[{"date_published":"2025-09-24T00:00:00Z","type":"dissertation","day":"24","page":"102","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"year":"2025","author":[{"full_name":"Kishi, Kasumi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","orcid":"0000-0001-6060-4795"}],"OA_place":"publisher","oa_version":"Published Version","article_processing_charge":"No","title":"Regulation of notochord and floor plate size during mouse development","publication_status":"published","publisher":"Institute of Science and Technology Austria","date_created":"2025-09-25T10:08:10Z","status":"public","date_updated":"2026-04-14T09:50:52Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18481","status":"public"}]},"alternative_title":["ISTA Thesis"],"corr_author":"1","_id":"20393","file":[{"creator":"kkishi","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","file_id":"20413","content_type":"application/x-zip-compressed","file_size":41847994,"date_created":"2025-09-30T14:33:17Z","relation":"source_file","access_level":"closed","date_updated":"2025-10-01T11:54:41Z","file_name":"2025-Kishi-Kasumi-Thesis.zip"},{"embargo":"2026-09-30","file_name":"2025-Kishi-Kasumi-Thesis.pdf","date_updated":"2025-10-02T07:51:21Z","access_level":"closed","relation":"main_file","embargo_to":"open_access","date_created":"2025-09-30T14:33:22Z","file_size":55747072,"content_type":"application/pdf","file_id":"20414","checksum":"88349b9177e1dcbe1242cd3884b36fdb","creator":"kkishi"}],"month":"09","supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"file_date_updated":"2025-10-02T07:51:21Z","citation":{"ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025.","chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-20393","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}]},{"project":[{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"date_created":"2025-05-30T09:14:58Z","status":"public","acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","article_processing_charge":"No","OA_place":"publisher","year":"2025","author":[{"first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093"}],"language":[{"iso":"eng"}],"type":"dissertation","day":"29","page":"129","ddc":["570"],"date_published":"2025-05-29T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/AT-ISTA-19763","has_accepted_license":"1","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2025-11-30T23:30:02Z","citation":{"short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025.","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>.","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>.","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025."},"supervisor":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"}],"department":[{"_id":"AnKi"},{"_id":"GradSch"}],"month":"05","abstract":[{"lang":"eng","text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation."}],"_id":"19763","file":[{"relation":"main_file","date_updated":"2025-11-30T23:30:02Z","access_level":"open_access","file_name":"Thesis_Lehr_PDFA.pdf","embargo":"2025-11-30","creator":"cchlebak","checksum":"8cd7fe3ca990adbcafdece119aa0973d","file_id":"19764","date_created":"2025-05-30T09:10:22Z","file_size":42879974,"content_type":"application/pdf"},{"checksum":"0c87dd5fc803450a47b20736b5f86a2f","creator":"cchlebak","file_size":18731094,"date_created":"2025-05-30T09:31:15Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19765","date_updated":"2025-11-30T23:30:02Z","access_level":"closed","relation":"source_file","embargo_to":"open_access","file_name":"Thesis_Lehr_emptyPages.docx"}],"oa":1,"corr_author":"1","date_updated":"2026-04-14T09:50:53Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18601","status":"public"},{"id":"17148","relation":"part_of_dissertation","status":"public"},{"id":"18807","relation":"part_of_dissertation","status":"public"},{"id":"13136","relation":"part_of_dissertation","status":"public"}]}},{"quality_controlled":"1","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Elsevier, pp. 567–580, 2025.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580."},"file_date_updated":"2025-04-16T10:54:07Z","publication_identifier":{"issn":["1534-5807"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1016/j.devcel.2024.10.024","corr_author":"1","oa":1,"related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-05-20T22:31:11Z","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"publication":"Developmental Cell","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"volume":60,"month":"02","article_type":"original","file":[{"file_name":"2025_DevelopmentalCell_Lehr.pdf","date_updated":"2025-04-16T10:54:07Z","access_level":"open_access","relation":"main_file","date_created":"2025-04-16T10:54:07Z","file_size":6994499,"success":1,"content_type":"application/pdf","file_id":"19584","checksum":"bb58db4a908a1f4aabe4004706154541","creator":"dernst"}],"_id":"18807","intvolume":"        60","abstract":[{"lang":"eng","text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues."}],"article_processing_charge":"Yes (via OA deal)","title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","oa_version":"Published Version","pmid":1,"OA_place":"publisher","author":[{"first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Thomas","full_name":"Minchington, Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"id":"48A59534-F248-11E8-B48F-1D18A9856A87","last_name":"Greunz","full_name":"Greunz, Martina","first_name":"Martina"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"year":"2025","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","status":"public","date_created":"2025-01-09T11:25:47Z","publisher":"Elsevier","publication_status":"published","issue":"4","date_published":"2025-02-24T00:00:00Z","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"ddc":["570"],"page":"567-580","day":"24","type":"journal_article"},{"status":"public","date_created":"2024-10-27T23:01:45Z","acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","publisher":"Public Library of Science","pmid":1,"oa_version":"Published Version","title":"Dynamics of morphogen source formation in a growing tissue","article_processing_charge":"No","year":"2024","author":[{"first_name":"Richard D.J.G.","full_name":"Ho, Richard D.J.G.","last_name":"Ho"},{"last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","orcid":"0000-0001-6060-4795"},{"full_name":"Majka, Maciej","first_name":"Maciej","last_name":"Majka"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"},{"orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P"}],"OA_place":"publisher","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"14","ddc":["570"],"date_published":"2024-10-14T00:00:00Z","APC_amount":"3197,23 EUR","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1012508","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_type":"gold","quality_controlled":"1","file_date_updated":"2024-10-29T11:59:09Z","citation":{"short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>.","ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.","apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024."},"article_number":"e1012508","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":20,"DOAJ_listed":"1","department":[{"_id":"AnKi"}],"publication":"PLoS Computational Biology","intvolume":"        20","_id":"18481","abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"file":[{"file_size":3732443,"success":1,"date_created":"2024-10-29T11:59:09Z","content_type":"application/pdf","file_id":"18487","checksum":"42fa714459943cb3961b40fab8fd82c8","creator":"dernst","file_name":"2024_PloSComBio_Ho.pdf","date_updated":"2024-10-29T11:59:09Z","access_level":"open_access","relation":"main_file"}],"article_type":"original","month":"10","oa":1,"corr_author":"1","external_id":{"pmid":["39401260"],"isi":["001331700300003"]},"date_updated":"2026-04-07T12:31:58Z","related_material":{"record":[{"relation":"dissertation_contains","id":"20393","status":"public"}]}},{"pmid":1,"oa_version":"Published Version","article_processing_charge":"Yes","title":"Assessing the precision of morphogen gradients in neural tube development","year":"2024","author":[{"last_name":"Zagorski","first_name":"Marcin","full_name":"Zagorski, Marcin"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"first_name":"Matthias","full_name":"Lutolf, Matthias","last_name":"Lutolf"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"OA_place":"publisher","status":"public","date_created":"2025-01-27T13:01:01Z","acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"}],"publication_status":"published","publisher":"Springer Nature","date_published":"2024-02-01T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"01","ddc":["570"],"OA_type":"gold","quality_controlled":"1","citation":{"ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>","ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929.","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>.","chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>","short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024)."},"file_date_updated":"2025-01-27T13:04:03Z","article_number":"929","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-024-45148-8","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"corr_author":"1","external_id":{"isi":["001156218500022"],"pmid":["38302459"]},"date_updated":"2025-12-30T10:57:08Z","volume":15,"DOAJ_listed":"1","department":[{"_id":"GaTk"},{"_id":"AnKi"}],"publication":"Nature Communications","intvolume":"        15","_id":"18902","file":[{"file_name":"2024_NatureComm_Zagorski.pdf","relation":"main_file","date_updated":"2025-01-27T13:04:03Z","access_level":"open_access","file_id":"18903","success":1,"file_size":4723831,"date_created":"2025-01-27T13:04:03Z","content_type":"application/pdf","creator":"dernst","checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7"}],"month":"02","article_type":"letter_note"},{"file":[{"file_name":"2024_DevelopmentalCell_Krammer.pdf","date_updated":"2025-01-13T10:59:12Z","access_level":"open_access","relation":"main_file","file_size":6249076,"date_created":"2025-01-13T10:59:12Z","success":1,"content_type":"application/pdf","file_id":"18841","checksum":"fefdea9c02862b4bb74de49b65ce638a","creator":"dernst"}],"intvolume":"        59","_id":"17148","abstract":[{"lang":"eng","text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering."}],"article_type":"original","month":"08","volume":59,"publication":"Developmental Cell","department":[{"_id":"AnKi"}],"date_updated":"2026-05-20T22:31:11Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"oa":1,"has_accepted_license":"1","doi":"10.1016/j.devcel.2024.04.021","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"file_date_updated":"2025-01-13T10:59:12Z","citation":{"ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","quality_controlled":"1","day":"01","page":"1940-1953.e10","ddc":["570"],"type":"journal_article","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2024-08-01T00:00:00Z","issue":"15","publication_status":"published","publisher":"Elsevier","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","status":"public","date_created":"2024-06-16T22:01:07Z","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"author":[{"last_name":"Krammer","full_name":"Krammer, Teresa","first_name":"Teresa"},{"first_name":"Hannah T.","full_name":"Stuart, Hannah T.","last_name":"Stuart"},{"full_name":"Gromberg, Elena","first_name":"Elena","last_name":"Gromberg"},{"first_name":"Keisuke","full_name":"Ishihara, Keisuke","last_name":"Ishihara"},{"last_name":"Cislo","full_name":"Cislo, Dillon","first_name":"Dillon"},{"full_name":"Melchionda, Manuela","first_name":"Manuela","last_name":"Melchionda"},{"full_name":"Becerril Perez, Fernando","first_name":"Fernando","last_name":"Becerril Perez"},{"last_name":"Wang","first_name":"Jingkui","full_name":"Wang, Jingkui"},{"last_name":"Costantini","first_name":"Elena","full_name":"Costantini, Elena"},{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093"},{"last_name":"Arbanas","full_name":"Arbanas, Laura","first_name":"Laura"},{"last_name":"Hörmann","full_name":"Hörmann, Alexandra","first_name":"Alexandra"},{"full_name":"Neumüller, Ralph A.","first_name":"Ralph A.","last_name":"Neumüller"},{"full_name":"Elvassore, Nicola","first_name":"Nicola","last_name":"Elvassore"},{"first_name":"Eric","full_name":"Siggia, Eric","last_name":"Siggia"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tanaka","first_name":"Elly M.","full_name":"Tanaka, Elly M."}],"year":"2024","OA_place":"publisher","pmid":1,"article_processing_charge":"Yes (in subscription journal)","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","oa_version":"Published Version"},{"article_processing_charge":"Yes","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","oa_version":"Published Version","pmid":1,"OA_place":"publisher","author":[{"orcid":"0000-0001-8703-1093","first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609"},{"id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","last_name":"Kulig","first_name":"Monika Aleksandra","full_name":"Kulig, Monika Aleksandra"},{"full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington"},{"orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna"}],"year":"2024","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","date_created":"2024-12-01T23:01:53Z","status":"public","publisher":"Elsevier","publication_status":"published","issue":"4","APC_amount":"804 EUR","date_published":"2024-12-20T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"ddc":["570"],"day":"20","type":"journal_article","quality_controlled":"1","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"103187","file_date_updated":"2024-12-03T10:53:23Z","citation":{"short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>.","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024."},"acknowledged_ssus":[{"_id":"NanoFab"}],"publication_identifier":{"eissn":["2666-1667"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1016/j.xpro.2024.103187","oa":1,"corr_author":"1","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"date_updated":"2026-05-20T22:31:11Z","external_id":{"pmid":["39602310"]},"publication":"STAR Protocols","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"DOAJ_listed":"1","volume":5,"month":"12","article_type":"original","file":[{"file_id":"18610","content_type":"application/pdf","success":1,"file_size":4989169,"date_created":"2024-12-03T10:53:23Z","creator":"dernst","checksum":"0c61a6f9978608a103865905e06f4581","file_name":"2024_STARProtoc_Lehr.pdf","relation":"main_file","access_level":"open_access","date_updated":"2024-12-03T10:53:23Z"}],"intvolume":"         5","_id":"18601","abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}]},{"day":"01","ddc":["570"],"type":"journal_article","isi":1,"language":[{"iso":"eng"}],"date_published":"2023-10-01T00:00:00Z","issue":"19","publication_status":"published","publisher":"The Company of Biologists","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","date_created":"2024-01-10T09:18:54Z","status":"public","author":[{"last_name":"Harish","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","full_name":"Harish, Rohit K","first_name":"Rohit K"},{"last_name":"Gupta","first_name":"Mansi","full_name":"Gupta, Mansi"},{"first_name":"Daniela","full_name":"Zöller, Daniela","last_name":"Zöller"},{"last_name":"Hartmann","full_name":"Hartmann, Hella","first_name":"Hella"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"last_name":"Machate","first_name":"Anja","full_name":"Machate, Anja"},{"full_name":"Hans, Stefan","first_name":"Stefan","last_name":"Hans"},{"first_name":"Michael","full_name":"Brand, Michael","last_name":"Brand"}],"year":"2023","pmid":1,"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","file":[{"creator":"dernst","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","file_id":"14790","success":1,"date_created":"2024-01-10T12:41:13Z","file_size":12836306,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2024-01-10T12:41:13Z","file_name":"2023_Development_Harish.pdf"}],"abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"_id":"14774","intvolume":"       150","month":"10","article_type":"original","volume":150,"keyword":["Developmental Biology","Molecular Biology"],"publication":"Development","department":[{"_id":"AnKi"}],"date_updated":"2024-01-10T12:45:25Z","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"oa":1,"has_accepted_license":"1","doi":"10.1242/dev.201559","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"article_number":"dev201559","file_date_updated":"2024-01-10T12:41:13Z","citation":{"short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. The Company of Biologists, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1"},{"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}],"status":"public","date_created":"2023-11-05T23:00:53Z","acknowledgement":"We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138).","publisher":"Annual Reviews","publication_status":"published","oa_version":"Published Version","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","title":"Control of tissue development by morphogens","pmid":1,"year":"2023","author":[{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"}],"scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","day":"16","page":"91-121","ddc":["570"],"date_published":"2023-10-16T00:00:00Z","publication_identifier":{"eissn":["1530-8995"],"issn":["1081-0706"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1146/annurev-cellbio-020823-011522","has_accepted_license":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2023-11-06T09:47:50Z","citation":{"chicago":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">https://doi.org/10.1146/annurev-cellbio-020823-011522</a>.","apa":"Kicheva, A., &#38; Briscoe, J. (2023). Control of tissue development by morphogens. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">https://doi.org/10.1146/annurev-cellbio-020823-011522</a>","ista":"Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121.","mla":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">10.1146/annurev-cellbio-020823-011522</a>.","ieee":"A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 39. Annual Reviews, pp. 91–121, 2023.","short":"A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121.","ama":"Kicheva A, Briscoe J. Control of tissue development by morphogens. <i>Annual Review of Cell and Developmental Biology</i>. 2023;39:91-121. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-020823-011522\">10.1146/annurev-cellbio-020823-011522</a>"},"department":[{"_id":"AnKi"}],"publication":"Annual Review of Cell and Developmental Biology","volume":39,"month":"10","article_type":"review","intvolume":"        39","_id":"14484","abstract":[{"lang":"eng","text":"Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling."}],"file":[{"relation":"main_file","date_updated":"2023-11-06T09:47:50Z","access_level":"open_access","file_name":"2023_AnnualReviews_Kicheva.pdf","creator":"dernst","checksum":"461726014cf5907010afbd418d3c13ec","file_id":"14491","file_size":434819,"success":1,"date_created":"2023-11-06T09:47:50Z","content_type":"application/pdf"}],"oa":1,"corr_author":"1","external_id":{"isi":["001082823000006"],"pmid":["37418774"]},"date_updated":"2025-12-30T10:57:08Z"},{"status":"public","date_created":"2023-09-13T10:07:18Z","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","oa_version":"Published Version","author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska"}],"year":"2023","OA_place":"publisher","language":[{"iso":"eng"}],"page":"151","ddc":["570"],"day":"13","type":"dissertation","date_published":"2023-09-13T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","doi":"10.15479/at:ista:14323","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2025-03-13T23:30:05Z","citation":{"short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"supervisor":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2023-09-13T09:52:52Z","file_size":10147911,"content_type":"application/pdf","file_id":"14324","checksum":"bd83596869c814b24aeff7077d031c0e","creator":"kkuzmicz","embargo":"2025-03-13","file_name":"PhDThesis_KK_final_pdfA.pdf","date_updated":"2025-03-13T23:30:05Z","access_level":"open_access","relation":"main_file"},{"creator":"kkuzmicz","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","file_id":"14325","file_size":103980668,"date_created":"2023-09-13T09:53:29Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","embargo_to":"open_access","access_level":"closed","date_updated":"2025-03-13T23:30:05Z","file_name":"thesis_KK_final_corrections_092023.docx"}],"_id":"14323","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"month":"09","oa":1,"corr_author":"1","date_updated":"2026-04-14T09:50:54Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7883"}]}},{"has_accepted_license":"1","doi":"10.1016/j.coisb.2023.100459","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_identifier":{"eissn":["2452-3100"]},"article_number":"100459","file_date_updated":"2024-01-29T11:06:45Z","citation":{"ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023.","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","file":[{"creator":"dernst","checksum":"8a75c4e29fd9b62e3c50663c2265b173","file_id":"14896","content_type":"application/pdf","success":1,"file_size":598842,"date_created":"2024-01-29T11:06:45Z","relation":"main_file","date_updated":"2024-01-29T11:06:45Z","access_level":"open_access","file_name":"2023_CurrOpSystBioloy_Minchington.pdf"}],"_id":"13136","intvolume":"        35","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"article_type":"original","month":"09","volume":35,"publication":"Current Opinion in Systems Biology","department":[{"_id":"AnKi"}],"related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-05-20T22:31:11Z","oa":1,"corr_author":"1","publication_status":"published","publisher":"Elsevier","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","status":"public","date_created":"2023-06-18T22:00:46Z","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"author":[{"last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","first_name":"Thomas"},{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","first_name":"Stefanie","full_name":"Rus, Stefanie"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"}],"year":"2023","title":"Control of tissue dimensions in the developing neural tube and somites","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","day":"01","ddc":["570"],"type":"journal_article","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2023-09-01T00:00:00Z"},{"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","status":"public","date_created":"2023-04-16T22:01:09Z","publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","ec_funded":1,"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Laura","full_name":"Bocanegra, Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singh, Amrita","first_name":"Amrita","last_name":"Singh","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","orcid":"0000-0001-7896-7762"},{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"}],"year":"2023","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"day":"01","ddc":["570"],"page":"1050-1058","type":"journal_article","date_published":"2023-07-01T00:00:00Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1038/s41567-023-01977-w","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. 2023;19:1050-1058. doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1050–1058, 2023.","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., &#38; Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>","ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>."},"file_date_updated":"2023-10-04T11:13:28Z","publication":"Nature Physics","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"volume":19,"article_type":"original","month":"07","file":[{"checksum":"858225a4205b74406e5045006cdd853f","creator":"dernst","date_created":"2023-10-04T11:13:28Z","file_size":5532285,"success":1,"content_type":"application/pdf","file_id":"14392","access_level":"open_access","date_updated":"2023-10-04T11:13:28Z","relation":"main_file","file_name":"2023_NaturePhysics_Boncanegra.pdf"}],"_id":"12837","abstract":[{"lang":"eng","text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues."}],"intvolume":"        19","corr_author":"1","oa":1,"date_updated":"2026-05-20T22:31:14Z","related_material":{"record":[{"id":"13081","relation":"dissertation_contains","status":"public"}]},"external_id":{"pmid":["37456593"],"isi":["000964029300003"]}},{"citation":{"ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>"},"file_date_updated":"2024-06-01T22:30:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","doi":"10.15479/at:ista:13081","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2026-04-14T09:50:54Z","related_material":{"record":[{"id":"9349","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12837","status":"public"}]},"alternative_title":["ISTA Thesis"],"oa":1,"corr_author":"1","abstract":[{"text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling.  Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.","lang":"eng"}],"_id":"13081","file":[{"file_id":"13089","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25615534,"date_created":"2023-05-25T06:32:12Z","creator":"lbocaneg","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_name":"Thesis_final_LauraBocanegra.docx","embargo_to":"open_access","relation":"source_file","access_level":"closed","date_updated":"2024-06-01T22:30:04Z"},{"checksum":"c6cdef6323eacfb4b7a8af20f32eae97","creator":"lbocaneg","file_size":12386046,"date_created":"2023-05-25T06:32:16Z","content_type":"application/pdf","file_id":"13090","date_updated":"2024-06-01T22:30:04Z","access_level":"open_access","relation":"main_file","embargo":"2024-05-31","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf"}],"month":"05","supervisor":[{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"year":"2023","author":[{"full_name":"Bocanegra, Laura","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","last_name":"Bocanegra"}],"OA_place":"publisher","oa_version":"Published Version","article_processing_charge":"No","title":"Epithelial dynamics during mouse neural tube development","publication_status":"published","publisher":"Institute of Science and Technology Austria","status":"public","date_created":"2023-05-23T19:10:42Z","date_published":"2023-05-23T00:00:00Z","type":"dissertation","ddc":["570"],"page":"93","day":"23","language":[{"iso":"eng"}]},{"volume":149,"keyword":["Developmental Biology","Molecular Biology"],"department":[{"_id":"AnKi"}],"publication":"Development","abstract":[{"text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.","lang":"eng"}],"_id":"12245","intvolume":"       149","file":[{"file_name":"2022_Development_Soto.pdf","relation":"main_file","access_level":"open_access","date_updated":"2023-01-30T08:35:44Z","file_id":"12438","success":1,"date_created":"2023-01-30T08:35:44Z","file_size":9348839,"content_type":"application/pdf","creator":"dernst","checksum":"d7c29b74e9e4032308228cc704a30e88"}],"article_type":"original","month":"10","oa":1,"external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"date_updated":"2023-08-04T09:41:08Z","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"doi":"10.1242/dev.200474","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","file_date_updated":"2023-01-30T08:35:44Z","citation":{"chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company of Biologists, 2022.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>"},"article_number":"dev200474","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"01","ddc":["570"],"issue":"19","date_published":"2022-10-01T00:00:00Z","status":"public","date_created":"2023-01-16T09:53:17Z","acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","publication_status":"published","publisher":"The Company of Biologists","pmid":1,"oa_version":"Published Version","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","article_processing_charge":"No","year":"2022","author":[{"last_name":"Soto","full_name":"Soto, Ximena","first_name":"Ximena"},{"first_name":"Joshua","full_name":"Burton, Joshua","last_name":"Burton"},{"full_name":"Manning, Cerys S.","first_name":"Cerys S.","last_name":"Manning"},{"full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington"},{"last_name":"Lea","full_name":"Lea, Robert","first_name":"Robert"},{"last_name":"Lee","first_name":"Jessica","full_name":"Lee, Jessica"},{"full_name":"Kursawe, Jochen","first_name":"Jochen","last_name":"Kursawe"},{"full_name":"Rattray, Magnus","first_name":"Magnus","last_name":"Rattray"},{"first_name":"Nancy","full_name":"Papalopulu, Nancy","last_name":"Papalopulu"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1242/dev.196121","has_accepted_license":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-04-03T13:58:51Z","citation":{"ama":"Vinter DJ, Hoppe C, Minchington T, Sutcliffe C, Ashe HL. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. <i>Development</i>. 2021;148(18). doi:<a href=\"https://doi.org/10.1242/dev.196121\">10.1242/dev.196121</a>","short":"D.J. Vinter, C. Hoppe, T. Minchington, C. Sutcliffe, H.L. Ashe, Development 148 (2021).","ieee":"D. J. Vinter, C. Hoppe, T. Minchington, C. Sutcliffe, and H. L. Ashe, “Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo,” <i>Development</i>, vol. 148, no. 18. The Company of Biologists, 2021.","mla":"Vinter, Daisy J., et al. “Dynamics of Hunchback Translation in Real-Time and at Single-MRNA Resolution in the Drosophila Embryo.” <i>Development</i>, vol. 148, no. 18, dev196121., The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/dev.196121\">10.1242/dev.196121</a>.","ista":"Vinter DJ, Hoppe C, Minchington T, Sutcliffe C, Ashe HL. 2021. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development. 148(18), dev196121.","apa":"Vinter, D. J., Hoppe, C., Minchington, T., Sutcliffe, C., &#38; Ashe, H. L. (2021). Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.196121\">https://doi.org/10.1242/dev.196121</a>","chicago":"Vinter, Daisy J., Caroline Hoppe, Thomas Minchington, Catherine Sutcliffe, and Hilary L. Ashe. “Dynamics of Hunchback Translation in Real-Time and at Single-MRNA Resolution in the Drosophila Embryo.” <i>Development</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/dev.196121\">https://doi.org/10.1242/dev.196121</a>."},"article_number":"dev196121.","quality_controlled":"1","month":"09","article_type":"original","_id":"15262","abstract":[{"lang":"eng","text":"The Hunchback (Hb) transcription factor is crucial for anterior-posterior patterning of the Drosophila embryo. The maternal hb mRNA acts as a paradigm for translational regulation due to its repression in the posterior of the embryo. However, little is known about the translatability of zygotically transcribed hb mRNAs. Here, we adapt the SunTag system, developed for imaging translation at single-mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using single-molecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. Whereas the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila."}],"intvolume":"       148","file":[{"file_name":"2021_CompanyBiologists_Vinter.pdf","relation":"main_file","date_updated":"2024-04-03T13:58:51Z","access_level":"open_access","file_id":"15290","content_type":"application/pdf","success":1,"file_size":16258500,"date_created":"2024-04-03T13:58:51Z","creator":"dernst","checksum":"6d0533fe9c712448b3f9feb15e05ec4b"}],"department":[{"_id":"AnKi"}],"publication":"Development","volume":148,"keyword":["Developmental Biology","Molecular Biology"],"external_id":{"pmid":["33722899 "]},"date_updated":"2024-04-03T14:00:33Z","oa":1,"publisher":"The Company of Biologists","publication_status":"published","date_created":"2024-04-03T07:26:41Z","status":"public","year":"2021","author":[{"first_name":"Daisy J.","full_name":"Vinter, Daisy J.","last_name":"Vinter"},{"first_name":"Caroline","full_name":"Hoppe, Caroline","last_name":"Hoppe"},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","first_name":"Thomas","full_name":"Minchington, Thomas"},{"last_name":"Sutcliffe","first_name":"Catherine","full_name":"Sutcliffe, Catherine"},{"last_name":"Ashe","full_name":"Ashe, Hilary L.","first_name":"Hilary L."}],"oa_version":"Published Version","article_processing_charge":"No","title":"Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo","pmid":1,"type":"journal_article","day":"01","ddc":["570"],"scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2021-09-01T00:00:00Z","issue":"18"},{"date_updated":"2026-05-20T22:31:12Z","related_material":{"record":[{"relation":"dissertation_contains","id":"14323","status":"public"}]},"external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"oa":1,"corr_author":"1","file":[{"access_level":"open_access","date_updated":"2020-11-24T13:11:39Z","relation":"main_file","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","checksum":"f0a7745d48afa09ea7025e876a0145a8","creator":"dernst","success":1,"date_created":"2020-11-24T13:11:39Z","file_size":2527276,"content_type":"application/pdf","file_id":"8800"}],"_id":"7883","abstract":[{"lang":"eng","text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern."}],"month":"04","article_type":"original","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","department":[{"_id":"AnKi"}],"article_number":"e383","file_date_updated":"2020-11-24T13:11:39Z","citation":{"ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","quality_controlled":"1","has_accepted_license":"1","doi":"10.1002/wdev.383","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["1759-7684"],"eissn":["1759-7692"]},"date_published":"2021-04-15T00:00:00Z","day":"15","ddc":["570"],"type":"journal_article","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","author":[{"last_name":"Kuzmicz-Kowalska","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna","full_name":"Kuzmicz-Kowalska, Katarzyna"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"year":"2021","OA_place":"publisher","pmid":1,"article_processing_charge":"Yes (via OA deal)","title":"Regulation of size and scale in vertebrate spinal cord development","oa_version":"Published Version","ec_funded":1,"publication_status":"published","publisher":"Wiley","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","status":"public","date_created":"2020-05-24T22:01:00Z","project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-04-27T08:38:35Z","citation":{"ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>.","ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021)."},"article_number":"041501","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1088/1478-3975/abd0db","has_accepted_license":"1","publication_identifier":{"eissn":["1478-3975"]},"external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13081"}]},"date_updated":"2026-05-20T22:31:14Z","oa":1,"month":"04","article_type":"original","_id":"9349","intvolume":"        18","abstract":[{"lang":"eng","text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development."}],"file":[{"checksum":"4f52082549d3561c4c15d4d8d84ca5d8","creator":"cziletti","date_created":"2021-04-27T08:38:35Z","success":1,"file_size":6296324,"content_type":"application/pdf","file_id":"9355","date_updated":"2021-04-27T08:38:35Z","access_level":"open_access","relation":"main_file","file_name":"2021_PhysBio_Lenne.pdf"}],"department":[{"_id":"AnKi"},{"_id":"EdHa"}],"publication":"Physical biology","volume":18,"year":"2021","author":[{"last_name":"Lenne","full_name":"Lenne, Pierre François","first_name":"Pierre François"},{"last_name":"Munro","first_name":"Edwin","full_name":"Munro, Edwin"},{"first_name":"Idse","full_name":"Heemskerk, Idse","last_name":"Heemskerk"},{"first_name":"Aryeh","full_name":"Warmflash, Aryeh","last_name":"Warmflash"},{"full_name":"Bocanegra, Laura","first_name":"Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6060-4795","full_name":"Kishi, Kasumi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"},{"last_name":"Long","full_name":"Long, Yuchen","first_name":"Yuchen"},{"first_name":"Antoine","full_name":"Fruleux, Antoine","last_name":"Fruleux"},{"last_name":"Boudaoud","full_name":"Boudaoud, Arezki","first_name":"Arezki"},{"last_name":"Saunders","full_name":"Saunders, Timothy E.","first_name":"Timothy E."},{"first_name":"Paolo","full_name":"Caldarelli, Paolo","last_name":"Caldarelli"},{"last_name":"Michaut","first_name":"Arthur","full_name":"Michaut, Arthur"},{"last_name":"Gros","full_name":"Gros, Jerome","first_name":"Jerome"},{"last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit","first_name":"Yonit"},{"last_name":"Keren","full_name":"Keren, Kinneret","first_name":"Kinneret"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Zev J.","full_name":"Gartner, Zev J.","last_name":"Gartner"},{"last_name":"Stormo","full_name":"Stormo, Benjamin","first_name":"Benjamin"},{"first_name":"Amy","full_name":"Gladfelter, Amy","last_name":"Gladfelter"},{"first_name":"Alan","full_name":"Rodrigues, Alan","last_name":"Rodrigues"},{"first_name":"Amy","full_name":"Shyer, Amy","last_name":"Shyer"},{"first_name":"Nicolas","full_name":"Minc, Nicolas","last_name":"Minc"},{"first_name":"Jean Léon","full_name":"Maître, Jean Léon","last_name":"Maître"},{"full_name":"Di Talia, Stefano","first_name":"Stefano","last_name":"Di Talia"},{"full_name":"Khamaisi, Bassma","first_name":"Bassma","last_name":"Khamaisi"},{"last_name":"Sprinzak","first_name":"David","full_name":"Sprinzak, David"},{"first_name":"Sham","full_name":"Tlili, Sham","last_name":"Tlili"}],"oa_version":"Published Version","ec_funded":1,"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","article_processing_charge":"No","pmid":1,"publisher":"IOP Publishing","publication_status":"published","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"status":"public","date_created":"2021-04-25T22:01:29Z","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","date_published":"2021-04-14T00:00:00Z","issue":"4","type":"journal_article","day":"14","ddc":["570"],"scopus_import":"1","language":[{"iso":"eng"}],"isi":1},{"ddc":["570"],"day":"04","type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"date_published":"2019-12-04T00:00:00Z","issue":"23","publisher":"The Company of Biologists","publication_status":"published","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"date_created":"2019-12-10T14:39:50Z","status":"public","author":[{"full_name":"Guerrero, Pilar","first_name":"Pilar","last_name":"Guerrero"},{"first_name":"Ruben","full_name":"Perez-Carrasco, Ruben","last_name":"Perez-Carrasco"},{"first_name":"Marcin P","full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762"},{"last_name":"Page","first_name":"David","full_name":"Page, David"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"first_name":"Karen M.","full_name":"Page, Karen M.","last_name":"Page"}],"year":"2019","article_processing_charge":"No","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","ec_funded":1,"oa_version":"Published Version","pmid":1,"article_type":"original","month":"12","file":[{"checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","creator":"dernst","content_type":"application/pdf","file_size":7797881,"date_created":"2019-12-13T07:34:06Z","file_id":"7177","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","relation":"main_file","file_name":"2019_Development_Guerrero.pdf"}],"_id":"7165","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"intvolume":"       146","publication":"Development","department":[{"_id":"AnKi"}],"volume":146,"date_updated":"2025-04-14T07:27:30Z","external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"corr_author":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1242/dev.176297","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"dev176297","file_date_updated":"2020-07-14T12:47:50Z","citation":{"chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>.","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>","ieee":"P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146, no. 23. The Company of Biologists, 2019.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. 2019;146(23). doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>"},"quality_controlled":"1"},{"doi":"10.1016/j.cels.2018.04.003","publication_identifier":{"eissn":["2405-4712"]},"publist_id":"7551","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2018.04.003"}],"citation":{"mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>.","ieee":"G. Bauer <i>et al.</i>, “The science of living matter for tomorrow,” <i>Cell Systems</i>, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. <i>Cell Systems</i>. 2018;6(4):400-402. doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>"},"quality_controlled":"1","month":"04","article_type":"letter_note","abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"_id":"314","intvolume":"         6","department":[{"_id":"AnKi"}],"publication":"Cell Systems","volume":6,"external_id":{"isi":["000432192100003"],"pmid":["29698645"]},"date_updated":"2023-09-19T10:11:25Z","oa":1,"publisher":"Cell Press","publication_status":"published","status":"public","date_created":"2018-12-11T11:45:46Z","year":"2018","author":[{"first_name":"Guntram","full_name":"Bauer, Guntram","last_name":"Bauer"},{"full_name":"Fakhri, Nikta","first_name":"Nikta","last_name":"Fakhri"},{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"last_name":"Kondev","full_name":"Kondev, Jané","first_name":"Jané"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"full_name":"Noji, Hiroyuki","first_name":"Hiroyuki","last_name":"Noji"},{"last_name":"Riveline","first_name":"Daniel","full_name":"Riveline, Daniel"},{"full_name":"Saunders, Timothy","first_name":"Timothy","last_name":"Saunders"},{"first_name":"Mukund","full_name":"Thatta, Mukund","last_name":"Thatta"},{"last_name":"Wieschaus","first_name":"Eric","full_name":"Wieschaus, Eric"}],"oa_version":"Published Version","title":"The science of living matter for tomorrow","article_processing_charge":"No","pmid":1,"type":"journal_article","day":"25","page":"400 - 402","scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"date_published":"2018-04-25T00:00:00Z","issue":"4"},{"date_updated":"2025-05-19T08:28:40Z","oa":1,"_id":"19706","abstract":[{"text":"The importance of astrocytic l-lactate (LL) for normal functioning of neural circuits such as those regulating learning/memory, sleep/wake state, autonomic homeostasis, or emotional behaviour is being increasingly recognised. l-Lactate can act on neurones as a metabolic or redox substrate, but transmembrane receptor targets are also emerging. A comparative review of the hydroxy-carboxylic acid receptor (HCA1, formerly known as GPR81), Olfactory Receptor Family 51 Subfamily E Member 2 (OR51E2), and orphan receptor GPR4 highlights differences in their LL sensitivity, pharmacology, intracellular coupling, and localisation in the brain. In addition, a putative Gs-coupled receptor on noradrenergic neurones, LLRx, which we previously postulated, remains to be identified. Next-generation sequencing revealed several orphan receptors expressed in locus coeruleus neurones. Screening of a selection of these suggests additional LL-sensitive receptors: GPR180 which inhibits and GPR137 which activates intracellular cyclic AMP signalling in response to LL in a heterologous expression system. To further characterise binding of LL at LLRx, we carried out a structure–activity relationship study which demonstrates that carboxyl and 2-hydroxyl moieties of LL are essential for triggering d-lactate-sensitive noradrenaline release in locus coeruleus, and that the size of the LL binding pocket is limited towards the methyl group position. The evidence accumulating to date suggests that LL acts via multiple receptor targets to modulate distinct brain functions.","lang":"eng"}],"intvolume":"         1","file":[{"file_size":1909402,"date_created":"2025-05-19T08:20:19Z","success":1,"content_type":"application/pdf","file_id":"19711","checksum":"cadb56618f72edf4703b6a9855e84baa","creator":"dernst","file_name":"2018_Neuroglia_Mosienko.pdf","date_updated":"2025-05-19T08:20:19Z","access_level":"open_access","relation":"main_file"}],"article_type":"original","month":"12","volume":1,"DOAJ_listed":"1","department":[{"_id":"AnKi"}],"publication":"Neuroglia","file_date_updated":"2025-05-19T08:20:19Z","citation":{"short":"V. Mosienko, S. Rasooli-Nejad, K. Kishi, M. De Both, D. Jane, M.J. Huentelman, S. Kasparov, A.G. Teschemacher, Neuroglia 1 (2018) 365–380.","ama":"Mosienko V, Rasooli-Nejad S, Kishi K, et al. Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. 2018;1(2):365-380. doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>","mla":"Mosienko, Valentina, et al. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>, vol. 1, no. 2, MDPI, 2018, pp. 365–80, doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>.","apa":"Mosienko, V., Rasooli-Nejad, S., Kishi, K., De Both, M., Jane, D., Huentelman, M. J., … Teschemacher, A. G. (2018). Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. MDPI. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>","ista":"Mosienko V, Rasooli-Nejad S, Kishi K, De Both M, Jane D, Huentelman MJ, Kasparov S, Teschemacher AG. 2018. Putative receptors underpinning L-Lactate signalling in locus coeruleus. Neuroglia. 1(2), 365–380.","chicago":"Mosienko, Valentina, Seyed Rasooli-Nejad, Kasumi Kishi, Matt De Both, David Jane, Matt J. Huentelman, Sergey Kasparov, and Anja G. Teschemacher. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>.","ieee":"V. Mosienko <i>et al.</i>, “Putative receptors underpinning L-Lactate signalling in locus coeruleus,” <i>Neuroglia</i>, vol. 1, no. 2. MDPI, pp. 365–380, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","quality_controlled":"1","doi":"10.3390/neuroglia1020025","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2571-6980"]},"date_published":"2018-12-01T00:00:00Z","issue":"2","type":"journal_article","ddc":["570"],"page":"365-380","day":"01","language":[{"iso":"eng"}],"scopus_import":"1","year":"2018","author":[{"first_name":"Valentina","full_name":"Mosienko, Valentina","last_name":"Mosienko"},{"first_name":"Seyed","full_name":"Rasooli-Nejad, Seyed","last_name":"Rasooli-Nejad"},{"full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matt","full_name":"De Both, Matt","last_name":"De Both"},{"first_name":"David","full_name":"Jane, David","last_name":"Jane"},{"last_name":"Huentelman","first_name":"Matt J.","full_name":"Huentelman, Matt J."},{"full_name":"Kasparov, Sergey","first_name":"Sergey","last_name":"Kasparov"},{"last_name":"Teschemacher","full_name":"Teschemacher, Anja G.","first_name":"Anja G."}],"OA_place":"publisher","oa_version":"Published Version","article_processing_charge":"Yes","title":"Putative receptors underpinning L-Lactate signalling in locus coeruleus","publication_status":"published","publisher":"MDPI","date_created":"2025-05-18T22:02:51Z","status":"public","acknowledgement":"This work was supported by grants from BBSRC BB/L019396/1, and MRC MR/L020661/1. David Kleinfeld for his gift of CNiFER cells, Lesley Arberry for expert technical support, Andrew Herman for support with FACS sorting."}]