--- _id: '17362' abstract: - lang: eng text: This is the supplementary data for the paper titled "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:10.15479/AT:ISTA:17362' apa: 'Elkrewi, M. N., & Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17362' chicago: 'Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17362.' ieee: 'M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.' ista: 'Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17362.' mla: 'Elkrewi, Marwan N., and Beatriz Vicoso. Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17362.' short: M.N. Elkrewi, B. Vicoso, (2024). corr_author: '1' date_created: 2024-08-02T07:27:45Z date_published: 2024-08-05T00:00:00Z date_updated: 2026-09-24T11:17:37Z day: '05' ddc: - '576' department: - _id: GradSch - _id: BeVi doi: 10.15479/AT:ISTA:17362 file: - access_level: open_access checksum: 26b5d41b3103f4284dd97d56e370a5b6 content_type: text/plain creator: melkrewi date_created: 2024-08-05T22:24:18Z date_updated: 2024-08-05T22:24:18Z file_id: '17394' file_name: README.txt file_size: 2465 relation: main_file success: 1 - access_level: open_access checksum: 95adab5e36148015da313505e3910707 content_type: application/x-zip-compressed creator: melkrewi date_created: 2024-08-05T23:28:52Z date_updated: 2024-08-05T23:28:52Z file_id: '17395' file_name: Data_artemia_single_nucleus_atlas.zip file_size: 2526735400 relation: main_file success: 1 file_date_updated: 2024-08-05T23:28:52Z fulldoi: https://doi.org/10.15479/AT:ISTA:17362 has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publisher: Institute of Science and Technology Austria related_material: record: - id: '17890' relation: used_in_publication status: public status: public title: 'Data for: "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome"' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18952' abstract: - lang: eng text: 'A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.' acknowledgement: "The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett, J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge numerous CCDC colleagues for\r\ntheir helpful feedback and suggestions on the manuscript (P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python knowledge (A. Moldovan), providing and maintaining internal compute resources (K. Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind test meeting (E. Clarke),and improvements to the Crystal Packing Similarity tool (M.\r\nRead). Data analysis was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/T022159/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). N. Francia thanks M. Salvalaglio for advice on the metadynamics simulations and the University College London for providing access to the Kathleen High Performance Computing Facility Kathleen@UCL) on which simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson for counselling on crystal structure similarity. I. Sugden and N. Francia participated in the blind test as members of Groups 1 and 24, respectively. They were involved in the analysis of the results.\r\nand in writing this paper only after all results were made\r\navailable to participants." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lily M. full_name: Hunnisett, Lily M. last_name: Hunnisett - first_name: Jonas full_name: Nyman, Jonas last_name: Nyman - first_name: Nicholas full_name: Francia, Nicholas last_name: Francia - first_name: Nathan S. full_name: Abraham, Nathan S. last_name: Abraham - first_name: Claire S. full_name: Adjiman, Claire S. last_name: Adjiman - first_name: Srinivasulu full_name: Aitipamula, Srinivasulu last_name: Aitipamula - first_name: Tamador full_name: Alkhidir, Tamador last_name: Alkhidir - first_name: Mubarak full_name: Almehairbi, Mubarak last_name: Almehairbi - first_name: Andrea full_name: Anelli, Andrea last_name: Anelli - first_name: Dylan M. full_name: Anstine, Dylan M. last_name: Anstine - first_name: John E. full_name: Anthony, John E. last_name: Anthony - first_name: Joseph E. full_name: Arnold, Joseph E. last_name: Arnold - first_name: Faezeh full_name: Bahrami, Faezeh last_name: Bahrami - first_name: Michael A. full_name: Bellucci, Michael A. last_name: Bellucci - first_name: Rajni M. full_name: Bhardwaj, Rajni M. last_name: Bhardwaj - first_name: Imanuel full_name: Bier, Imanuel last_name: Bier - first_name: Joanna A. full_name: Bis, Joanna A. last_name: Bis - first_name: A. Daniel full_name: Boese, A. Daniel last_name: Boese - first_name: David H. full_name: Bowskill, David H. last_name: Bowskill - first_name: James full_name: Bramley, James last_name: Bramley - first_name: Jan Gerit full_name: Brandenburg, Jan Gerit last_name: Brandenburg - first_name: Doris E. full_name: Braun, Doris E. last_name: Braun - first_name: Patrick W. V. full_name: Butler, Patrick W. V. last_name: Butler - first_name: Joseph full_name: Cadden, Joseph last_name: Cadden - first_name: Stephen full_name: Carino, Stephen last_name: Carino - first_name: Eric J. full_name: Chan, Eric J. last_name: Chan - first_name: Chao full_name: Chang, Chao last_name: Chang - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Sarah M. full_name: Clarke, Sarah M. last_name: Clarke - first_name: Simon J. full_name: Coles, Simon J. last_name: Coles - first_name: Richard I. full_name: Cooper, Richard I. last_name: Cooper - first_name: Ricky full_name: Couch, Ricky last_name: Couch - first_name: Ramon full_name: Cuadrado, Ramon last_name: Cuadrado - first_name: Tom full_name: Darden, Tom last_name: Darden - first_name: Graeme M. full_name: Day, Graeme M. last_name: Day - first_name: Hanno full_name: Dietrich, Hanno last_name: Dietrich - first_name: Yiming full_name: Ding, Yiming last_name: Ding - first_name: Antonio full_name: DiPasquale, Antonio last_name: DiPasquale - first_name: Bhausaheb full_name: Dhokale, Bhausaheb last_name: Dhokale - first_name: Bouke P. full_name: van Eijck, Bouke P. last_name: van Eijck - first_name: Mark R. J. full_name: Elsegood, Mark R. J. last_name: Elsegood - first_name: Dzmitry full_name: Firaha, Dzmitry last_name: Firaha - first_name: Wenbo full_name: Fu, Wenbo last_name: Fu - first_name: Kaori full_name: Fukuzawa, Kaori last_name: Fukuzawa - first_name: Joseph full_name: Glover, Joseph last_name: Glover - first_name: Hitoshi full_name: Goto, Hitoshi last_name: Goto - first_name: Chandler full_name: Greenwell, Chandler last_name: Greenwell - first_name: Rui full_name: Guo, Rui last_name: Guo - first_name: Jürgen full_name: Harter, Jürgen last_name: Harter - first_name: Julian full_name: Helfferich, Julian last_name: Helfferich - first_name: Detlef W. M. full_name: Hofmann, Detlef W. M. last_name: Hofmann - first_name: Johannes full_name: Hoja, Johannes last_name: Hoja - first_name: John full_name: Hone, John last_name: Hone - first_name: Richard full_name: Hong, Richard last_name: Hong - first_name: Geoffrey full_name: Hutchison, Geoffrey last_name: Hutchison - first_name: Yasuhiro full_name: Ikabata, Yasuhiro last_name: Ikabata - first_name: Olexandr full_name: Isayev, Olexandr last_name: Isayev - first_name: Ommair full_name: Ishaque, Ommair last_name: Ishaque - first_name: Varsha full_name: Jain, Varsha last_name: Jain - first_name: Yingdi full_name: Jin, Yingdi last_name: Jin - first_name: Aling full_name: Jing, Aling last_name: Jing - first_name: Erin R. full_name: Johnson, Erin R. last_name: Johnson - first_name: Ian full_name: Jones, Ian last_name: Jones - first_name: K. V. Jovan full_name: Jose, K. V. Jovan last_name: Jose - first_name: Elena A. full_name: Kabova, Elena A. last_name: Kabova - first_name: Adam full_name: Keates, Adam last_name: Keates - first_name: Paul F. full_name: Kelly, Paul F. last_name: Kelly - first_name: Dmitry full_name: Khakimov, Dmitry last_name: Khakimov - first_name: Stefanos full_name: Konstantinopoulos, Stefanos last_name: Konstantinopoulos - first_name: Liudmila N. full_name: Kuleshova, Liudmila N. last_name: Kuleshova - first_name: He full_name: Li, He last_name: Li - first_name: Xiaolu full_name: Lin, Xiaolu last_name: Lin - first_name: Alexander full_name: List, Alexander last_name: List - first_name: Congcong full_name: Liu, Congcong last_name: Liu - first_name: Yifei Michelle full_name: Liu, Yifei Michelle last_name: Liu - first_name: Zenghui full_name: Liu, Zenghui last_name: Liu - first_name: Zhi-Pan full_name: Liu, Zhi-Pan last_name: Liu - first_name: Joseph W. full_name: Lubach, Joseph W. last_name: Lubach - first_name: Noa full_name: Marom, Noa last_name: Marom - first_name: Alexander A. full_name: Maryewski, Alexander A. last_name: Maryewski - first_name: Hiroyuki full_name: Matsui, Hiroyuki last_name: Matsui - first_name: Alessandra full_name: Mattei, Alessandra last_name: Mattei - first_name: R. Alex full_name: Mayo, R. Alex last_name: Mayo - first_name: John W. full_name: Melkumov, John W. last_name: Melkumov - first_name: Sharmarke full_name: Mohamed, Sharmarke last_name: Mohamed - first_name: Zahrasadat full_name: Momenzadeh Abardeh, Zahrasadat last_name: Momenzadeh Abardeh - first_name: Hari S. full_name: Muddana, Hari S. last_name: Muddana - first_name: Naofumi full_name: Nakayama, Naofumi last_name: Nakayama - first_name: Kamal Singh full_name: Nayal, Kamal Singh last_name: Nayal - first_name: Marcus A. full_name: Neumann, Marcus A. last_name: Neumann - first_name: Rahul full_name: Nikhar, Rahul last_name: Nikhar - first_name: Shigeaki full_name: Obata, Shigeaki last_name: Obata - first_name: Dana full_name: O'Connor, Dana last_name: O'Connor - first_name: Artem R. full_name: Oganov, Artem R. last_name: Oganov - first_name: Koji full_name: Okuwaki, Koji last_name: Okuwaki - first_name: Alberto full_name: Otero-de-la-Roza, Alberto last_name: Otero-de-la-Roza - first_name: Constantinos C. full_name: Pantelides, Constantinos C. last_name: Pantelides - first_name: Sean full_name: Parkin, Sean last_name: Parkin - first_name: Chris J. full_name: Pickard, Chris J. last_name: Pickard - first_name: Luca full_name: Pilia, Luca last_name: Pilia - first_name: Tatyana full_name: Pivina, Tatyana last_name: Pivina - first_name: Rafał full_name: Podeszwa, Rafał last_name: Podeszwa - first_name: Alastair J. A. full_name: Price, Alastair J. A. last_name: Price - first_name: Louise S. full_name: Price, Louise S. last_name: Price - first_name: Sarah L. full_name: Price, Sarah L. last_name: Price - first_name: Michael R. full_name: Probert, Michael R. last_name: Probert - first_name: Angeles full_name: Pulido, Angeles last_name: Pulido - first_name: Gunjan Rajendra full_name: Ramteke, Gunjan Rajendra last_name: Ramteke - first_name: Atta Ur full_name: Rehman, Atta Ur last_name: Rehman - first_name: Susan M. full_name: Reutzel-Edens, Susan M. last_name: Reutzel-Edens - first_name: Jutta full_name: Rogal, Jutta last_name: Rogal - first_name: Marta J. full_name: Ross, Marta J. last_name: Ross - first_name: Adrian F. full_name: Rumson, Adrian F. last_name: Rumson - first_name: Ghazala full_name: Sadiq, Ghazala last_name: Sadiq - first_name: Zeinab M. full_name: Saeed, Zeinab M. last_name: Saeed - first_name: Alireza full_name: Salimi, Alireza last_name: Salimi - first_name: Matteo full_name: Salvalaglio, Matteo last_name: Salvalaglio - first_name: Leticia full_name: Sanders de Almada, Leticia last_name: Sanders de Almada - first_name: Kiran full_name: Sasikumar, Kiran last_name: Sasikumar - first_name: Sivakumar full_name: Sekharan, Sivakumar last_name: Sekharan - first_name: Cheng full_name: Shang, Cheng last_name: Shang - first_name: Kenneth full_name: Shankland, Kenneth last_name: Shankland - first_name: Kotaro full_name: Shinohara, Kotaro last_name: Shinohara - first_name: Baimei full_name: Shi, Baimei last_name: Shi - first_name: Xuekun full_name: Shi, Xuekun last_name: Shi - first_name: A. Geoffrey full_name: Skillman, A. Geoffrey last_name: Skillman - first_name: Hongxing full_name: Song, Hongxing last_name: Song - first_name: Nina full_name: Strasser, Nina last_name: Strasser - first_name: Jacco full_name: van de Streek, Jacco last_name: van de Streek - first_name: Isaac J. full_name: Sugden, Isaac J. last_name: Sugden - first_name: Guangxu full_name: Sun, Guangxu last_name: Sun - first_name: Krzysztof full_name: Szalewicz, Krzysztof last_name: Szalewicz - first_name: Benjamin I. full_name: Tan, Benjamin I. last_name: Tan - first_name: Lu full_name: Tan, Lu last_name: Tan - first_name: Frank full_name: Tarczynski, Frank last_name: Tarczynski - first_name: Christopher R. full_name: Taylor, Christopher R. last_name: Taylor - first_name: Alexandre full_name: Tkatchenko, Alexandre last_name: Tkatchenko - first_name: Rithwik full_name: Tom, Rithwik last_name: Tom - first_name: Mark E. full_name: Tuckerman, Mark E. last_name: Tuckerman - first_name: Yohei full_name: Utsumi, Yohei last_name: Utsumi - first_name: Leslie full_name: Vogt-Maranto, Leslie last_name: Vogt-Maranto - first_name: Jake full_name: Weatherston, Jake last_name: Weatherston - first_name: Luke J. full_name: Wilkinson, Luke J. last_name: Wilkinson - first_name: Robert D. full_name: Willacy, Robert D. last_name: Willacy - first_name: Lukasz full_name: Wojtas, Lukasz last_name: Wojtas - first_name: Grahame R. full_name: Woollam, Grahame R. last_name: Woollam - first_name: Zhuocen full_name: Yang, Zhuocen last_name: Yang - first_name: Etsuo full_name: Yonemochi, Etsuo last_name: Yonemochi - first_name: Xin full_name: Yue, Xin last_name: Yue - first_name: Qun full_name: Zeng, Qun last_name: Zeng - first_name: Yizu full_name: Zhang, Yizu last_name: Zhang - first_name: Tian full_name: Zhou, Tian last_name: Zhou - first_name: Yunfei full_name: Zhou, Yunfei last_name: Zhou - first_name: Roman full_name: Zubatyuk, Roman last_name: Zubatyuk - first_name: Jason C. full_name: Cole, Jason C. last_name: Cole citation: ama: 'Hunnisett LM, Nyman J, Francia N, et al. The seventh blind test of crystal structure prediction: Structure generation methods. Acta Crystallographica Section B. 2024;80(6):517-547. doi:10.1107/s2052520624007492' apa: 'Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S., Aitipamula, S., … Cole, J. C. (2024). The seventh blind test of crystal structure prediction: Structure generation methods. Acta Crystallographica Section B. International Union of Crystallography. https://doi.org/10.1107/s2052520624007492' chicago: 'Hunnisett, Lily M., Jonas Nyman, Nicholas Francia, Nathan S. Abraham, Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” Acta Crystallographica Section B. International Union of Crystallography, 2024. https://doi.org/10.1107/s2052520624007492.' ieee: 'L. M. Hunnisett et al., “The seventh blind test of crystal structure prediction: Structure generation methods,” Acta Crystallographica Section B, vol. 80, no. 6. International Union of Crystallography, pp. 517–547, 2024.' ista: 'Hunnisett LM et al. 2024. The seventh blind test of crystal structure prediction: Structure generation methods. Acta Crystallographica Section B. 80(6), 517–547.' mla: 'Hunnisett, Lily M., et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” Acta Crystallographica Section B, vol. 80, no. 6, International Union of Crystallography, 2024, pp. 517–47, doi:10.1107/s2052520624007492.' short: L.M. Hunnisett, J. Nyman, N. Francia, N.S. Abraham, C.S. Adjiman, S. Aitipamula, T. Alkhidir, M. Almehairbi, A. Anelli, D.M. Anstine, J.E. Anthony, J.E. Arnold, F. Bahrami, M.A. Bellucci, R.M. Bhardwaj, I. Bier, J.A. Bis, A.D. Boese, D.H. Bowskill, J. Bramley, J.G. Brandenburg, D.E. Braun, P.W.V. Butler, J. Cadden, S. Carino, E.J. Chan, C. Chang, B. Cheng, S.M. Clarke, S.J. Coles, R.I. Cooper, R. Couch, R. Cuadrado, T. Darden, G.M. Day, H. Dietrich, Y. Ding, A. DiPasquale, B. Dhokale, B.P. van Eijck, M.R.J. Elsegood, D. Firaha, W. Fu, K. Fukuzawa, J. Glover, H. Goto, C. Greenwell, R. Guo, J. Harter, J. Helfferich, D.W.M. Hofmann, J. Hoja, J. Hone, R. Hong, G. Hutchison, Y. Ikabata, O. Isayev, O. Ishaque, V. Jain, Y. Jin, A. Jing, E.R. Johnson, I. Jones, K.V.J. Jose, E.A. Kabova, A. Keates, P.F. Kelly, D. Khakimov, S. Konstantinopoulos, L.N. Kuleshova, H. Li, X. Lin, A. List, C. Liu, Y.M. Liu, Z. Liu, Z.-P. Liu, J.W. Lubach, N. Marom, A.A. Maryewski, H. Matsui, A. Mattei, R.A. Mayo, J.W. Melkumov, S. Mohamed, Z. Momenzadeh Abardeh, H.S. Muddana, N. Nakayama, K.S. Nayal, M.A. Neumann, R. Nikhar, S. Obata, D. O’Connor, A.R. Oganov, K. Okuwaki, A. Otero-de-la-Roza, C.C. Pantelides, S. Parkin, C.J. Pickard, L. Pilia, T. Pivina, R. Podeszwa, A.J.A. Price, L.S. Price, S.L. Price, M.R. Probert, A. Pulido, G.R. Ramteke, A.U. Rehman, S.M. Reutzel-Edens, J. Rogal, M.J. Ross, A.F. Rumson, G. Sadiq, Z.M. Saeed, A. Salimi, M. Salvalaglio, L. Sanders de Almada, K. Sasikumar, S. Sekharan, C. Shang, K. Shankland, K. Shinohara, B. Shi, X. Shi, A.G. Skillman, H. Song, N. Strasser, J. van de Streek, I.J. Sugden, G. Sun, K. Szalewicz, B.I. Tan, L. Tan, F. Tarczynski, C.R. Taylor, A. Tkatchenko, R. Tom, M.E. Tuckerman, Y. Utsumi, L. Vogt-Maranto, J. Weatherston, L.J. Wilkinson, R.D. Willacy, L. Wojtas, G.R. Woollam, Z. Yang, E. Yonemochi, X. Yue, Q. Zeng, Y. Zhang, T. Zhou, Y. Zhou, R. Zubatyuk, J.C. Cole, Acta Crystallographica Section B 80 (2024) 517–547. das_tickbox: '0' date_created: 2025-01-29T11:07:36Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-09-24T11:31:46Z day: '01' ddc: - '540' department: - _id: BiCh doi: 10.1107/s2052520624007492 external_id: isi: - '001388840500003' pmid: - '39405196' file: - access_level: open_access checksum: 33b8083e76564cc918182b0b0b2cc023 content_type: application/pdf creator: dernst date_created: 2025-01-29T11:09:48Z date_updated: 2025-01-29T11:09:48Z file_id: '18954' file_name: 2024_ActaCrystallographicaB_Hunnisett.pdf file_size: 10061037 relation: main_file success: 1 file_date_updated: 2025-01-29T11:09:48Z fulldoi: https://doi.org/10.1107/s2052520624007492 has_accepted_license: '1' intvolume: ' 80' isi: 1 issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 517-547 pmid: 1 publication: Acta Crystallographica Section B publication_identifier: issn: - 2052-5206 publication_status: published publisher: International Union of Crystallography quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'The seventh blind test of crystal structure prediction: Structure generation methods' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 80 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '15311' abstract: - lang: eng text: Materials with low thermal conductivity usually have complex crystal structures. Herein we experimentally find that a simple crystal structure material AgTlI2 (I4/mcm) owns an extremely low thermal conductivity of 0.25 W/mK at room temperature. To understand this anomaly, we perform in-depth theoretical studies based on ab initio molecular dynamics simulations and anharmonic lattice dynamics. We find that the unique atomic arrangement and weak chemical bonding provide a permissive environment for strong oscillations of Ag atoms, leading to a considerable rattling behaviour and giant lattice anharmonicity. This feature is also verified by the experimental probability density function refinement of single-crystal diffraction. The particularly strong anharmonicity breaks down the conventional phonon gas model, giving rise to non-negligible wavelike phonon behaviours in AgTlI2 at 300 K. Intriguingly, unlike many strongly anharmonic materials where a small propagative thermal conductivity is often accompanied by a large diffusive thermal conductivity, we find an unusual coexistence of ultralow propagative and diffusive thermal conductivities in AgTlI2 based on the thermal transport unified theory. This study underscores the potential of simple crystal structures in achieving low thermal conductivity and encourages further experimental research to enrich the family of materials with ultralow thermal conductivity. acknowledgement: "We thank Bingqing Cheng (IST Austria) and Terumasa Tadano (NIMS\r\nJapan) for reading the manuscript and providing insightful comments.\r\nThis work is supported by the Research Grants Council of Hong Kong\r\n(C7002-22Y and 17318122). ZZ acknowledges the European Union’s\r\nHorizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 101034413. XS acknowledges\r\nfunding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo. 101034329, and the WINNING Normandy Programme supported by\r\nthe Normandy Region. The computations were performed using\r\nresearch computing facilities offered by Information Technology Services, at the University of Hong Kong." article_number: '3007' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Xingchen full_name: Shen, Xingchen last_name: Shen - first_name: Ruihuan full_name: Cheng, Ruihuan last_name: Cheng - first_name: Olivier full_name: Perez, Olivier last_name: Perez - first_name: Niuchang full_name: Ouyang, Niuchang last_name: Ouyang - first_name: Zheyong full_name: Fan, Zheyong last_name: Fan - first_name: Pierric full_name: Lemoine, Pierric last_name: Lemoine - first_name: Bernard full_name: Raveau, Bernard last_name: Raveau - first_name: Emmanuel full_name: Guilmeau, Emmanuel last_name: Guilmeau - first_name: Yue full_name: Chen, Yue last_name: Chen citation: ama: Zeng Z, Shen X, Cheng R, et al. Pushing thermal conductivity to its lower limit in crystals with simple structures. Nature Communications. 2024;15. doi:10.1038/s41467-024-46799-3 apa: Zeng, Z., Shen, X., Cheng, R., Perez, O., Ouyang, N., Fan, Z., … Chen, Y. (2024). Pushing thermal conductivity to its lower limit in crystals with simple structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-46799-3 chicago: Zeng, Zezhu, Xingchen Shen, Ruihuan Cheng, Olivier Perez, Niuchang Ouyang, Zheyong Fan, Pierric Lemoine, Bernard Raveau, Emmanuel Guilmeau, and Yue Chen. “Pushing Thermal Conductivity to Its Lower Limit in Crystals with Simple Structures.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-46799-3. ieee: Z. Zeng et al., “Pushing thermal conductivity to its lower limit in crystals with simple structures,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Zeng Z, Shen X, Cheng R, Perez O, Ouyang N, Fan Z, Lemoine P, Raveau B, Guilmeau E, Chen Y. 2024. Pushing thermal conductivity to its lower limit in crystals with simple structures. Nature Communications. 15, 3007. mla: Zeng, Zezhu, et al. “Pushing Thermal Conductivity to Its Lower Limit in Crystals with Simple Structures.” Nature Communications, vol. 15, 3007, Springer Nature, 2024, doi:10.1038/s41467-024-46799-3. short: Z. Zeng, X. Shen, R. Cheng, O. Perez, N. Ouyang, Z. Fan, P. Lemoine, B. Raveau, E. Guilmeau, Y. Chen, Nature Communications 15 (2024). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "All necessary source data files generated for this study are available in the SI repository https://github.com/ZengZezhu/Thermal-conductivity-AgTlI2 see ref 72.\r\n72. Zeng, Z. et al. Source data for pushing thermal conductivity to its lower limit in crystals with simple structures. Zenodo (2024)." date_created: 2024-04-14T22:01:00Z date_published: 2024-04-08T00:00:00Z date_updated: 2026-09-24T11:20:55Z day: '08' ddc: - '530' department: - _id: BiCh doi: 10.1038/s41467-024-46799-3 ec_funded: 1 external_id: arxiv: - '2310.01838' isi: - '001198902100029' pmid: - '38589376' file: - access_level: open_access checksum: f81bd6ba42f740d060fb446eeebc1035 content_type: application/pdf creator: cchlebak date_created: 2024-04-26T10:34:07Z date_updated: 2024-04-26T10:34:07Z file_id: '15346' file_name: 2024_NatComm_Zeng.pdf file_size: 3049375 relation: main_file success: 1 file_date_updated: 2024-04-26T10:34:07Z fulldoi: https://doi.org/10.1038/s41467-024-46799-3 has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Pushing thermal conductivity to its lower limit in crystals with simple structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18452' abstract: - lang: eng text: 'Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.' acknowledgement: B.C. thanks Chris Pickard for enlightening discussions. article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Cheng B. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 2024;20(20):9259-9266. doi:10.1021/acs.jctc.4c00998 apa: Cheng, B. (2024). Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.4c00998 chicago: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” Journal of Chemical Theory and Computation. American Chemical Society, 2024. https://doi.org/10.1021/acs.jctc.4c00998. ieee: B. Cheng, “Response matching for generating materials and molecules,” Journal of Chemical Theory and Computation, vol. 20, no. 20. American Chemical Society, pp. 9259–9266, 2024. ista: Cheng B. 2024. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 20(20), 9259–9266. mla: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” Journal of Chemical Theory and Computation, vol. 20, no. 20, American Chemical Society, 2024, pp. 9259–66, doi:10.1021/acs.jctc.4c00998. short: B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training scripts, trained models, and training data are available at https://github.com/BingqingCheng/cace-rm. date_created: 2024-10-20T22:02:07Z date_published: 2024-10-22T00:00:00Z date_updated: 2026-09-24T11:30:58Z day: '22' ddc: - '540' department: - _id: BiCh doi: 10.1021/acs.jctc.4c00998 external_id: arxiv: - '2405.09057' isi: - '001330001500001' pmid: - '39365029' file: - access_level: open_access checksum: aca0011bba4846140809b5af583daa9a content_type: application/pdf creator: dernst date_created: 2025-01-13T09:11:09Z date_updated: 2025-01-13T09:11:09Z file_id: '18832' file_name: 2024_JCTC_Cheng.pdf file_size: 4758251 relation: main_file success: 1 file_date_updated: 2025-01-13T09:11:09Z fulldoi: https://doi.org/10.1021/acs.jctc.4c00998 has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '20' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 9259-9266 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/BingqingCheng/cace researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Response matching for generating materials and molecules tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17322' abstract: - lang: eng text: Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys. acknowledgement: B.C. thanks Ralf Drautz and Ngoc Cuong Nguyen for illuminating discussions. article_number: '157' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Cheng B. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 2024;10. doi:10.1038/s41524-024-01332-4 apa: Cheng, B. (2024). Cartesian atomic cluster expansion for machine learning interatomic potentials. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-024-01332-4 chicago: Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” Npj Computational Materials. Springer Nature, 2024. https://doi.org/10.1038/s41524-024-01332-4. ieee: B. Cheng, “Cartesian atomic cluster expansion for machine learning interatomic potentials,” npj Computational Materials, vol. 10. Springer Nature, 2024. ista: Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 10, 157. mla: Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” Npj Computational Materials, vol. 10, 157, Springer Nature, 2024, doi:10.1038/s41524-024-01332-4. short: B. Cheng, Npj Computational Materials 10 (2024). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The water dataset is from https://github.com/BingqingCheng/ab-initio-thermodynamics-of-water. MD17-ethanol is from http://www.sgdml.org/#datasets. BPA is from ref. 43, downloaded from https://github.com/davkovacs/BOTNet-datasets. The HEA25 dataset is from ref. 45, downloaded from https://archive.materialscloud.org/record/2023.57. The training scripts, trained CACE potentials, and MD input files are available at https://github.com/BingqingCheng/cacefit. date_created: 2024-07-28T22:01:08Z date_published: 2024-07-18T00:00:00Z date_updated: 2026-09-24T11:30:25Z day: '18' ddc: - '000' department: - _id: BiCh doi: 10.1038/s41524-024-01332-4 external_id: arxiv: - '2402.07472' isi: - '001271730700001' file: - access_level: open_access checksum: e6b4d1a45a9ef1e9be35b313d96ebd6f content_type: application/pdf creator: dernst date_created: 2025-01-09T12:36:48Z date_updated: 2025-01-09T12:36:48Z file_id: '18813' file_name: 2024_npjComputationalMaterials_Cheng.pdf file_size: 1659509 relation: main_file success: 1 file_date_updated: 2025-01-09T12:36:48Z fulldoi: https://doi.org/10.1038/s41524-024-01332-4 has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: npj Computational Materials publication_identifier: eissn: - 2057-3960 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Cartesian atomic cluster expansion for machine learning interatomic potentials tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 10 year: '2024' ... --- _id: '15052' abstract: - lang: eng text: "Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications." acknowledgement: "This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413." article_number: '054305' article_processing_charge: No article_type: original author: - first_name: Ruihuan full_name: Cheng, Ruihuan last_name: Cheng - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Chen full_name: Wang, Chen last_name: Wang - first_name: Niuchang full_name: Ouyang, Niuchang last_name: Ouyang - first_name: Yue full_name: Chen, Yue last_name: Chen citation: ama: Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 2024;109(5). doi:10.1103/physrevb.109.054305 apa: Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305 chicago: Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/physrevb.109.054305. ieee: R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024. ista: Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305. mla: Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305. short: R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024). das_tickbox: '0' date_created: 2024-03-04T07:41:23Z date_published: 2024-02-14T00:00:00Z date_updated: 2026-09-24T11:19:44Z day: '14' department: - _id: BiCh doi: 10.1103/physrevb.109.054305 ec_funded: 1 external_id: isi: - '001198615900003' fulldoi: https://doi.org/10.1103/physrevb.109.054305 intvolume: ' 109' isi: 1 issue: '5' language: - iso: eng month: '02' oa_version: None project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 109 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18553' abstract: - lang: eng text: Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component. acknowledged_ssus: - _id: LifeSc - _id: PreCl acknowledgement: We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research. article_processing_charge: No article_type: original author: - first_name: Anisha R. full_name: Ramadhin, Anisha R. last_name: Ramadhin - first_name: Shun-Hsiao full_name: Lee, Shun-Hsiao last_name: Lee - first_name: Di full_name: Zhou, Di last_name: Zhou - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Camila full_name: Gonzalo-Hansen, Camila last_name: Gonzalo-Hansen - first_name: Marjolein full_name: van Sluis, Marjolein last_name: van Sluis - first_name: Cindy M.A. full_name: Blom, Cindy M.A. last_name: Blom - first_name: Roel C. full_name: Janssens, Roel C. last_name: Janssens - first_name: Anja full_name: Raams, Anja last_name: Raams - first_name: Dick full_name: Dekkers, Dick last_name: Dekkers - first_name: Karel full_name: Bezstarosti, Karel last_name: Bezstarosti - first_name: Dea full_name: Slade, Dea last_name: Slade - first_name: Wim full_name: Vermeulen, Wim last_name: Vermeulen - first_name: Alex full_name: Pines, Alex last_name: Pines - first_name: Jeroen A.A. full_name: Demmers, Jeroen A.A. last_name: Demmers - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Titia K. full_name: Sixma, Titia K. last_name: Sixma - first_name: Jurgen A. full_name: Marteijn, Jurgen A. last_name: Marteijn citation: ama: Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 2024;84(24):4740-4757.e12. doi:10.1016/j.molcel.2024.10.030 apa: Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2024.10.030 chicago: Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” Molecular Cell. Elsevier, 2024. https://doi.org/10.1016/j.molcel.2024.10.030. ieee: A. R. Ramadhin et al., “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” Molecular Cell, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024. ista: Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12. mla: Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” Molecular Cell, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:10.1016/j.molcel.2024.10.030. short: A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12. das_tickbox: '1' dataavailabilitystatement: "Proteomics data is deposited at the ProteomeXchange Consortium through the PRIDE partner repository with dataset identifier PXD051720. Imaging data are deposited at Mendeley Data at https://doi.org/10.17632/wp9sf6sp4z.1. Cryo-EM reconstructions and structure coordinates are deposited to the Electron Microscopy Database (EMDB) and to the PDB under the following accession codes: for RNA Pol II-TC-NER-STK19 complex model (PDB: 9FD2), composite map (EMD-50325) and consensus map (EMD-50292). Focused maps of CSA-DDB1-DDA1-UVSSA-STK19 (EMD-50293), RNA Pol II-ELOF1 (EMD-50294), CRL4CSA (EMD-50295), and CSA-DDB1-DDA1-CSB (EMD-50306).\r\nThis paper does not report original code.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2024-11-15T12:12:54Z date_published: 2024-12-19T00:00:00Z date_updated: 2026-10-01T08:20:39Z day: '19' ddc: - '570' department: - _id: CaBe doi: 10.1016/j.molcel.2024.10.030 external_id: isi: - '001395711300001' pmid: - '39547223' file: - access_level: open_access checksum: e051e2766b2d424983778f742cb7c5ed content_type: application/pdf creator: dernst date_created: 2025-01-13T11:17:35Z date_updated: 2025-01-13T11:17:35Z file_id: '18844' file_name: 2024_MolecularCell_Ramadhin.pdf file_size: 25071994 relation: main_file success: 1 file_date_updated: 2025-01-13T11:17:35Z fulldoi: https://doi.org/10.1016/j.molcel.2024.10.030 has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4740-4757.e12 pmid: 1 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '23013' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 84 year: '2024' ... --- OA_type: closed access _id: '18945' abstract: - lang: eng text: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division. acknowledgement: "R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0), Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by the Structural Genomics Consortium, a registered charity (1097737) that receives funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck & Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7), A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C. (2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00) and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis. We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We thank the staff at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24. The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang (KI) for valuable discussions and technical support." article_processing_charge: No article_type: original author: - first_name: Fernando H. full_name: de Souza Gama, Fernando H. last_name: de Souza Gama - first_name: Luiz A. full_name: Dutra, Luiz A. last_name: Dutra - first_name: Michael full_name: Hawgood, Michael last_name: Hawgood - first_name: Caio Vinícius full_name: dos Reis, Caio Vinícius last_name: dos Reis - first_name: Ricardo A. M. full_name: Serafim, Ricardo A. M. last_name: Serafim - first_name: Marcos A. full_name: Ferreira, Marcos A. last_name: Ferreira - first_name: Bruno V. M. full_name: Teodoro, Bruno V. M. last_name: Teodoro - first_name: Jéssica Emi full_name: Takarada, Jéssica Emi last_name: Takarada - first_name: André S. full_name: Santiago, André S. last_name: Santiago - first_name: Dimitrios-Ilias full_name: Balourdas, Dimitrios-Ilias last_name: Balourdas - first_name: Ann-Sofie full_name: Nilsson, Ann-Sofie last_name: Nilsson - first_name: Bruno full_name: Urien, Bruno last_name: Urien - first_name: Vitor M. full_name: Almeida, Vitor M. last_name: Almeida - first_name: Carina full_name: Gileadi, Carina last_name: Gileadi - first_name: Priscila Z. full_name: Ramos, Priscila Z. last_name: Ramos - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Stanley N. S. full_name: Vasconcelos, Stanley N. S. last_name: Vasconcelos - first_name: Micael R. full_name: Cunha, Micael R. last_name: Cunha - first_name: Susanne full_name: Mueller, Susanne last_name: Mueller - first_name: Stefan full_name: Knapp, Stefan last_name: Knapp - first_name: Katlin B. full_name: Massirer, Katlin B. last_name: Massirer - first_name: Jonathan M. full_name: Elkins, Jonathan M. last_name: Elkins - first_name: Opher full_name: Gileadi, Opher last_name: Gileadi - first_name: Alessandra full_name: Mascarello, Alessandra last_name: Mascarello - first_name: Bennie B. L. G. full_name: Lemmens, Bennie B. L. G. last_name: Lemmens - first_name: Cristiano R. W. full_name: Guimarães, Cristiano R. W. last_name: Guimarães - first_name: Hatylas full_name: Azevedo, Hatylas last_name: Azevedo - first_name: Rafael M. full_name: Couñago, Rafael M. last_name: Couñago citation: ama: de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 2024;67(11):8609-8629. doi:10.1021/acs.jmedchem.3c02250 apa: de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim, R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. American Chemical Society. https://doi.org/10.1021/acs.jmedchem.3c02250 chicago: Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry. American Chemical Society, 2024. https://doi.org/10.1021/acs.jmedchem.3c02250. ieee: F. H. de Souza Gama et al., “Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε,” Journal of Medicinal Chemistry, vol. 67, no. 11. American Chemical Society, pp. 8609–8629, 2024. ista: de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B, Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629. mla: de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry, vol. 67, no. 11, American Chemical Society, 2024, pp. 8609–29, doi:10.1021/acs.jmedchem.3c02250. short: F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim, M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas, A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo, S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins, O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M. Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629. das_tickbox: '1' dataavailabilitystatement: 'Atomic coordinates and experimental data have been deposited in the PDB with the following PDB ID codes: 6CNX (VRK1 bound to 2); 6CFM (VRK1 bound to 3); 6CQH (VRK1 bound to 4); 6CMM (VRK1 bound to 7); 6VXU (VRK1 bound to 8); 6VZH (VRK1 bound to 11); 6CSW (VRK1 bound to 13); 8V42 (VRK1 bound to 21); 6NPN (VRK1 bound to 24).' date_created: 2025-01-29T09:14:19Z date_published: 2024-05-23T00:00:00Z date_updated: 2026-10-01T08:26:28Z day: '23' department: - _id: CaBe doi: 10.1021/acs.jmedchem.3c02250 external_id: pmid: - '38780468' fulldoi: https://doi.org/10.1021/acs.jmedchem.3c02250 intvolume: ' 67' issue: '11' language: - iso: eng month: '05' oa_version: None page: 8609-8629 pmid: 1 publication: Journal of Medicinal Chemistry publication_identifier: eissn: - 1520-4804 issn: - 0022-2623 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 67 year: '2024' ... --- APC_amount: 3534 EUR OA_place: publisher OA_type: gold _id: '17407' abstract: - lang: eng text: The ability to control forces between sub-micron-scale building blocks offers significant potential for designing new materials through self-assembly. Traditionally, this involves identifying a crystal structure with a desired property and then designing building-block interactions so that it assembles spontaneously. However, this paradigm fails for structurally disordered solids, which lack a well-defined structure. Here, we show that disordered solids can still be treated from an inverse self-assembly perspective by bypassing structure and directly targeting material properties. Using the Poisson’s ratio as a primary example, we demonstrate how differentiable programming links interaction parameters with emergent behavior, enabling iterative training to achieve the desired Poisson’s ratio. We also tune other properties, including pressure and local 8-fold structural order, and can even control multiple properties simultaneously. This robust, transferable, and scalable approach can handle a wide variety of systems and properties, demonstrating the utility of disordered solids as a practical avenue for self-assembly platforms. acknowledgement: We thank M. Lechner for helpful discussions. article_number: '141' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Mengjie full_name: Zu, Mengjie id: 26dd9e7c-e86a-11eb-a854-82ac731c9ae2 last_name: Zu - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: Zu M, Goodrich CP. Designing athermal disordered solids with automatic differentiation. Communications Materials. 2024;5. doi:10.1038/s43246-024-00583-4 apa: Zu, M., & Goodrich, C. P. (2024). Designing athermal disordered solids with automatic differentiation. Communications Materials. Springer Nature. https://doi.org/10.1038/s43246-024-00583-4 chicago: Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” Communications Materials. Springer Nature, 2024. https://doi.org/10.1038/s43246-024-00583-4. ieee: M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic differentiation,” Communications Materials, vol. 5. Springer Nature, 2024. ista: Zu M, Goodrich CP. 2024. Designing athermal disordered solids with automatic differentiation. Communications Materials. 5, 141. mla: Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” Communications Materials, vol. 5, 141, Springer Nature, 2024, doi:10.1038/s43246-024-00583-4. short: M. Zu, C.P. Goodrich, Communications Materials 5 (2024). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The authors declare that the data supporting the findings of this study are available within the paper and its Supplementary Information files date_created: 2024-08-11T22:01:11Z date_published: 2024-08-01T00:00:00Z date_updated: 2026-10-01T08:28:59Z day: '01' ddc: - '530' department: - _id: CaGo doi: 10.1038/s43246-024-00583-4 external_id: arxiv: - '2404.15101' file: - access_level: open_access checksum: d6f74e242db5f46bb0e380ee23a268af content_type: application/pdf creator: dernst date_created: 2024-08-12T07:56:38Z date_updated: 2024-08-12T07:56:38Z file_id: '17416' file_name: 2024_CommMaterials_Zu.pdf file_size: 9824134 relation: main_file success: 1 file_date_updated: 2024-08-12T07:56:38Z fulldoi: https://doi.org/10.1038/s43246-024-00583-4 has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications Materials publication_identifier: eissn: - 2662-4443 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: yes title: Designing athermal disordered solids with automatic differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 5 year: '2024' ... --- _id: '17325' abstract: - lang: eng text: Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology. acknowledgement: We would like to thank all members of the Pilizota lab, as well as Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L. were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Wei Chang full_name: Lo, Wei Chang last_name: Lo - first_name: Ekaterina full_name: Krasnopeeva, Ekaterina id: 1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A last_name: Krasnopeeva - first_name: Teuta full_name: Pilizota, Teuta last_name: Pilizota citation: ama: Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annual Review of Biophysics. 2024;53:487-510. doi:10.1146/annurev-biophys-030822-032215 apa: Lo, W. C., Krasnopeeva, E., & Pilizota, T. (2024). Bacterial Electrophysiology. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-030822-032215 chicago: Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.” Annual Review of Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-030822-032215. ieee: W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,” Annual Review of Biophysics, vol. 53. Annual Reviews, pp. 487–510, 2024. ista: Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510. mla: Lo, Wei Chang, et al. “Bacterial Electrophysiology.” Annual Review of Biophysics, vol. 53, Annual Reviews, 2024, pp. 487–510, doi:10.1146/annurev-biophys-030822-032215. short: W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510. das_tickbox: '0' date_created: 2024-07-28T22:01:09Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-10-01T08:29:37Z day: '01' ddc: - '570' department: - _id: CaGu doi: 10.1146/annurev-biophys-030822-032215 external_id: isi: - '001278237500021' pmid: - '38382113' file: - access_level: open_access checksum: e0505553b3cee624fa865f0cc5a99ecc content_type: application/pdf creator: dernst date_created: 2024-07-29T10:56:01Z date_updated: 2024-07-29T10:56:01Z file_id: '17339' file_name: 2024_AnnualReviewBiophys_Lo.pdf file_size: 1276645 relation: main_file success: 1 file_date_updated: 2024-07-29T10:56:01Z fulldoi: https://doi.org/10.1146/annurev-biophys-030822-032215 has_accepted_license: '1' intvolume: ' 53' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 487-510 pmid: 1 project: - _id: eb872896-77a9-11ec-83b8-f59a38ec17f8 grant_number: ALTF 44-2021 name: 'Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy' publication: Annual Review of Biophysics publication_identifier: eissn: - 1936-1238 issn: - 1936-122X publication_status: published publisher: Annual Reviews quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: unclear title: Bacterial Electrophysiology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 53 year: '2024' ... --- _id: '17128' abstract: - lang: eng text: The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases. acknowledgement: We gratefully acknowledge the assistance of J. M. Lopez with DNSs at an early stage of this work. This work was partially supported by two grants from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST 111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing resources of CRIANN (Normandy, France). article_processing_charge: No article_type: original author: - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Hong Yan full_name: Shih, Hong Yan last_name: Shih - first_name: Gaute full_name: Linga, Gaute last_name: Linga - first_name: Joachim full_name: Mathiesen, Joachim last_name: Mathiesen - first_name: Nigel full_name: Goldenfeld, Nigel last_name: Goldenfeld - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 2024;20:1339-1345. doi:10.1038/s41567-024-02513-0 apa: Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld, N., & Hof, B. (2024). Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02513-0 chicago: Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02513-0. ieee: G. M. Lemoult et al., “Directed percolation and puff jamming near the transition to pipe turbulence,” Nature Physics, vol. 20. Springer Nature, pp. 1339–1345, 2024. ista: Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 20, 1339–1345. mla: Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1339–45, doi:10.1038/s41567-024-02513-0. short: G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld, B. Hof, Nature Physics 20 (2024) 1339–1345. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All experimental data presented in this article are available online in the Zenodo repository at https://doi.org/10.5281/zenodo.10308791 date_created: 2024-06-09T22:01:03Z date_published: 2024-08-01T00:00:00Z date_updated: 2026-10-01T07:50:32Z day: '01' department: - _id: BjHo doi: 10.1038/s41567-024-02513-0 external_id: isi: - '001232300600001' fulldoi: https://doi.org/10.1038/s41567-024-02513-0 intvolume: ' 20' isi: 1 language: - iso: eng month: '08' oa_version: None page: 1339-1345 project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: Revisiting the Turbulence Problem Using Statistical Mechanics publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '23012' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Directed percolation and puff jamming near the transition to pipe turbulence type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- OA_type: closed access _id: '18651' abstract: - lang: eng text: Embryo axis formation begins with the localized expression of biochemical signals, which organize cell movements and determine cell fate. A quail study finds that tissue contraction and resulting long-range changes in tissue tension restrict the area where these biochemical signals are expressed. article_processing_charge: No article_type: letter_note author: - first_name: Naoya full_name: Hino, Naoya id: 5299a9ce-7679-11eb-a7bc-d1e62b936307 last_name: Hino - first_name: Carolina full_name: Santos Fernandes Lasbarrères Camelo, Carolina id: 6347dca5-074c-11ed-af92-a80f860d9d5b last_name: Santos Fernandes Lasbarrères Camelo - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Hino N, Santos Fernandes Lasbarrères Camelo C, Heisenberg C-PJ. Development: Turing mechanics. Current Biology. 2024;34(24):R1230-R1232. doi:10.1016/j.cub.2024.10.065' apa: 'Hino, N., Santos Fernandes Lasbarrères Camelo, C., & Heisenberg, C.-P. J. (2024). Development: Turing mechanics. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.10.065' chicago: 'Hino, Naoya, Carolina Santos Fernandes Lasbarrères Camelo, and Carl-Philipp J Heisenberg. “Development: Turing Mechanics.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.10.065.' ieee: 'N. Hino, C. Santos Fernandes Lasbarrères Camelo, and C.-P. J. Heisenberg, “Development: Turing mechanics,” Current Biology, vol. 34, no. 24. Elsevier, pp. R1230–R1232, 2024.' ista: 'Hino N, Santos Fernandes Lasbarrères Camelo C, Heisenberg C-PJ. 2024. Development: Turing mechanics. Current Biology. 34(24), R1230–R1232.' mla: 'Hino, Naoya, et al. “Development: Turing Mechanics.” Current Biology, vol. 34, no. 24, Elsevier, 2024, pp. R1230–32, doi:10.1016/j.cub.2024.10.065.' short: N. Hino, C. Santos Fernandes Lasbarrères Camelo, C.-P.J. Heisenberg, Current Biology 34 (2024) R1230–R1232. corr_author: '1' das_tickbox: '0' date_created: 2024-12-15T23:01:49Z date_published: 2024-12-16T00:00:00Z date_updated: 2026-10-01T08:30:45Z day: '16' department: - _id: CaHe doi: 10.1016/j.cub.2024.10.065 external_id: isi: - '001392077000001' pmid: - '39689690' fulldoi: https://doi.org/10.1016/j.cub.2024.10.065 intvolume: ' 34' isi: 1 issue: '24' language: - iso: eng month: '12' oa_version: None page: R1230-R1232 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Development: Turing mechanics' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2024' ... --- OA_place: repository OA_type: green _id: '23013' abstract: - lang: eng text: 'Raw data of figures in our manuscript ''Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment'' by Ramadhin et al. ' article_processing_charge: No author: - first_name: ' Jurgen' full_name: Marteijn, Jurgen last_name: Marteijn citation: ama: Marteijn Jurgen. Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al. 2024. doi:10.17632/wp9sf6sp4z.1 apa: Marteijn, Jurgen. (2024). Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al. Mendeley Data. https://doi.org/10.17632/wp9sf6sp4z.1 chicago: Marteijn, Jurgen. “Study of STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, Pol II Ubiquitylation and TFIIH Recruitment by Ramadhin et Al.” Mendeley Data, 2024. https://doi.org/10.17632/wp9sf6sp4z.1. ieee: Jurgen Marteijn, “Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al.” Mendeley Data, 2024. ista: Marteijn Jurgen. 2024. Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al., Mendeley Data, 10.17632/wp9sf6sp4z.1. mla: Marteijn, Jurgen. Study of STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, Pol II Ubiquitylation and TFIIH Recruitment by Ramadhin et Al. Mendeley Data, 2024, doi:10.17632/wp9sf6sp4z.1. short: Jurgen Marteijn, (2024). date_created: 2026-10-01T08:20:32Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-10-01T08:20:39Z day: '01' ddc: - '570' department: - _id: CaBe doi: 10.17632/wp9sf6sp4z.1 fulldoi: https://doi.org/10.17632/wp9sf6sp4z.1 main_file_link: - open_access: '1' url: https://doi.org/10.17632/wp9sf6sp4z.1 month: '10' oa: 1 oa_version: None publisher: Mendeley Data related_material: record: - id: '18553' relation: used_in_publication status: public status: public title: Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al. type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '14846' abstract: - lang: eng text: Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces. acknowledged_ssus: - _id: EM-Fac - _id: Bio - _id: NanoFab acknowledgement: We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 - first_name: Rushikesh full_name: Shinde, Rushikesh last_name: Shinde - first_name: Madison full_name: Bolger-Munro, Madison id: 516F03FA-93A3-11EA-A7C5-D6BE3DDC885E last_name: Bolger-Munro orcid: 0000-0002-8176-4824 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Gregory full_name: Szep, Gregory id: 4BFB7762-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Irene full_name: Steccari, Irene id: 2705C766-9FE2-11EA-B224-C6773DDC885E last_name: Steccari - first_name: David full_name: Labrousse Arias, David id: CD573DF4-9ED3-11E9-9D77-3223E6697425 last_name: Labrousse Arias - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden orcid: 0000-0002-9438-4783 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Andrew full_name: Callan-Jones, Andrew last_name: Callan-Jones - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024;20:310-321. doi:10.1038/s41567-023-02302-1 apa: Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1 chicago: Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1. ieee: S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics, vol. 20. Springer Nature, pp. 310–321, 2024. ista: Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 20, 310–321. mla: Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 310–21, doi:10.1038/s41567-023-02302-1. short: S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics 20 (2024) 310–321. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on request date_created: 2024-01-21T23:00:57Z date_published: 2024-02-01T00:00:00Z date_updated: 2026-10-01T08:33:51Z day: '01' ddc: - '530' department: - _id: CaHe - _id: JoFi - _id: MiSi - _id: EM-Fac - _id: NanoFab doi: 10.1038/s41567-023-02302-1 external_id: isi: - '001138880800005' pmid: - '38370025' file: - access_level: open_access checksum: 7891ebe7c900ae47469ab127031dd1ec content_type: application/pdf creator: dernst date_created: 2024-07-16T12:12:43Z date_updated: 2024-07-16T12:12:43Z file_id: '17267' file_name: 2024_NaturePhysics_CaballeroMancebo.pdf file_size: 9897883 relation: main_file success: 1 file_date_updated: 2024-07-16T12:12:43Z fulldoi: https://doi.org/10.1038/s41567-023-02302-1 has_accepted_license: '1' intvolume: ' 20' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 310-321 pmid: 1 project: - _id: 2646861A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03601 name: Control of embryonic cleavage pattern publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/ researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- _id: '14795' abstract: - lang: eng text: Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067 apa: Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067 chicago: Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067. ieee: F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024. ista: Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8. mla: Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067. short: F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All original microscopy data any additional information reported in this paper is available from the lead contact upon request. All original code is available from the lead contact upon request date_created: 2024-01-14T23:00:56Z date_published: 2024-01-08T00:00:00Z date_updated: 2026-10-01T08:33:05Z day: '08' ddc: - '570' department: - _id: CaHe - _id: EdHa - _id: MaLo - _id: NanoFab doi: 10.1016/j.cub.2023.11.067 ec_funded: 1 external_id: isi: - '001154500400001' pmid: - '38134934' file: - access_level: open_access checksum: 51220b76d72a614208f84bdbfbaf9b72 content_type: application/pdf creator: dernst date_created: 2024-01-16T10:53:31Z date_updated: 2024-01-16T10:53:31Z file_id: '14813' file_name: 2024_CurrentBiology_Arslan.pdf file_size: 5183861 relation: main_file success: 1 file_date_updated: 2024-01-16T10:53:31Z fulldoi: https://doi.org/10.1016/j.cub.2023.11.067 has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 171-182.e8 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2024' ... --- _id: '15048' abstract: - lang: eng text: Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Kornelija full_name: Pranjic-Ferscha, Kornelija id: 4362B3C2-F248-11E8-B48F-1D18A9856A87 last_name: Pranjic-Ferscha - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316 apa: Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. Company of Biologists. https://doi.org/10.1242/dev.202316 chicago: Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. Company of Biologists, 2024. https://doi.org/10.1242/dev.202316. ieee: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. Company of Biologists, pp. 1–18, 2024. ista: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18. mla: Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316. short: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: A custom MATLAB script for analyzing cell dispersal has been deposited in the ISTA library (doi:10.15479/AT:ISTA:14926) date_created: 2024-03-03T23:00:50Z date_published: 2024-02-01T00:00:00Z date_updated: 2026-10-01T08:32:34Z day: '01' ddc: - '570' department: - _id: CaHe - _id: Bio doi: 10.1242/dev.202316 ec_funded: 1 external_id: isi: - '001170580200001' pmid: - '38372390' file: - access_level: open_access checksum: 6961ea10012bf0d266681f9628bb8f13 content_type: application/pdf creator: dernst date_created: 2024-03-04T07:24:43Z date_updated: 2024-03-04T07:24:43Z file_id: '15050' file_name: 2024_Development_Schauer.pdf file_size: 14839986 relation: main_file success: 1 file_date_updated: 2024-03-04T07:24:43Z fulldoi: https://doi.org/10.1242/dev.202316 has_accepted_license: '1' intvolume: ' 151' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1-18 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 26B1E39C-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues' publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: Company of Biologists quality_controlled: '1' related_material: record: - id: '14926' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Robust axis elongation by Nodal-dependent restriction of BMP signaling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 151 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '15047' abstract: - lang: eng text: Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling. acknowledgement: This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041). article_number: eadj6801 article_processing_charge: Yes article_type: original author: - first_name: Jiawei full_name: Bao, Jiawei id: bb9a7399-fefd-11ed-be3c-ae648fd1d160 last_name: Bao - first_name: Bjorn full_name: Stevens, Bjorn last_name: Stevens - first_name: Lukas full_name: Kluft, Lukas last_name: Kluft - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801 apa: Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801 chicago: Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801. ieee: J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024. ista: Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801. mla: Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801. short: J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024). das_tickbox: '1' dataavailabilitystatement: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The ICONA/O simulations were done with the ICON branch nextgems_cycle1_dpp0066 as commit 62dbfc. The source code is available here (https://doi.org/10.17617/3.1XTSR6). The ICON model is available to individuals under licenses (https://mpimet.mpg.de/en/science/modeling-with-icon/code-availability). IMERG was provided by the NASA Goddard Space Flight Center’s IMERG and PPS teams, which develop and compute IMERG as a contribution to the GPM mission, and archived at the NASA GES DISC (https://disc.gsfc.nasa.gov/datasets/GPM_3IMERGHH_V06/summary). The data and scripts for reproducing the plots are available on MPG publication repository (https://hdl.handle.net/21.11116/0000-000C-7F2B-7). date_created: 2024-03-03T23:00:50Z date_published: 2024-02-23T00:00:00Z date_updated: 2026-10-01T08:36:23Z day: '23' ddc: - '550' department: - _id: CaMu doi: 10.1126/sciadv.adj6801 ec_funded: 1 external_id: isi: - '001300045100007' pmid: - '38394192' file: - access_level: open_access checksum: d4ec4f05a6d14745057e14d1b8bf45ae content_type: application/pdf creator: dernst date_created: 2024-03-04T07:34:00Z date_updated: 2024-03-04T07:34:00Z file_id: '15051' file_name: 2024_ScienceAdv_Bao.pdf file_size: 800926 relation: main_file success: 1 file_date_updated: 2024-03-04T07:34:00Z fulldoi: https://doi.org/10.1126/sciadv.adj6801 has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '8' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/ researchdata_availability: yes (supplementary data) scopus_import: '1' status: public supplementarymaterial: yes title: Intensification of daily tropical precipitation extremes from more organized convection tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 10 year: '2024' ... --- _id: '17396' abstract: - lang: eng text: Wildfire intensity and severity have been increasing in the Iberian Peninsula in recent years, particularly in the Galicia region, due to rising temperatures and accumulating drier combustible vegetation in unmanaged lands. This leads to substantial emissions of air pollutants, notably fine particles (PM2.5), posing a risk to public health. This study aims to assess the impact of local and regional wildfires on PM2.5 levels in Galicia's main cities and their implications for air quality and public health. Over a decade (2013–2022), PM2.5 data during wildfire seasons were analyzed using statistical methods and Lagrangian tracking to monitor smoke plume evolution. The results reveal a notable increase in PM2.5 concentration during the wildfire season (June–November) in Galicia, surpassing health guidelines during extreme events and posing a significant health risk to the population. Regional wildfire analyses indicate that smoke plumes from Northern Portugal contribute to pollution in Galician cities, influencing the seasonality of heightened PM2.5 levels. During extensive wildfires, elevated PM2.5 concentration values persisted for several days, potentially exacerbating health concerns in Galicia. These findings underscore the urgency of implementing air pollution prevention and management measures in the region, including developing effective alerts for large-scale events and improved wildfire management strategies to mitigate their impact on air quality in Galician cities. acknowledgement: 'Alejandro Casallas was partially funded by a fellowship from the Abdus Salam International Centre for Theoretical Physics – ICTP. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 awarded to Alejandro Casallas. ' article_number: '122093' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: César full_name: Quishpe-Vásquez, César last_name: Quishpe-Vásquez - first_name: Patricia full_name: Oliva, Patricia last_name: Oliva - first_name: Ellie Anne full_name: López-Barrera, Ellie Anne last_name: López-Barrera - first_name: Alejandro full_name: Casallas Garcia, Alejandro id: 92081129-2d75-11ef-a48d-b04dd7a2385a last_name: Casallas Garcia orcid: 0000-0002-1988-5035 citation: ama: Quishpe-Vásquez C, Oliva P, López-Barrera EA, Casallas Garcia A. Wildfires impact on PM2.5 concentration in galicia Spain. Journal of Environmental Management. 2024;367. doi:10.1016/j.jenvman.2024.122093 apa: Quishpe-Vásquez, C., Oliva, P., López-Barrera, E. A., & Casallas Garcia, A. (2024). Wildfires impact on PM2.5 concentration in galicia Spain. Journal of Environmental Management. Elsevier. https://doi.org/10.1016/j.jenvman.2024.122093 chicago: Quishpe-Vásquez, César, Patricia Oliva, Ellie Anne López-Barrera, and Alejandro Casallas Garcia. “Wildfires Impact on PM2.5 Concentration in Galicia Spain.” Journal of Environmental Management. Elsevier, 2024. https://doi.org/10.1016/j.jenvman.2024.122093. ieee: C. Quishpe-Vásquez, P. Oliva, E. A. López-Barrera, and A. Casallas Garcia, “Wildfires impact on PM2.5 concentration in galicia Spain,” Journal of Environmental Management, vol. 367. Elsevier, 2024. ista: Quishpe-Vásquez C, Oliva P, López-Barrera EA, Casallas Garcia A. 2024. Wildfires impact on PM2.5 concentration in galicia Spain. Journal of Environmental Management. 367, 122093. mla: Quishpe-Vásquez, César, et al. “Wildfires Impact on PM2.5 Concentration in Galicia Spain.” Journal of Environmental Management, vol. 367, 122093, Elsevier, 2024, doi:10.1016/j.jenvman.2024.122093. short: C. Quishpe-Vásquez, P. Oliva, E.A. López-Barrera, A. Casallas Garcia, Journal of Environmental Management 367 (2024). das_tickbox: '1' dataavailabilitystatement: Data will be made available on request date_created: 2024-08-06T05:54:52Z date_published: 2024-09-01T00:00:00Z date_updated: 2026-10-01T08:34:24Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1016/j.jenvman.2024.122093 ec_funded: 1 external_id: isi: - '001289532100001' pmid: - '39106804' file: - access_level: open_access checksum: 6fa476a4c08aded413844d92336b0e52 content_type: application/pdf creator: acasalla date_created: 2024-08-09T13:37:23Z date_updated: 2024-08-09T13:37:23Z file_id: '17405' file_name: Fires_Galicia_SM.pdf file_size: 1595118 relation: main_file success: 1 - access_level: open_access checksum: 859dcdef9555c383b702cf8cc7da66f2 content_type: application/pdf creator: acasalla date_created: 2024-08-09T13:37:24Z date_updated: 2024-08-09T13:37:24Z file_id: '17406' file_name: Fires_Galicia.pdf file_size: 13662676 relation: main_file success: 1 file_date_updated: 2024-08-09T13:37:24Z fulldoi: https://doi.org/10.1016/j.jenvman.2024.122093 has_accepted_license: '1' intvolume: ' 367' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Journal of Environmental Management publication_identifier: issn: - 0301-4797 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Wildfires impact on PM2.5 concentration in galicia Spain tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 367 year: '2024' ... --- _id: '17435' abstract: - lang: eng text: 'The Mediterranean region is experiencing pronounced aridification and in certain areas higher occurrence of intense precipitation. In this work, we analyze the evolution of the precipitation probability distribution in terms of precipitating days (or “wet-days”) and all-days quantile trends, in Europe and the Mediterranean, using the ERA5 reanalysis. Looking at the form of wet-days quantile trends curves, we identify four regimes. Two are predominant: in most of northern Europe the precipitation quantiles all intensify, while in the Mediterranean the low-medium quantiles are mostly decreasing as extremes intensify or decrease. The wet-days distribution is then modeled by a Weibull law with two parameters, whose changes capture the four regimes. Assessing the significance of the parameters'' changes over 1950–2020 shows that a signal on wet-days distribution has already emerged in northern Europe (where the distribution shifts to more intense precipitation), but not yet in the Mediterranean, where the natural variability is stronger. We extend the results by describing the all-days distribution change as the wet-days’ change plus a contribution from the dry-days frequency change, and study their relative contribution. In northern Europe, the wet-days distribution change is the dominant driver, and the contribution of dry-days frequency change can be neglected for wet-days percentiles above about 50%. In the Mediterranean, however, the change of precipitation distribution comes from the significant increase of dry-days frequency instead of an intensity change during wet-days. Therefore, in the Mediterranean the increase of dry-days frequency is crucial for all-days trends, even for heavy precipitation.' acknowledgement: CJM gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No 805041). The authors also thank Samuel Somot (Centre National de Recherches Météorologiques, Toulouse) and Juliette Blanchet (Institut des Géosciences de l’Environnement, Grenoble) for their fruitful discussions on the project. article_number: e2023JD040413 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julie full_name: André, Julie last_name: André - first_name: Fabio full_name: D'Andrea, Fabio last_name: D'Andrea - first_name: Philippe full_name: Drobinski, Philippe last_name: Drobinski - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: 'André J, D’Andrea F, Drobinski P, Muller CJ. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 2024;129(15). doi:10.1029/2023JD040413' apa: 'André, J., D’Andrea, F., Drobinski, P., & Muller, C. J. (2024). Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040413' chicago: 'André, Julie, Fabio D’Andrea, Philippe Drobinski, and Caroline J Muller. “Regimes of Precipitation Change over Europe and the Mediterranean.” Journal of Geophysical Research: Atmospheres. Wiley, 2024. https://doi.org/10.1029/2023JD040413.' ieee: 'J. André, F. D’Andrea, P. Drobinski, and C. J. Muller, “Regimes of precipitation change over Europe and the Mediterranean,” Journal of Geophysical Research: Atmospheres, vol. 129, no. 15. Wiley, 2024.' ista: 'André J, D’Andrea F, Drobinski P, Muller CJ. 2024. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 129(15), e2023JD040413.' mla: 'André, Julie, et al. “Regimes of Precipitation Change over Europe and the Mediterranean.” Journal of Geophysical Research: Atmospheres, vol. 129, no. 15, e2023JD040413, Wiley, 2024, doi:10.1029/2023JD040413.' short: 'J. André, F. D’Andrea, P. Drobinski, C.J. Muller, Journal of Geophysical Research: Atmospheres 129 (2024).' das_tickbox: '1' dataavailabilitystatement: The hourly precipitation variable in ERA5 reanalysis Hersbach et al. (2018) was downloaded from the Copernicus Climate Change Service (C3S) accessed in July 2022. It is freely available on C3S website. The results contain modified Copernicus Climate Change Service information 2020. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains. date_created: 2024-08-18T22:01:04Z date_published: 2024-08-16T00:00:00Z date_updated: 2026-10-01T08:35:09Z day: '16' ddc: - '550' department: - _id: CaMu doi: 10.1029/2023JD040413 ec_funded: 1 external_id: isi: - '001285897600001' file: - access_level: open_access checksum: 71d7f966318e11ce474737f4e37405ef content_type: application/pdf creator: dernst date_created: 2024-08-19T06:32:21Z date_updated: 2024-08-19T06:32:21Z file_id: '17438' file_name: 2024_JGRAtmospheres_Andre.pdf file_size: 8126046 relation: main_file success: 1 file_date_updated: 2024-08-19T06:32:21Z fulldoi: https://doi.org/10.1029/2023JD040413 has_accepted_license: '1' intvolume: ' 129' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: 'Journal of Geophysical Research: Atmospheres' publication_identifier: eissn: - 2169-8996 issn: - 2169-897X publication_status: published publisher: Wiley quality_controlled: '1' researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: yes title: Regimes of precipitation change over Europe and the Mediterranean tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 129 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18940' abstract: - lang: eng text: BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression. acknowledgement: This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope. article_processing_charge: Yes article_type: original author: - first_name: Paul full_name: Knabl, Paul last_name: Knabl - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Autumn P full_name: Pomreinke, Autumn P last_name: Pomreinke - first_name: Bob full_name: Zimmermann, Bob last_name: Zimmermann - first_name: Katherine W full_name: Rogers, Katherine W last_name: Rogers - first_name: Daniel full_name: Čapek, Daniel last_name: Čapek - first_name: Patrick full_name: Müller, Patrick last_name: Müller - first_name: Grigory full_name: Genikhovich, Grigory last_name: Genikhovich citation: ama: Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 2024;13. doi:10.7554/elife.80803 apa: Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.80803 chicago: Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803. ieee: P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13. mla: Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.80803. short: P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024). das_tickbox: '1' dataavailabilitystatement: The data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 6D-F', Figure 6Q, Figure 5—figure supplement 1D, Figure 6—figure supplement 2G, Figure 6—figure supplement 3E and F. All the sequencing data are available at NCBI as an SRA project PRJNA820593. date_created: 2025-01-29T08:48:34Z date_published: 2024-02-07T00:00:00Z date_updated: 2026-10-01T08:31:50Z day: '07' ddc: - '570' department: - _id: CaHe doi: 10.7554/elife.80803 file: - access_level: open_access checksum: 24548a184215d3f4547bba535ccfd7b1 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:50:18Z date_updated: 2025-01-29T08:50:18Z file_id: '18941' file_name: 2024_eLife_Knabl.pdf file_size: 11855972 relation: main_file success: 1 file_date_updated: 2025-01-29T08:50:18Z fulldoi: https://doi.org/10.7554/elife.80803 has_accepted_license: '1' intvolume: ' 13' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 13 year: '2024' ...