular Cell","OA_place":"publisher"},{"publisher":"Institute of Science and Technology Austria","citation":{"mla":"Kishi, Kasumi. Regulation of Notochord and Floor Plate Size during Mouse Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20393.","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria.","apa":"Kishi, K. (2025). Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20393","chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20393.","ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:10.15479/AT-ISTA-20393","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025."},"oa_version":"Published Version","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"status":"public","related_material":{"record":[{"id":"18481","relation":"part_of_dissertation","status":"public"}]},"title":"Regulation of notochord and floor plate size during mouse development","article_processing_charge":"No","date_published":"2025-09-24T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"month":"09","date_updated":"2026-04-14T09:50:52Z","page":"102","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"supervisor":[{"orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"20393","department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"OA_place":"publisher","corr_author":"1","day":"24","date_created":"2025-09-25T10:08:10Z","alternative_title":["ISTA Thesis"],"year":"2025","publication_status":"published","file":[{"date_created":"2025-09-30T14:33:17Z","file_id":"20413","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","creator":"kkishi","access_level":"closed","file_name":"2025-Kishi-Kasumi-Thesis.zip","file_size":41847994,"date_updated":"2025-10-01T11:54:41Z","content_type":"application/x-zip-compressed","relation":"source_file"},{"date_created":"2025-09-30T14:33:22Z","file_id":"20414","checksum":"88349b9177e1dcbe1242cd3884b36fdb","creator":"kkishi","access_level":"closed","file_name":"2025-Kishi-Kasumi-Thesis.pdf","embargo_to":"open_access","embargo":"2026-09-30","file_size":55747072,"relation":"main_file","content_type":"application/pdf","date_updated":"2025-10-02T07:51:21Z"}],"doi":"10.15479/AT-ISTA-20393","file_date_updated":"2025-10-02T07:51:21Z","degree_awarded":"PhD","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"first_name":"Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi"}]},{"oa_version":"Published Version","abstract":[{"text":"The recent classification of the onset of turbulence as a directed percolation (DP) phase transition has been applied to all major shear flows including pipe, channel, Couette and boundary layer flows. A cornerstone of the DP analogy is the memoryless (Poisson) property of turbulent sites. We here show that, for the classic case of channel flow, neither the decay nor the proliferation of turbulent stripes is memoryless. As demonstrated by a standard analysis of the respective survival curves, isolated channel stripes, in the immediate vicinity of the critical point, age. Consequently, the one to one mapping between turbulent stripes and active DP-sites is not fulfilled in this low Reynolds number regime. In addition, the interpretation of turbulence as a chaotic saddle with supertransient properties, the basis of recent theoretical progress, does not apply to individual localized stripes. The discrepancy between channel flow and the transition models established for pipe and Couette flow, illustrates that seemingly minor geometrical differences between flows can give rise to instabilities and growth mechanisms that fundamentally alter the nature of the transition to turbulence.","lang":"eng"}],"article_number":"8447","citation":{"mla":"Vasudevan, Mukund, et al. “Aging and Memory of Transitional Turbulence.” Nature Communications, vol. 16, 8447, Springer Nature, 2025, doi:10.1038/s41467-025-63044-7.","ista":"Vasudevan M, Paranjape CS, Sitte MP, Yalniz G, Hof B. 2025. Aging and memory of transitional turbulence. Nature Communications. 16, 8447.","short":"M. Vasudevan, C.S. Paranjape, M.P. Sitte, G. Yalniz, B. Hof, Nature Communications 16 (2025).","apa":"Vasudevan, M., Paranjape, C. S., Sitte, M. P., Yalniz, G., & Hof, B. (2025). Aging and memory of transitional turbulence. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-63044-7","chicago":"Vasudevan, Mukund, Chaitanya S Paranjape, Michael Philip Sitte, Gökhan Yalniz, and Björn Hof. “Aging and Memory of Transitional Turbulence.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-63044-7.","ama":"Vasudevan M, Paranjape CS, Sitte MP, Yalniz G, Hof B. Aging and memory of transitional turbulence. Nature Communications. 2025;16. doi:10.1038/s41467-025-63044-7","ieee":"M. Vasudevan, C. S. Paranjape, M. P. Sitte, G. Yalniz, and B. Hof, “Aging and memory of transitional turbulence,” Nature Communications, vol. 16. Springer Nature, 2025."},"scopus_import":"1","publisher":"Springer Nature","OA_type":"gold","status":"public","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","volume":16,"isi":1,"acknowledgement":"This work was supported by a grant from the Simons Foundation (662960, BH). We thank Yohann Duguet for helpful discussions, Baofang Song for the initial adaptation of openpipeflow57 to the channel geometry, and Ashley P. Willis for openpipeflow57.","arxiv":1,"date_published":"2025-09-26T00:00:00Z","article_processing_charge":"Yes","title":"Aging and memory of transitional turbulence","PlanS_conform":"1","date_updated":"2026-05-20T07:56:59Z","quality_controlled":"1","external_id":{"isi":["001582555200041"],"arxiv":["2112.06537"]},"month":"09","department":[{"_id":"BjHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20402","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","publication":"Nature Communications","corr_author":"1","OA_place":"publisher","DOAJ_listed":"1","year":"2025","article_type":"original","date_created":"2025-09-27T13:27:31Z","author":[{"full_name":"Vasudevan, Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","first_name":"Mukund","last_name":"Vasudevan"},{"first_name":"Chaitanya S","last_name":"Paranjape","full_name":"Paranjape, Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sitte","first_name":"Michael Philip","id":"0ba0f1f2-9cfe-11f0-bee6-f95318d225b0","full_name":"Sitte, Michael Philip"},{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","first_name":"Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"ddc":["532"],"language":[{"iso":"eng"}],"file_date_updated":"2025-09-27T13:32:03Z","APC_amount":"7068 EUR","intvolume":" 16","doi":"10.1038/s41467-025-63044-7","file":[{"file_size":2226082,"relation":"main_file","date_updated":"2025-09-27T13:32:03Z","content_type":"application/pdf","checksum":"945926ead9cde464435d456427e2869e","creator":"gyalniz","file_name":"s41467-025-63044-7.pdf","access_level":"open_access","date_created":"2025-09-27T13:32:03Z","file_id":"20403"}],"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_status":"published","oa":1},{"volume":141,"date_published":"2025-11-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","isi":1,"acknowledgement":"This project was supported by the All May See Foundation 7031,182 to YI, the Louisiana Board of Regents Support Fund: Research Competitiveness Subprogram to MAT, Austrian science fund (FWF) as part of the SFB Meiosis consortium FWF SFB F88-10 to Beatriz Vicoso (supported ME), American Heart Association 16POST2726018 and American Cancer Society 132,123-PF-18–025–01-CSM postdoctoral fellowships to ALZ, National Institutes of Health R01 GM136961 and R35 GM148485 to SH-B, and the Academy of Medical Sciences/the Wellcome Trust/ the Government Department of Business, Energy and Industrial Strategy/the British Heart Foundation/Diabetes UK Springboard Award SBF008\\1115 to YM. \r\nComputational analyses of single-nucleus transcriptome data were performed on the high performance computer (HPC) at Bournemouth University, the HPC at Institute of Science and Technology Austria, and the high-performance computational resources provided by the Louisiana Optical Network Infrastructure (http://www.loni.org). The authors are grateful to the researchers who published the transcriptome datasets [48,49,52,55] that became the essential bases for this study, to FlyBase for curating the datasets in an easily accessible format, and the Drosophila Genomics Resource Center (DGRC), supported by NIH grant 2P40OD010949, for providing the D17 cell line used in this research. The authors thank Kristian Koski (University of Oulu, Finland) for crucial advice on the domain structure of collagen P4H⍺s, and Ryusuke Niwa and Ryo Hoshino (University of Tsukuba, Japan) for helpful discussions on SP.","PlanS_conform":"1","title":"Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV","date_updated":"2026-01-05T13:09:08Z","quality_controlled":"1","external_id":{"isi":["001583892100002"],"pmid":["40946811"]},"month":"11","citation":{"ieee":"Y. Ishikawa, M. A. Toups, M. N. Elkrewi, A. L. Zajac, S. Horne-Badovinac, and Y. Matsubayashi, “Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV,” Matrix Biology, vol. 141, no. 11. Springer Nature, pp. 101–113, 2025.","ama":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. 2025;141(11):101-113. doi:10.1016/j.matbio.2025.09.002","chicago":"Ishikawa, Yoshihiro, Melissa A Toups, Marwan N Elkrewi, Allison L. Zajac, Sally Horne-Badovinac, and Yutaka Matsubayashi. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” Matrix Biology. Springer Nature, 2025. https://doi.org/10.1016/j.matbio.2025.09.002.","apa":"Ishikawa, Y., Toups, M. A., Elkrewi, M. N., Zajac, A. L., Horne-Badovinac, S., & Matsubayashi, Y. (2025). Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. Springer Nature. https://doi.org/10.1016/j.matbio.2025.09.002","short":"Y. Ishikawa, M.A. Toups, M.N. Elkrewi, A.L. Zajac, S. Horne-Badovinac, Y. Matsubayashi, Matrix Biology 141 (2025) 101–113.","ista":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. 2025. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. 141(11), 101–113.","mla":"Ishikawa, Yoshihiro, et al. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” Matrix Biology, vol. 141, no. 11, Springer Nature, 2025, pp. 101–13, doi:10.1016/j.matbio.2025.09.002."},"abstract":[{"text":"Collagens are fundamental components of extracellular matrices, requiring precise intracellular post-translational modifications for proper function. Among the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases (P4Hs). While humans possess three genes encoding these enzymes (P4H⍺s), Drosophila melanogaster harbour at least 26 candidates for collagen P4H⍺s despite its simple genome, and it is poorly understood which of them are actually working on collagen in the fly. In this study, we addressed this question by carrying out thorough bioinformatic and biochemical analyses. We demonstrate that among the 26 potential collagen P4H⍺s, PH4⍺EFB shares the highest homology with vertebrate collagen P4H⍺s. Furthermore, while collagen P4Hs and their substrates must exist in the same cells, our transcriptomic analyses at the tissue and single cell levels showed a global co-expression of PH4⍺EFB but not the other P4H⍺-related genes with the collagen IV genes. Moreover, expression of PH4⍺EFB during embryogenesis was found to precede that of collagen IV, presumably enabling efficient collagen modification by PH4⍺EFB. Finally, biochemical assays confirm that PH4⍺EFB binds collagen, supporting its direct role in collagen IV modification. Collectively, we identify PH4⍺EFB as the primary and potentially constitutive prolyl 4-hydroxylase responsible for collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint for defining the minimal requirements for collagen engineering.","lang":"eng"}],"scopus_import":"1","oa_version":"Published Version","publisher":"Springer Nature","OA_type":"hybrid","status":"public","type":"journal_article","publication_identifier":{"issn":["0945-053X"],"eissn":["1569-1802"]},"year":"2025","article_type":"original","date_created":"2025-09-28T22:01:26Z","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"full_name":"Ishikawa, Yoshihiro","first_name":"Yoshihiro","last_name":"Ishikawa"},{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"first_name":"Allison L.","last_name":"Zajac","full_name":"Zajac, Allison L."},{"full_name":"Horne-Badovinac, Sally","last_name":"Horne-Badovinac","first_name":"Sally"},{"full_name":"Matsubayashi, Yutaka","first_name":"Yutaka","last_name":"Matsubayashi"}],"file_date_updated":"2026-01-05T13:09:01Z","intvolume":" 141","publication_status":"published","oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2026-01-05T13:09:01Z","file_size":5844254,"access_level":"open_access","file_name":"2025_MatrixBiology_Ishikawa.pdf","creator":"dernst","checksum":"764257db41865d19daec1935788f72d7","file_id":"20948","success":1,"date_created":"2026-01-05T13:09:01Z"}],"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"doi":"10.1016/j.matbio.2025.09.002","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20404","issue":"11","department":[{"_id":"BeVi"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"101-113","day":"01","publication":"Matrix Biology","OA_place":"publisher"},{"day":"11","corr_author":"1","OA_place":"publisher","publication":"ACS Photonics","_id":"20405","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"},{"_id":"MiLe"},{"_id":"ZhAl"}],"issue":"9","page":"5220-5230","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","file_date_updated":"2025-10-20T11:02:21Z","language":[{"iso":"eng"}],"ddc":["540","530"],"author":[{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem"},{"last_name":"Zhumekenov","first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A."},{"orcid":"0000-0002-6962-8598","last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"}],"oa":1,"publication_status":"published","file":[{"creator":"dernst","checksum":"d42476279287a9a2f8aeafaef032f4a7","file_name":"2025_ACSPhotonics_Lorenc.pdf","access_level":"open_access","date_created":"2025-10-20T11:02:21Z","success":1,"file_id":"20502","file_size":6609950,"date_updated":"2025-10-20T11:02:21Z","relation":"main_file","content_type":"application/pdf"}],"doi":"10.1021/acsphotonics.5c01360","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"intvolume":" 12","year":"2025","date_created":"2025-09-28T22:01:26Z","article_type":"original","OA_type":"hybrid","type":"journal_article","publication_identifier":{"eissn":["2330-4022"]},"status":"public","abstract":[{"text":"Dielectric breakdown of physical vacuum (Schwinger effect) is the textbook demonstration of compatibility of Relativity and Quantum theory. Although observing this effect is still practically unachievable, its analogue generalizations have been shown to be more readily attainable. This paper demonstrates that a gapped Dirac semiconductor, methylammonium lead-bromide perovskite (MAPbBr3), exhibits analogue dynamic Schwinger effect. Tunneling ionization under deep subgap mid-infrared irradiation leads to intense photoluminescence in the visible range, in full agreement with quasi-adiabatic theory. In addition to revealing a gapped extended system suitable for studying the analogue Schwinger effect, this observation holds great potential for nonperturbative field sensing, i.e., sensing electric fields through nonperturbative light-matter interactions. First, this paper illustrates this by measuring the local deviation from the nominally cubic phase of a perovskite single crystal, which can be interpreted in terms of frozen-in fields. Next, it is shown that analogue dynamic Schwinger effect can be used for nonperturbative amplification of nonparametric upconversion process in perovskites driven simultaneously by multiple optical fields. This discovery demonstrates the potential for material response beyond perturbation theory in the tunneling regime, offering extremely sensitive light detection and amplification across an ultrabroad spectral range not accessible by conventional devices.","lang":"eng"}],"citation":{"short":"D. Lorenc, A. Volosniev, A.A. Zhumekenov, S. Lee, M. Ibáñez, O.M. Bakr, M. Lemeshko, Z. Alpichshev, ACS Photonics 12 (2025) 5220–5230.","ista":"Lorenc D, Volosniev A, Zhumekenov AA, Lee S, Ibáñez M, Bakr OM, Lemeshko M, Alpichshev Z. 2025. Observation of analogue dynamic Schwinger effect and non-perturbative light sensing in lead halide perovskites. ACS Photonics. 12(9), 5220–5230.","mla":"Lorenc, Dusan, et al. “Observation of Analogue Dynamic Schwinger Effect and Non-Perturbative Light Sensing in Lead Halide Perovskites.” ACS Photonics, vol. 12, no. 9, American Chemical Society, 2025, pp. 5220–30, doi:10.1021/acsphotonics.5c01360.","chicago":"Lorenc, Dusan, Artem Volosniev, Ayan A. Zhumekenov, Seungho Lee, Maria Ibáñez, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Observation of Analogue Dynamic Schwinger Effect and Non-Perturbative Light Sensing in Lead Halide Perovskites.” ACS Photonics. American Chemical Society, 2025. https://doi.org/10.1021/acsphotonics.5c01360.","apa":"Lorenc, D., Volosniev, A., Zhumekenov, A. A., Lee, S., Ibáñez, M., Bakr, O. M., … Alpichshev, Z. (2025). Observation of analogue dynamic Schwinger effect and non-perturbative light sensing in lead halide perovskites. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.5c01360","ama":"Lorenc D, Volosniev A, Zhumekenov AA, et al. Observation of analogue dynamic Schwinger effect and non-perturbative light sensing in lead halide perovskites. ACS Photonics. 2025;12(9):5220-5230. doi:10.1021/acsphotonics.5c01360","ieee":"D. Lorenc et al., “Observation of analogue dynamic Schwinger effect and non-perturbative light sensing in lead halide perovskites,” ACS Photonics, vol. 12, no. 9. American Chemical Society, pp. 5220–5230, 2025."},"scopus_import":"1","oa_version":"Published Version","publisher":"American Chemical Society","external_id":{"isi":["001547359300001"],"arxiv":["2406.05032"]},"quality_controlled":"1","date_updated":"2025-12-01T12:59:51Z","month":"08","volume":12,"acknowledged_ssus":[{"_id":"EM-Fac"}],"PlanS_conform":"1","title":"Observation of analogue dynamic Schwinger effect and non-perturbative light sensing in lead halide perovskites","arxiv":1,"date_published":"2025-08-11T00:00:00Z","article_processing_charge":"Yes (via OA deal)","isi":1,"acknowledgement":"A.G.V. thanks Peter Balling for useful discussions. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), and by the Werner Siemens Foundation (WSS) for financial support."},{"year":"2025","date_created":"2025-09-28T22:01:27Z","article_type":"original","file_date_updated":"2025-09-29T06:59:14Z","author":[{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"full_name":"Rix, Hans Walter","last_name":"Rix","first_name":"Hans Walter"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"first_name":"Ivo","last_name":"Labbé","full_name":"Labbé, Ivo"},{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"last_name":"Leja","first_name":"Joel","full_name":"Leja, Joel"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X"},{"full_name":"Katz, Harley","first_name":"Harley","last_name":"Katz"},{"last_name":"Greene","first_name":"Jenny E.","full_name":"Greene, Jenny E."},{"last_name":"Hviding","first_name":"Raphael E.","full_name":"Hviding, Raphael E."},{"last_name":"Baggen","first_name":"Josephine","full_name":"Baggen, Josephine"},{"first_name":"Rachel","last_name":"Bezanson","full_name":"Bezanson, Rachel"},{"full_name":"Boogaard, Leindert A.","first_name":"Leindert A.","last_name":"Boogaard"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"first_name":"Pratika","last_name":"Dayal","full_name":"Dayal, Pratika"},{"full_name":"Van Dokkum, Pieter","first_name":"Pieter","last_name":"Van Dokkum"},{"full_name":"Goulding, Andy D.","last_name":"Goulding","first_name":"Andy D."},{"full_name":"Hirschmann, Michaela","last_name":"Hirschmann","first_name":"Michaela"},{"last_name":"Maseda","first_name":"Michael V.","full_name":"Maseda, Michael V."},{"first_name":"Ian","last_name":"Mcconachie","full_name":"Mcconachie, Ian"},{"first_name":"Tim B.","last_name":"Miller","full_name":"Miller, Tim B."},{"last_name":"Nelson","first_name":"Erica","full_name":"Nelson, Erica"},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."},{"last_name":"Setton","first_name":"David J.","full_name":"Setton, David J."},{"full_name":"Shivaei, Irene","last_name":"Shivaei","first_name":"Irene"},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"full_name":"Whitaker, Katherine E.","last_name":"Whitaker","first_name":"Katherine E."},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."}],"ddc":["520"],"language":[{"iso":"eng"}],"file":[{"date_created":"2025-09-29T06:59:14Z","file_id":"20409","success":1,"checksum":"cf93d635121dbf4865fd080c517927d0","creator":"dernst","access_level":"open_access","file_name":"2025_AstronomyAstrophysics_deGraaff2.pdf","file_size":1218479,"relation":"main_file","content_type":"application/pdf","date_updated":"2025-09-29T06:59:14Z"}],"doi":"10.1051/0004-6361/202554681","publication_status":"published","oa":1,"intvolume":" 701","department":[{"_id":"JoMa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20406","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","OA_place":"publisher","publication":"Astronomy & Astrophysics","volume":701,"PlanS_conform":"1","title":"A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5","acknowledgement":"We thank the PRIMER team for making their imaging data publicly available immediately. We thank Jaime Villaseñor and Friedrich Röpke for helpful discussions. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs #1837 and #4233. Support for program #4233 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. REH acknowledges support by the German Aerospace Center (DLR) and the Federal Ministry for Economic Affairs and Energy (BMWi) through program 50OR2403 ‘RUBIES’. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #562. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. Support for this work for RPN was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. TBM was supported by a CIERA fellowship. Open Access funding provided by Max Planck Society.","isi":1,"arxiv":1,"date_published":"2025-09-01T00:00:00Z","article_processing_charge":"No","external_id":{"isi":["001570450900004"],"arxiv":["2503.16600"]},"date_updated":"2026-02-16T12:13:12Z","quality_controlled":"1","month":"09","oa_version":"Published Version","citation":{"ama":"De Graaff A, Rix HW, Naidu RP, et al. A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5. Astronomy & Astrophysics. 2025;701. doi:10.1051/0004-6361/202554681","ieee":"A. De Graaff et al., “A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5,” Astronomy & Astrophysics, vol. 701. EDP Sciences, 2025.","ista":"De Graaff A, Rix HW, Naidu RP, Labbé I, Wang B, Leja J, Matthee JJ, Katz H, Greene JE, Hviding RE, Baggen J, Bezanson R, Boogaard LA, Brammer G, Dayal P, Van Dokkum P, Goulding AD, Hirschmann M, Maseda MV, Mcconachie I, Miller TB, Nelson E, Oesch PA, Setton DJ, Shivaei I, Weibel A, Whitaker KE, Williams CC. 2025. A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5. Astronomy & Astrophysics. 701, A168.","short":"A. De Graaff, H.W. Rix, R.P. Naidu, I. Labbé, B. Wang, J. Leja, J.J. Matthee, H. Katz, J.E. Greene, R.E. Hviding, J. Baggen, R. Bezanson, L.A. Boogaard, G. Brammer, P. Dayal, P. Van Dokkum, A.D. Goulding, M. Hirschmann, M.V. Maseda, I. Mcconachie, T.B. Miller, E. Nelson, P.A. Oesch, D.J. Setton, I. Shivaei, A. Weibel, K.E. Whitaker, C.C. Williams, Astronomy & Astrophysics 701 (2025).","mla":"De Graaff, Anna, et al. “A Remarkable Ruby: Absorption in Dense Gas, Rather than Evolved Stars, Drives the Extreme Balmer Break of a Little Red Dot at z = 3.5.” Astronomy & Astrophysics, vol. 701, A168, EDP Sciences, 2025, doi:10.1051/0004-6361/202554681.","chicago":"De Graaff, Anna, Hans Walter Rix, Rohan P. Naidu, Ivo Labbé, Bingjie Wang, Joel Leja, Jorryt J Matthee, et al. “A Remarkable Ruby: Absorption in Dense Gas, Rather than Evolved Stars, Drives the Extreme Balmer Break of a Little Red Dot at z = 3.5.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202554681.","apa":"De Graaff, A., Rix, H. W., Naidu, R. P., Labbé, I., Wang, B., Leja, J., … Williams, C. C. (2025). A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202554681"},"scopus_import":"1","article_number":"A168","abstract":[{"lang":"eng","text":"The origin of the rest-optical emission of compact, red, high-redshift sources known as little red dots (LRDs) poses a major puzzle. If interpreted as starlight, it would imply that LRDs constitute the densest stellar systems in the Universe. However, alternative models suggest active galactic nuclei (AGN) may instead power the rest-optical continuum. Here, we present JWST/NIRSpec, NIRCam, and MIRI observations from the RUBIES and PRIMER programs of The Cliff: a bright LRD at z = 3.55 with an exceptional Balmer break, twice as strong as that of any high-redshift source previously observed. The spectra also reveal broad hydrogen (Hα FWHM ∼ 1500 km s−1) and He I emission, but no significant metal lines. We demonstrate that massive evolved stellar populations cannot explain the observed spectrum, even when considering unusually steep and strong dust attenuation or reasonable variations in the initial mass function. Moreover, the formally best-fit stellar mass and compact size (M* ∼ 1010.5 M⊙, re ∼ 40 pc) would imply densities at which near-monthly stellar collisions might lead to significant X-ray emission. We argue that the Balmer break, emission lines, and Hα absorption line are instead most plausibly explained by a black hole star (BH*) scenario, in which dense gas surrounds a powerful ionising source. In contrast to recently proposed BH* models of dust-reddened AGN, we show that spectral fits in the rest UV to near-infrared favour an intrinsically redder continuum over strong dust reddening. This may point to a super-Eddington accreting massive black hole or, possibly, the presence of (super)massive stars in a nuclear star cluster. The Cliff is the clearest evidence to date that at least some LRDs are not ultra-dense massive galaxies, and are instead powered by a central ionising source embedded in dense, absorbing gas."}],"publisher":"EDP Sciences","OA_type":"diamond","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"type":"journal_article","status":"public"},{"year":"2025","date_created":"2025-09-28T22:01:27Z","article_type":"original","author":[{"full_name":"Ennes, Henrique","last_name":"Ennes","first_name":"Henrique"},{"orcid":"0000-0002-1404-1095","last_name":"Tinarrage","first_name":"Raphaël","full_name":"Tinarrage, Raphaël","id":"40ebcc9d-905f-11ef-bf0a-dc475da8a04e"}],"language":[{"iso":"eng"}],"ddc":["500"],"doi":"10.1007/s10208-025-09728-4","oa":1,"publication_status":"epub_ahead","department":[{"_id":"UlWa"}],"_id":"20407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","OA_place":"publisher","corr_author":"1","publication":"Foundations of Computational Mathematics","title":"LieDetect: Detection of representation orbits of compact Lie groups from point clouds","PlanS_conform":"1","acknowledgement":"The original work behind this article was developed for HE’s master’s thesis, supervised by RT. We are mostly in debt to César Camacho, who was HE’s co-advisor, as well as the members of the thesis jury, Clément Maria, Eduardo Mendes, and Jameson Cahill, not only for agreeing to evaluate the original work but also for many valuable inputs. Finally, we are indebted to the anonymous reviewers for their important feedback and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","isi":1,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","date_published":"2025-09-15T00:00:00Z","external_id":{"isi":["001571197200001"],"arxiv":["2309.03086"]},"quality_controlled":"1","date_updated":"2026-06-18T18:22:42Z","month":"09","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We suggest a new algorithm to estimate representations of compact Lie groups from finite samples of their orbits. Different from other reported techniques, our method allows the retrieval of the precise representation type as a direct sum of irreducible representations. Moreover, the knowledge of the representation type permits the reconstruction of its orbit, which is useful for identifying the Lie group that generates the action, from a finite list of candidates. Our algorithm is general for any compact Lie group, but only instantiations for SO(2), T^d, SU(2), and SO(3) are considered. Theoretical guarantees of robustness in terms of Hausdorff and Wasserstein distances are derived. Our tools are drawn from geometric measure theory, computational geometry, and optimization on matrix manifolds. The algorithm is tested for synthetic data up to dimension 32, as well as real-life applications in image analysis, harmonic analysis, density estimation, equivariant neural networks, chemical conformational spaces, and classical mechanics systems, achieving very accurate results."}],"scopus_import":"1","citation":{"apa":"Ennes, H., & Tinarrage, R. (2025). LieDetect: Detection of representation orbits of compact Lie groups from point clouds. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-025-09728-4","chicago":"Ennes, Henrique, and Raphaël Tinarrage. “LieDetect: Detection of Representation Orbits of Compact Lie Groups from Point Clouds.” Foundations of Computational Mathematics. Springer Nature, 2025. https://doi.org/10.1007/s10208-025-09728-4.","mla":"Ennes, Henrique, and Raphaël Tinarrage. “LieDetect: Detection of Representation Orbits of Compact Lie Groups from Point Clouds.” Foundations of Computational Mathematics, Springer Nature, 2025, doi:10.1007/s10208-025-09728-4.","short":"H. Ennes, R. Tinarrage, Foundations of Computational Mathematics (2025).","ista":"Ennes H, Tinarrage R. 2025. LieDetect: Detection of representation orbits of compact Lie groups from point clouds. Foundations of Computational Mathematics.","ieee":"H. Ennes and R. Tinarrage, “LieDetect: Detection of representation orbits of compact Lie groups from point clouds,” Foundations of Computational Mathematics. Springer Nature, 2025.","ama":"Ennes H, Tinarrage R. LieDetect: Detection of representation orbits of compact Lie groups from point clouds. Foundations of Computational Mathematics. 2025. doi:10.1007/s10208-025-09728-4"},"publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1007/s10208-025-09728-4","open_access":"1"}],"OA_type":"hybrid","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"type":"journal_article","status":"public"},{"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_processing_charge":"No","date_published":"2025-10-01T00:00:00Z","title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids","date_updated":"2026-04-07T11:52:32Z","month":"10","citation":{"ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:10.15479/AT-ISTA-20415","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025.","mla":"Lee, Seungho. Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20415.","chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20415.","apa":"Lee, S. (2025). Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20415"},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"15357","relation":"part_of_dissertation","status":"public"},{"id":"12237","relation":"part_of_dissertation","status":"public"}]},"status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","alternative_title":["ISTA Thesis"],"date_created":"2025-10-01T09:04:00Z","ddc":["540"],"language":[{"iso":"eng"}],"author":[{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"}],"file_date_updated":"2025-10-07T08:57:14Z","degree_awarded":"PhD","publication_status":"published","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"file":[{"access_level":"closed","file_name":"2025_Lee_Seungho_Thesis.docx","checksum":"fa6d5946feb37b678ee1c6dffb4fa167","creator":"slee","file_id":"20420","date_created":"2025-10-03T12:29:43Z","date_updated":"2025-10-07T08:57:14Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":88706648},{"date_updated":"2025-10-03T12:29:25Z","relation":"main_file","content_type":"application/pdf","embargo":"2026-10-03","file_size":14587276,"file_id":"20421","date_created":"2025-10-03T12:29:25Z","access_level":"closed","embargo_to":"open_access","file_name":"2025_Lee_Seungho_Thesis__.pdf","creator":"slee","checksum":"c5ba6d464113ad0c5812a9d24b539b86"}],"doi":"10.15479/AT-ISTA-20415","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"20415","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"has_accepted_license":"1","supervisor":[{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria"},{"full_name":"Protesescu, Loredana","last_name":"Protesescu","first_name":"Loredana"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319"}],"page":"144","day":"01","corr_author":"1","OA_place":"publisher"},{"pmid":1,"ec_funded":1,"department":[{"_id":"EdHa"}],"_id":"20424","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"26","publication":"Nature Communications","OA_place":"publisher","corr_author":"1","DOAJ_listed":"1","year":"2025","article_type":"original","date_created":"2025-10-05T22:01:34Z","author":[{"last_name":"Sahu","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","full_name":"Sahu, Preeti"},{"full_name":"Monteiro-Ferreira, Sara","first_name":"Sara","last_name":"Monteiro-Ferreira"},{"last_name":"Canato","first_name":"Sara","full_name":"Canato, Sara"},{"last_name":"Soares","first_name":"Raquel Maia","full_name":"Soares, Raquel Maia"},{"full_name":"Sánchez-Danés, Adriana","first_name":"Adriana","last_name":"Sánchez-Danés"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"language":[{"iso":"eng"}],"file_date_updated":"2025-10-13T12:37:04Z","APC_amount":"7068 EUR","intvolume":" 16","project":[{"_id":"628f3fb1-2b32-11ec-9570-83ce778803f7","grant_number":"ALTF 522-2021","name":"Biomechanics of stem cell fate determination"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"file":[{"file_id":"20464","success":1,"date_created":"2025-10-13T12:37:04Z","access_level":"open_access","file_name":"2025_NatureComm_Sahu.pdf","creator":"dernst","checksum":"d1656576883b23902545328e2d640234","relation":"main_file","date_updated":"2025-10-13T12:37:04Z","content_type":"application/pdf","file_size":2816813}],"doi":"10.1038/s41467-025-62882-9","oa":1,"publication_status":"published","oa_version":"Published Version","abstract":[{"text":"Homeostasis relies on a precise balance of fate choices between renewal and differentiation. Although progress has been done to characterize the dynamics of single-cell fate choices, their underlying mechanistic basis often remains unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation in the basal layer, showing that mechanical competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical heterogeneities between cellular subpopulations. We uncover that relatively small tension heterogeneities, reflected by distinct morphological changes in single-cell shapes, can be sufficient to heavily tilt cellular dynamics towards exponential growth. We thus derive a master relationship between cell shape and long-term clonal dynamics, which we validated during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues.","lang":"eng"}],"article_number":"8440","citation":{"ama":"Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. 2025;16. doi:10.1038/s41467-025-62882-9","ieee":"P. Sahu, S. Monteiro-Ferreira, S. Canato, R. M. Soares, A. Sánchez-Danés, and E. B. Hannezo, “Mechanical control of cell fate decisions in the skin epidermis,” Nature Communications, vol. 16. Springer Nature, 2025.","mla":"Sahu, Preeti, et al. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” Nature Communications, vol. 16, 8440, Springer Nature, 2025, doi:10.1038/s41467-025-62882-9.","short":"P. Sahu, S. Monteiro-Ferreira, S. Canato, R.M. Soares, A. Sánchez-Danés, E.B. Hannezo, Nature Communications 16 (2025).","ista":"Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. 2025. Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. 16, 8440.","apa":"Sahu, P., Monteiro-Ferreira, S., Canato, S., Soares, R. M., Sánchez-Danés, A., & Hannezo, E. B. (2025). Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-62882-9","chicago":"Sahu, Preeti, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares, Adriana Sánchez-Danés, and Edouard B Hannezo. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-62882-9."},"scopus_import":"1","publisher":"Springer Nature","OA_type":"gold","status":"public","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","acknowledged_ssus":[{"_id":"Bio"}],"volume":16,"isi":1,"acknowledgement":"We thank Alois Schlögl, Paula Sanematsu, Susana Moreno Flores, Bernat Corominas-Murtra, Stefania Tavano, Gayathri Singharaju, and Hannezo group members for helpful discussions, the Bioimaging facility at ISTA, as well as Matthias Merkel and Lisa Manning for sharing the 3D Voronoi code. We also thank the Champalimaud animal facility, Anna Pezzarossa and the Champalimaud ABBE platform for the help with microscopy and image processing. This work was supported by EMBO (ALTF 522-2021), a Fundação para a Ciência e Tecnologia grant to A.S.D. (PTDC/MED-ONC/5553/2020), as well as the European Research Council (grant 851288 to EH). A.S.D., S.C., and R.M.S. are supported by QuantOCancer Project Horizon European Union’s Horizon 2020 program (grant agreement No 810653).","article_processing_charge":"Yes","date_published":"2025-09-26T00:00:00Z","title":"Mechanical control of cell fate decisions in the skin epidermis","quality_controlled":"1","date_updated":"2026-05-20T08:52:01Z","external_id":{"pmid":["41006218"],"isi":["001582555200011"]},"month":"09"},{"external_id":{"isi":["001581023000001"],"arxiv":["2509.05417"]},"quality_controlled":"1","date_updated":"2026-02-16T12:44:42Z","month":"09","volume":991,"title":"The light echo of a high-redshift quasar mapped with Lyα tomography","PlanS_conform":"1","date_published":"2025-09-25T00:00:00Z","arxiv":1,"article_processing_charge":"Yes","isi":1,"acknowledgement":"This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs #1243 and #4713.\r\n\r\nAll of the data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/w7hm-qb39.\r\nJ.M. is supported by the European Union (ERC, AGENTS, 101076224).","OA_type":"gold","type":"journal_article","publication_identifier":{"eissn":["2041-8213"],"issn":["2041-8205"]},"status":"public","citation":{"mla":"Eilers, Anna Christina, et al. “The Light Echo of a High-Redshift Quasar Mapped with Lyα Tomography.” The Astrophysical Journal Letters, vol. 991, no. 2, L40, IOP Publishing, 2025, doi:10.3847/2041-8213/ae057a.","short":"A.C. Eilers, M. Yue, J.J. Matthee, J.F. Hennawi, F.B. Davies, R.A. Simcoe, R. Teague, R. Bordoloi, G. Brammer, Y. Kang, D. Kashino, R. Mackenzie, R.P. Naidu, B. Navarrete, The Astrophysical Journal Letters 991 (2025).","ista":"Eilers AC, Yue M, Matthee JJ, Hennawi JF, Davies FB, Simcoe RA, Teague R, Bordoloi R, Brammer G, Kang Y, Kashino D, Mackenzie R, Naidu RP, Navarrete B. 2025. The light echo of a high-redshift quasar mapped with Lyα tomography. The Astrophysical Journal Letters. 991(2), L40.","apa":"Eilers, A. C., Yue, M., Matthee, J. J., Hennawi, J. F., Davies, F. B., Simcoe, R. A., … Navarrete, B. (2025). The light echo of a high-redshift quasar mapped with Lyα tomography. The Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ae057a","chicago":"Eilers, Anna Christina, Minghao Yue, Jorryt J Matthee, Joseph F. Hennawi, Frederick B. Davies, Robert A. Simcoe, Richard Teague, et al. “The Light Echo of a High-Redshift Quasar Mapped with Lyα Tomography.” The Astrophysical Journal Letters. IOP Publishing, 2025. https://doi.org/10.3847/2041-8213/ae057a.","ama":"Eilers AC, Yue M, Matthee JJ, et al. The light echo of a high-redshift quasar mapped with Lyα tomography. The Astrophysical Journal Letters. 2025;991(2). doi:10.3847/2041-8213/ae057a","ieee":"A. C. Eilers et al., “The light echo of a high-redshift quasar mapped with Lyα tomography,” The Astrophysical Journal Letters, vol. 991, no. 2. IOP Publishing, 2025."},"article_number":"L40","abstract":[{"lang":"eng","text":"Ultraviolet (UV) radiation from accreting black holes ionizes the intergalactic gas around early quasars, carving out highly ionized bubbles in their surroundings. Any changes in a quasar’s luminosity are therefore predicted to produce outward-propagating ionization gradients, affecting the Lyα absorption opacity near the quasar’s systemic redshift. This “proximity effect” is well-documented in rest-UV quasar spectra but only provides a one-dimensional probe along our line of sight. Here we present deep spectroscopic observations with the James Webb Space Telescope (JWST) of galaxies in the background of a superluminous quasar at zQSO ≈ 6.3, which reveal the quasar’s “light echo” with Lyα tomography in the transverse direction. This transverse proximity effect is detected for the first time toward multiple galaxy sightlines, allowing us to map the extent and geometry of the quasar’s ionization cone. We obtain constraints on the orientation and inclination of the cone, as well as an upper limit on the obscured solid angle fraction of fobsc < 91%. Additionally, we find a timescale of the quasar’s UV radiation of tqso = 10^5.6+0.1-0.3 yr, which is significantly shorter than would be required to build up the central supermassive black hole (SMBH) with conventional growth models, but is consistent with independent measurements of the quasars’ duty cycle. Our inferred obscured fraction disfavors a scenario where short quasar lifetimes can be explained exclusively by geometric obscuration, and instead supports the idea that radiatively inefficient accretion or growth in initially heavily enshrouded cocoons plays a pivotal role in early SMBH growth. Our results pave the way for novel studies of quasars’ ionizing geometries and radiative histories at early cosmic times."}],"scopus_import":"1","oa_version":"Published Version","publisher":"IOP Publishing","file_date_updated":"2025-10-13T09:25:12Z","ddc":["520"],"language":[{"iso":"eng"}],"author":[{"last_name":"Eilers","first_name":"Anna Christina","full_name":"Eilers, Anna Christina"},{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J"},{"full_name":"Hennawi, Joseph F.","first_name":"Joseph F.","last_name":"Hennawi"},{"last_name":"Davies","first_name":"Frederick B.","full_name":"Davies, Frederick B."},{"first_name":"Robert A.","last_name":"Simcoe","full_name":"Simcoe, Robert A."},{"full_name":"Teague, Richard","first_name":"Richard","last_name":"Teague"},{"full_name":"Bordoloi, Rongmon","last_name":"Bordoloi","first_name":"Rongmon"},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"full_name":"Kang, Yi","last_name":"Kang","first_name":"Yi"},{"full_name":"Kashino, Daichi","last_name":"Kashino","first_name":"Daichi"},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"id":"aa14a535-50c9-11ef-b52e-e0c373d10148","full_name":"Navarrete, Benjamín","first_name":"Benjamín","last_name":"Navarrete"}],"publication_status":"published","oa":1,"project":[{"name":"Young galaxies as tracers and agents of cosmic reionization","_id":"bd9b2118-d553-11ed-ba76-db24564edfea","grant_number":"101076224"}],"file":[{"relation":"main_file","date_updated":"2025-10-13T09:25:12Z","content_type":"application/pdf","file_size":23585591,"success":1,"file_id":"20461","date_created":"2025-10-13T09:25:12Z","file_name":"2025_AstrophysicalJour_Eilers.pdf","access_level":"open_access","checksum":"3cb8099b9a915755164e5675b33f8a03","creator":"dernst"}],"doi":"10.3847/2041-8213/ae057a","intvolume":" 991","year":"2025","DOAJ_listed":"1","date_created":"2025-10-05T22:01:35Z","article_type":"original","day":"25","OA_place":"publisher","publication":"The Astrophysical Journal Letters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20425","issue":"2","department":[{"_id":"JoMa"},{"_id":"GradSch"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1"},{"volume":19,"date_published":"2025-09-30T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grant No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002), and the Fundamental Research Funds for the Central Universities (JZ2024HGTB0239). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293) and the National Foreign Expert Project (Y20240175). Y.Z. acknowledges funding from the NSFC (Grant No. 52502313) and Wenzhou Basic Scientific Research Project (Grant No. G20240034). Q.W. acknowledges the financial support from the NSFC (Grant No. 22208292) and the “Pioneer” and “Leading Goose” R&D Program of Zhejiang (2025C04021). K.H.L. and Q.W. also acknowledge the Research Funds of the Institute of Zhejiang University-Quzhou (Nos. IZQ2022RCZX101, IZQ2021RCZX003, and IZQ2021RCZX002). M.H. acknowledges the funding from the Australian Research Council and the iLAuNCH Trailblazer, Department of Education, Australia. M.H. acknowledges the computational support from the National Computational Infrastructure (NCI), Australia and Pawsey Supercomputing Centre, Australia. The author also thanks Dr. Lijian Huang and Mr. Mincheng Yu at the Institute of Zhejiang University for the swift technical assistance during XPS characterization and quantification.","title":"Thiol-Amine complexes for the synthesis and surface engineering of SnTe nanomaterials toward high thermoelectric performance","quality_controlled":"1","date_updated":"2025-12-01T12:50:24Z","external_id":{"pmid":["40974325"],"isi":["001575398100001"]},"month":"09","citation":{"ieee":"W. Meng et al., “Thiol-Amine complexes for the synthesis and surface engineering of SnTe nanomaterials toward high thermoelectric performance,” ACS Nano, vol. 19, no. 38. American Chemical Society, pp. 34395–34407, 2025.","ama":"Meng W, Xu L, Lu S, et al. Thiol-Amine complexes for the synthesis and surface engineering of SnTe nanomaterials toward high thermoelectric performance. ACS Nano. 2025;19(38):34395-34407. doi:10.1021/acsnano.5c12627","chicago":"Meng, Weite, Lixiang Xu, Shaoqing Lu, Mingquan Li, Mengyao Li, Yu Zhang, Qingyue Wang, et al. “Thiol-Amine Complexes for the Synthesis and Surface Engineering of SnTe Nanomaterials toward High Thermoelectric Performance.” ACS Nano. American Chemical Society, 2025. https://doi.org/10.1021/acsnano.5c12627.","apa":"Meng, W., Xu, L., Lu, S., Li, M., Li, M., Zhang, Y., … Lim, K. H. (2025). Thiol-Amine complexes for the synthesis and surface engineering of SnTe nanomaterials toward high thermoelectric performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.5c12627","ista":"Meng W, Xu L, Lu S, Li M, Li M, Zhang Y, Wang Q, Wang WJ, Huo S, Bañares MA, Martin-Gonzalez M, Ibáñez M, Cabot A, Hong M, Liu Y, Lim KH. 2025. Thiol-Amine complexes for the synthesis and surface engineering of SnTe nanomaterials toward high thermoelectric performance. ACS Nano. 19(38), 34395–34407.","short":"W. Meng, L. Xu, S. Lu, M. Li, M. Li, Y. Zhang, Q. Wang, W.J. Wang, S. Huo, M.A. Bañares, M. Martin-Gonzalez, M. Ibáñez, A. Cabot, M. Hong, Y. Liu, K.H. Lim, ACS Nano 19 (2025) 34395–34407.","mla":"Meng, Weite, et al. “Thiol-Amine Complexes for the Synthesis and Surface Engineering of SnTe Nanomaterials toward High Thermoelectric Performance.” ACS Nano, vol. 19, no. 38, American Chemical Society, 2025, pp. 34395–407, doi:10.1021/acsnano.5c12627."},"abstract":[{"text":"SnTe has attracted significant research interest as a lead-free alternative to PbTe; however, its intrinsically high hole concentration results in an undesirably low Seebeck coefficient and elevated electronic thermal conductivity, thus significantly limiting its thermoelectric (TE) performance. Herein, we present a cost-effective, binary thiol-amine-mediated colloidal synthesis method to synthesize Bi-doped SnTe nanoparticles, eliminating the use of tri-n-octylphosphine-based precursors. The introduction of an electron-rich Bi dopant reduces the hole concentration and increases the Seebeck coefficient. Furthermore, post-synthetic surface treatment with chalcogenidocadmate complexes promotes atomic interdiffusion during annealing and consolidation, leading to compositional redistribution and modulation of the electronic band structure. Density functional theory (DFT) calculations reveal that co-modification via Bi doping and CdSe-derived chalcogen incorporation reduces the energy offset at the valence band maxima from 0.30 eV to 0.10 eV, thereby enhancing valence band degeneracy. The synergistic structural and electronic band structure modulations produce an SnTe-based material with a record high power factor of 2.1 mW m–1 K–2 at 900 K, a maximum TE figure of merit (zT) of 1.2, and a promising theoretical conversion efficiency of 8.3%. This study reports a versatile and scalable colloidal synthesis strategy that integrates hierarchical structural modulation with electronic band engineering, offering a synergistic route to significantly enhance the TE performance.","lang":"eng"}],"scopus_import":"1","oa_version":"None","publisher":"American Chemical Society","OA_type":"closed access","status":"public","type":"journal_article","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"year":"2025","article_type":"original","date_created":"2025-10-05T22:01:35Z","language":[{"iso":"eng"}],"author":[{"last_name":"Meng","first_name":"Weite","full_name":"Meng, Weite"},{"full_name":"Xu, Lixiang","first_name":"Lixiang","last_name":"Xu"},{"full_name":"Lu, Shaoqing","first_name":"Shaoqing","last_name":"Lu"},{"first_name":"Mingquan","last_name":"Li","full_name":"Li, Mingquan"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Wang, Qingyue","first_name":"Qingyue","last_name":"Wang"},{"full_name":"Wang, Wen Jun","first_name":"Wen Jun","last_name":"Wang"},{"full_name":"Huo, Siqi","last_name":"Huo","first_name":"Siqi"},{"full_name":"Bañares, Miguel A.","first_name":"Miguel A.","last_name":"Bañares"},{"last_name":"Martin-Gonzalez","first_name":"Marisol","full_name":"Martin-Gonzalez, Marisol"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"},{"full_name":"Hong, Min","last_name":"Hong","first_name":"Min"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"}],"intvolume":" 19","publication_status":"published","doi":"10.1021/acsnano.5c12627","pmid":1,"_id":"20426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"38","department":[{"_id":"MaIb"}],"page":"34395-34407","day":"30","publication":"ACS Nano"},{"volume":35,"article_processing_charge":"No","date_published":"2025-09-22T00:00:00Z","isi":1,"title":"Cell migration: How animal cells run and tumble","quality_controlled":"1","date_updated":"2025-12-01T12:54:02Z","external_id":{"isi":["001592664700001"],"pmid":["40987270"]},"month":"09","abstract":[{"lang":"eng","text":"Animal cells migrating up chemotactic gradients often show speed oscillations. A new study describes a molecular circuit that switches zebrafish germ cells between phases of straight runs, tumbling and directional reorientation."}],"scopus_import":"1","citation":{"mla":"LI, ZIQIANG, and Michael K. Sixt. “Cell Migration: How Animal Cells Run and Tumble.” Current Biology, vol. 35, no. 18, Elsevier, 2025, pp. R890–92, doi:10.1016/j.cub.2025.08.016.","short":"Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892.","ista":"LI Z, Sixt MK. 2025. Cell migration: How animal cells run and tumble. Current Biology. 35(18), R890–R892.","apa":"LI, Z., & Sixt, M. K. (2025). Cell migration: How animal cells run and tumble. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2025.08.016","chicago":"LI, ZIQIANG, and Michael K Sixt. “Cell Migration: How Animal Cells Run and Tumble.” Current Biology. Elsevier, 2025. https://doi.org/10.1016/j.cub.2025.08.016.","ama":"LI Z, Sixt MK. Cell migration: How animal cells run and tumble. Current Biology. 2025;35(18):R890-R892. doi:10.1016/j.cub.2025.08.016","ieee":"Z. LI and M. K. Sixt, “Cell migration: How animal cells run and tumble,” Current Biology, vol. 35, no. 18. Elsevier, pp. R890–R892, 2025."},"oa_version":"None","publisher":"Elsevier","OA_type":"closed access","status":"public","type":"journal_article","publication_identifier":{"eissn":["1879-0445"]},"year":"2025","article_type":"letter_note","date_created":"2025-10-05T22:01:35Z","language":[{"iso":"eng"}],"author":[{"id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","full_name":"Li, Ziqiang","last_name":"Li","first_name":"Ziqiang"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"intvolume":" 35","publication_status":"published","doi":"10.1016/j.cub.2025.08.016","pmid":1,"_id":"20427","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"}],"issue":"18","page":"R890-R892","day":"22","publication":"Current Biology","corr_author":"1"},{"article_type":"editorial","date_created":"2025-10-05T22:01:35Z","DOAJ_listed":"1","year":"2025","intvolume":" 21","file":[{"file_id":"20462","success":1,"date_created":"2025-10-13T11:18:02Z","access_level":"open_access","file_name":"2025_BeilsteinJourOrgChemistry_Noel.pdf","checksum":"45a4ac237e55fdcad168aeb5bd5be61d","creator":"dernst","date_updated":"2025-10-13T11:18:02Z","content_type":"application/pdf","relation":"main_file","file_size":117869}],"doi":"10.3762/bjoc.21.128","publication_status":"published","oa":1,"author":[{"first_name":"Timothy","last_name":"Noël","full_name":"Noël, Timothy"},{"orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","last_name":"Pieber","full_name":"Pieber, Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"}],"ddc":["540"],"language":[{"iso":"eng"}],"file_date_updated":"2025-10-13T11:18:02Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"1645-1647","pmid":1,"department":[{"_id":"BaPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20428","publication":"Beilstein Journal of Organic Chemistry","OA_place":"publisher","corr_author":"1","day":"18","acknowledgement":"The Graphical Abstract was created with the AI tool https://wordart.com. This content is not subject to CC BY 4.0.","article_processing_charge":"No","date_published":"2025-08-18T00:00:00Z","PlanS_conform":"1","title":"Photocatalysis and photochemistry in organic synthesis","volume":21,"month":"08","date_updated":"2025-10-13T11:21:01Z","quality_controlled":"1","external_id":{"pmid":["40927207"]},"publisher":"Beilstein Institut","oa_version":"Published Version","citation":{"ama":"Noël T, Pieber B. Photocatalysis and photochemistry in organic synthesis. Beilstein Journal of Organic Chemistry. 2025;21:1645-1647. doi:10.3762/bjoc.21.128","ieee":"T. Noël and B. Pieber, “Photocatalysis and photochemistry in organic synthesis,” Beilstein Journal of Organic Chemistry, vol. 21. Beilstein Institut, pp. 1645–1647, 2025.","mla":"Noël, Timothy, and Bartholomäus Pieber. “Photocatalysis and Photochemistry in Organic Synthesis.” Beilstein Journal of Organic Chemistry, vol. 21, Beilstein Institut, 2025, pp. 1645–47, doi:10.3762/bjoc.21.128.","ista":"Noël T, Pieber B. 2025. Photocatalysis and photochemistry in organic synthesis. Beilstein Journal of Organic Chemistry. 21, 1645–1647.","short":"T. Noël, B. Pieber, Beilstein Journal of Organic Chemistry 21 (2025) 1645–1647.","apa":"Noël, T., & Pieber, B. (2025). Photocatalysis and photochemistry in organic synthesis. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.21.128","chicago":"Noël, Timothy, and Bartholomäus Pieber. “Photocatalysis and Photochemistry in Organic Synthesis.” Beilstein Journal of Organic Chemistry. Beilstein Institut, 2025. https://doi.org/10.3762/bjoc.21.128."},"scopus_import":"1","status":"public","publication_identifier":{"eissn":["1860-5397"]},"type":"journal_article","OA_type":"diamond"},{"article_type":"original","date_created":"2025-10-05T22:01:36Z","year":"2025","intvolume":" 226","doi":"10.1007/s11258-025-01568-0","publication_status":"published","author":[{"full_name":"Bustamante, Gimena Noemí","last_name":"Bustamante","first_name":"Gimena Noemí"},{"full_name":"Arena, Miriam Elisabet","last_name":"Arena","first_name":"Miriam Elisabet"},{"full_name":"Selzer, Luciano","last_name":"Selzer","first_name":"Luciano"},{"last_name":"Ruggirello","first_name":"Matthew","full_name":"Ruggirello, Matthew"},{"full_name":"Rodríguez, Paula","first_name":"Paula","last_name":"Rodríguez"},{"full_name":"Pedrazzani, Samuele","last_name":"Pedrazzani","first_name":"Samuele"},{"first_name":"Jose Antonio","last_name":"Navarro-Cano","full_name":"Navarro-Cano, Jose Antonio"},{"last_name":"Soler Schaller","first_name":"Rosina Matilde","full_name":"Soler Schaller, Rosina Matilde","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803"}],"language":[{"iso":"eng"}],"page":"1301-1313","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20429","publication":"Plant Ecology","day":"01","isi":1,"date_published":"2025-12-01T00:00:00Z","article_processing_charge":"No","title":"Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests","volume":226,"month":"12","quality_controlled":"1","date_updated":"2026-01-05T13:23:57Z","external_id":{"isi":["001581599800001"]},"publisher":"Springer Nature","oa_version":"None","scopus_import":"1","citation":{"ista":"Bustamante GN, Arena ME, Selzer L, Ruggirello M, Rodríguez P, Pedrazzani S, Navarro-Cano JA, Soler Schaller RM. 2025. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. Plant Ecology. 226, 1301–1313.","short":"G.N. Bustamante, M.E. Arena, L. Selzer, M. Ruggirello, P. Rodríguez, S. Pedrazzani, J.A. Navarro-Cano, R.M. Soler Schaller, Plant Ecology 226 (2025) 1301–1313.","mla":"Bustamante, Gimena Noemí, et al. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” Plant Ecology, vol. 226, Springer Nature, 2025, pp. 1301–13, doi:10.1007/s11258-025-01568-0.","chicago":"Bustamante, Gimena Noemí, Miriam Elisabet Arena, Luciano Selzer, Matthew Ruggirello, Paula Rodríguez, Samuele Pedrazzani, Jose Antonio Navarro-Cano, and Rosina Matilde Soler Schaller. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” Plant Ecology. Springer Nature, 2025. https://doi.org/10.1007/s11258-025-01568-0.","apa":"Bustamante, G. N., Arena, M. E., Selzer, L., Ruggirello, M., Rodríguez, P., Pedrazzani, S., … Soler Schaller, R. M. (2025). Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. Plant Ecology. Springer Nature. https://doi.org/10.1007/s11258-025-01568-0","ama":"Bustamante GN, Arena ME, Selzer L, et al. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. Plant Ecology. 2025;226:1301-1313. doi:10.1007/s11258-025-01568-0","ieee":"G. N. Bustamante et al., “Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests,” Plant Ecology, vol. 226. Springer Nature, pp. 1301–1313, 2025."},"abstract":[{"lang":"eng","text":"Plant–plant interactions are key to understanding ecosystem services and shaping restoration strategies, as they can produce either negative or positive effects, determining species establishment and growth. Recognizing these interactions during early-life stages provides valuable insights for restoration in human-disturbed areas. One promising approach is nucleation planting, which establishes small clusters of native species in strategically selected sites, being particularly useful in sites with large herbivores. In southern Patagonia, livestock production has historically been the main economic activity, severely impacting extensive areas of Nothofagus antarctica forest through grazing and intentional burning to increase forage. In this context, nucleation planting with Berberis microphylla, a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate this, we conducted an experiment testing the response of trees to varying shrub number, while also assessing intraspecific effects in both species. We measured survival, biomass, and functional traits. Results showed that the combination of four shrubs surrounding a single tree maintained tree survival at levels comparable to trees growing alone, while seedlings exhibited conspecific negative plant number dependence. Additionally, B. microphylla increased its below- to above-ground biomass ratio under higher plant number, indicating resource reallocation and niche differentiation through spatial separation of root systems."}],"status":"public","publication_identifier":{"eissn":["1573-5052"],"issn":["1385-0237"]},"type":"journal_article","OA_type":"closed access"},{"article_type":"original","date_created":"2025-10-05T22:01:36Z","year":"2025","intvolume":" 647","oa":1,"publication_status":"published","file":[{"file_size":22099921,"content_type":"application/pdf","date_updated":"2026-01-05T13:17:47Z","relation":"main_file","date_created":"2026-01-05T13:17:47Z","file_id":"20951","success":1,"checksum":"b4ec44134e2eb320a724dc29158dfda2","creator":"dernst","access_level":"open_access","file_name":"2025_Nature_Broerman.pdf"}],"doi":"10.1038/s41586-025-09549-z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"first_name":"Adam J.","last_name":"Broerman","full_name":"Broerman, Adam J."},{"last_name":"Pollmann","first_name":"Christoph","full_name":"Pollmann, Christoph"},{"first_name":"Yang","last_name":"Zhao","full_name":"Zhao, Yang"},{"full_name":"Lichtenstein, Mauriz A.","first_name":"Mauriz A.","last_name":"Lichtenstein"},{"first_name":"Mark D.","last_name":"Jackson","full_name":"Jackson, Mark D."},{"first_name":"Maxx H.","last_name":"Tessmer","full_name":"Tessmer, Maxx H."},{"last_name":"Ryu","first_name":"Won Hee","full_name":"Ryu, Won Hee"},{"full_name":"Ogishi, Masato","first_name":"Masato","last_name":"Ogishi"},{"last_name":"Abedi","first_name":"Mohamad H.","full_name":"Abedi, Mohamad H."},{"last_name":"Sahtoe","first_name":"Danny D.","full_name":"Sahtoe, Danny D."},{"first_name":"Aza","last_name":"Allen","full_name":"Allen, Aza"},{"first_name":"Alex","last_name":"Kang","full_name":"Kang, Alex"},{"full_name":"De La Cruz, Joshmyn","last_name":"De La Cruz","first_name":"Joshmyn"},{"full_name":"Brackenbrough, Evans","last_name":"Brackenbrough","first_name":"Evans"},{"full_name":"Sankaran, Banumathi","first_name":"Banumathi","last_name":"Sankaran"},{"last_name":"Bera","first_name":"Asim K.","full_name":"Bera, Asim K."},{"full_name":"Zuckerman, Daniel M.","first_name":"Daniel M.","last_name":"Zuckerman"},{"last_name":"Stoll","first_name":"Stefan","full_name":"Stoll, Stefan"},{"full_name":"Garcia, K. Christopher","first_name":"K. Christopher","last_name":"Garcia"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius","orcid":"0000-0002-0806-8101"},{"last_name":"Piehler","first_name":"Jacob","full_name":"Piehler, Jacob"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"file_date_updated":"2026-01-05T13:17:47Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","page":"528-535","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20430","department":[{"_id":"FlPr"}],"publication":"Nature","corr_author":"1","OA_place":"publisher","day":"13","article_processing_charge":"Yes (in subscription journal)","date_published":"2025-11-13T00:00:00Z","isi":1,"acknowledgement":"We thank P. J. Y. Leung, K. L. Shelley, A. Pillai, C. Demakis, M. Exposit, K. Thompson, C. Savvides, R. J. Ragotte, G. Ahn and M. Glögl for discussions and technical support; K. VanWormer and L. Goldschmidt for technical support; S. R. Gerben and A. Murray for protein production support; and X. Li, M. Lamb, Z. Taylor and V. Adebomi for LC–MS support. This work was supported by the Audacious Project at the Institute for Protein Design (A.J.B., A.K., J.D.L.C., E.B. and A.K.B.); by a gift from Microsoft (A.J.B.); by the Nordstrom Barrier Institute for Protein Design Directors Fund (M.H.A. and F.P.); by Bill and Melinda Gates Foundation OPP1156262 (A.K. and J.D.L.C.); by the Open Philanthropy Project Improving Protein Design Fund (E.B. and A.K.B.); by the National Institutes of Health (NIH) National Institute of Allergy and Infectious Disease grant R0AI160052 (A.K.B.); by CRI Irvington Postdoctoral Fellowship 315511 (Y.Z.); by National Cancer Institute K00 award 4K00CA274708 (M.O.); by National Science Foundation grant MCB 2119837 and NIH grant GM115805 (W.H.R. and D.M.Z.); by NIH grant GM151956 (S.S.); by NIH AI-51321 (K.C.G.); by the DFG grants PI 405/15 and SFB 1557 (C.P. and J.P.); and by the Howard Hughes Medical Institute (A.K.B., K.C.G. and D.B.). The EPR spectrometer used for the DEER experiments was in part supported by NIH grant S10OD021557. This research used resources (FMX/AMX) of the National Synchrotron Light Source II, a US Department of Energy (DoE) Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under contract DE-SC0012704. The Center for BioMolecular Structure (CBMS) is supported mainly by the NIH National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DoE Office of Biological and Environmental Research (KP1607011). This work is based on research performed at the Northeastern Collaborative Access Team beamlines, which are funded by the NIGMS (P30 GM124165). The research used resources of the Advanced Photon Source, a US DoE Office of Science User Facility operated for the DoE Office of Science by Argonne National Laboratory under contract DE-AC02-06CH11357. The Berkeley Center for Structural Biology is supported by the NIH, NIGMS and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences and US DoE (DE-AC02-05CH11231).","title":"Design of facilitated dissociation enables timing of cytokine signalling","PlanS_conform":"1","volume":647,"month":"11","quality_controlled":"1","date_updated":"2026-01-05T13:18:17Z","external_id":{"isi":["001577755600001"],"pmid":["40993395"]},"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Protein design has focused on the design of ground states, ensuring that they are sufficiently low energy to be highly populated1. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another2,3. This is a challenging task because such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have focused on generating near-ideal structures4,5,6,7. Here we describe a general approach for designing systems that use an induced-fit power stroke8 to generate a structurally frustrated9 and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron–electron resonance spectroscopy and kinetic binding measurements show that incorporating excited states enables the design of effector-induced increases in dissociation rates as high as 5,700-fold. We highlight the power of this approach by designing rapid biosensors, kinetically controlled circuits and cytokine mimics that can be dissociated from their receptors within seconds, enabling dissection of the temporal dynamics of interleukin-2 signalling."}],"citation":{"ieee":"A. J. Broerman et al., “Design of facilitated dissociation enables timing of cytokine signalling,” Nature, vol. 647. Springer Nature, pp. 528–535, 2025.","ama":"Broerman AJ, Pollmann C, Zhao Y, et al. Design of facilitated dissociation enables timing of cytokine signalling. Nature. 2025;647:528-535. doi:10.1038/s41586-025-09549-z","chicago":"Broerman, Adam J., Christoph Pollmann, Yang Zhao, Mauriz A. Lichtenstein, Mark D. Jackson, Maxx H. Tessmer, Won Hee Ryu, et al. “Design of Facilitated Dissociation Enables Timing of Cytokine Signalling.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-09549-z.","apa":"Broerman, A. J., Pollmann, C., Zhao, Y., Lichtenstein, M. A., Jackson, M. D., Tessmer, M. H., … Baker, D. (2025). Design of facilitated dissociation enables timing of cytokine signalling. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09549-z","ista":"Broerman AJ, Pollmann C, Zhao Y, Lichtenstein MA, Jackson MD, Tessmer MH, Ryu WH, Ogishi M, Abedi MH, Sahtoe DD, Allen A, Kang A, De La Cruz J, Brackenbrough E, Sankaran B, Bera AK, Zuckerman DM, Stoll S, Garcia KC, Praetorius FM, Piehler J, Baker D. 2025. Design of facilitated dissociation enables timing of cytokine signalling. Nature. 647, 528–535.","short":"A.J. Broerman, C. Pollmann, Y. Zhao, M.A. Lichtenstein, M.D. Jackson, M.H. Tessmer, W.H. Ryu, M. Ogishi, M.H. Abedi, D.D. Sahtoe, A. Allen, A. Kang, J. De La Cruz, E. Brackenbrough, B. Sankaran, A.K. Bera, D.M. Zuckerman, S. Stoll, K.C. Garcia, F.M. Praetorius, J. Piehler, D. Baker, Nature 647 (2025) 528–535.","mla":"Broerman, Adam J., et al. “Design of Facilitated Dissociation Enables Timing of Cytokine Signalling.” Nature, vol. 647, Springer Nature, 2025, pp. 528–35, doi:10.1038/s41586-025-09549-z."},"scopus_import":"1","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"OA_type":"hybrid"},{"publication":"Nature Physics","corr_author":"1","OA_place":"repository","day":"01","page":"1638-1647","_id":"20431","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EdHa"}],"intvolume":" 21","oa":1,"publication_status":"published","doi":"10.1038/s41567-025-03015-3","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Isabela Corina","last_name":"Fortunato","full_name":"Fortunato, Isabela Corina"},{"orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Steffen","last_name":"Grosser","full_name":"Grosser, Steffen"},{"full_name":"Nautiyal, Rohit","first_name":"Rohit","last_name":"Nautiyal"},{"full_name":"Rossetti, Leone","last_name":"Rossetti","first_name":"Leone"},{"first_name":"Miquel","last_name":"Bosch-Padrós","full_name":"Bosch-Padrós, Miquel"},{"first_name":"Jonel","last_name":"Trebicka","full_name":"Trebicka, Jonel"},{"first_name":"Pere","last_name":"Roca-Cusachs","full_name":"Roca-Cusachs, Pere"},{"full_name":"Sunyer, Raimon","last_name":"Sunyer","first_name":"Raimon"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Trepat, Xavier","first_name":"Xavier","last_name":"Trepat"}],"article_type":"original","date_created":"2025-10-05T22:01:36Z","year":"2025","status":"public","type":"journal_article","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.12.02.626413"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Haptotaxis is the process of directed cell migration along gradients of extracellular matrix density and is central to morphogenesis, immune responses and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a wide range of complex trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behaviour, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. Although initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer timescales arise from the interplay between differential friction, persistence and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework for understanding how cells navigate complex environments."}],"citation":{"ama":"Fortunato IC, Brückner D, Grosser S, et al. Single-cell migration along and against confined haptotactic gradients. Nature Physics. 2025;21:1638-1647. doi:10.1038/s41567-025-03015-3","ieee":"I. C. Fortunato et al., “Single-cell migration along and against confined haptotactic gradients,” Nature Physics, vol. 21. Springer Nature, pp. 1638–1647, 2025.","ista":"Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell migration along and against confined haptotactic gradients. Nature Physics. 21, 1638–1647.","short":"I.C. Fortunato, D. Brückner, S. Grosser, R. Nautiyal, L. Rossetti, M. Bosch-Padrós, J. Trebicka, P. Roca-Cusachs, R. Sunyer, E.B. Hannezo, X. Trepat, Nature Physics 21 (2025) 1638–1647.","mla":"Fortunato, Isabela Corina, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” Nature Physics, vol. 21, Springer Nature, 2025, pp. 1638–47, doi:10.1038/s41567-025-03015-3.","chicago":"Fortunato, Isabela Corina, David Brückner, Steffen Grosser, Rohit Nautiyal, Leone Rossetti, Miquel Bosch-Padrós, Jonel Trebicka, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” Nature Physics. Springer Nature, 2025. https://doi.org/10.1038/s41567-025-03015-3.","apa":"Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós, M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic gradients. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03015-3"},"scopus_import":"1","oa_version":"Preprint","month":"10","date_updated":"2026-01-05T14:26:28Z","quality_controlled":"1","external_id":{"isi":["001581659900001"]},"date_published":"2025-10-01T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"We thank all the members of our groups for discussions and support. We thank A. Menéndez, S. Usieto, M. Purciolas and E. Coderch for technical assistance. We thank G. Charras (London Centre for Nanotechnology, UK) and M. Sheetz (Columbia University, USA) for sharing cells used in this work. We thank J. Ivaska (University of Turku, Finland) for sharing integrin α5-GFP DNA plasmid. We thank P. Guillamat for technical advice and A. Labernardie for providing the microfluidic channels. We thank M. Gómez-González for sharing the 2D traction microscopy algorithm. Finally, we thank P. Guillamat, J. Abenza, G. Ceada, L. Faure, E. Dalaka, M. Matejčić, A. Beedle, I. Granero, O. Baguer, A. Albajar and N. Chahare for discussions. This paper was funded by the Generalitat de Catalunya (Grant Nos. AGAUR SGR-2017-01602 to X.T. and 2021 SGR 00523 to R.S. and the CERCA Programme and ICREA Academia awards to P.R.-C.), the Spanish Ministry for Science and Innovation MICCINN/FEDER (Grant Nos. PID2021-128635NB-I00, MCIN/AEI/10.13039/501100011033 and ERDF-EU A way of making Europe to X.T., PID2021-128674OB-I00 and CNS2022-135533 to R.S. and PID2019-110298GB-I00 to P.R.-C.), the European Research Council (Grant Nos. 101097753 to P.R.-C. and Adv-883739 to X.T.), Fundació la Marató de TV3 (Project Award 201903-30-31-32 to X.T.), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957 to P.R.-C. and X.T.) and La Caixa Foundation (Grant No. LCF/PR/HR20/52400004 to P.R.-C. and X.T.). R.S. is a Serra-Hunter fellow. D.B.B. was supported by the NOMIS foundation as a NOMIS fellow, by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and by the Austrian Academy of Sciences through an APART-MINT Fellowship. I.C.F. acknowledges support from the European Foundation for the Study of Chronic Liver Failure. IBEC is recipient of a Severo Ochoa Award of Excellence from MINECO.","title":"Single-cell migration along and against confined haptotactic gradients","volume":21}]