[{"acknowledgement":"We thank Pierre Léopold, Tatsushi Igaki, Erik Storkebaum, Tobias Reiff, Masayuki Miura, Xiaohang Yang, Mikio Furuse, Bloomington Drosophila Stock Center and Developmental Studies Hybridoma Bank for providing us with fly stocks and reagents. We are also grateful to Hiromi Yanagisawa, Satoru Kobayashi, Md Al Amin Sheikh and Yaxuan Cui for allowing us to use their equipment, and to Allison Bardin, Pierre Léopold and Tadashi Uemura for helpful discussions.","intvolume":"       153","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.07.05.662934"}],"OA_place":"repository","date_created":"2026-01-25T23:01:39Z","issue":"2","author":[{"first_name":"Qingyin","last_name":"Qian","full_name":"Qian, Qingyin"},{"full_name":"Nagai, Hiroki","orcid":"0000-0003-1671-9434","last_name":"Nagai","id":"608df3e6-e2ab-11ed-8890-c9318cec7da4","first_name":"Hiroki"},{"full_name":"Sanaki, Yuya","first_name":"Yuya","last_name":"Sanaki"},{"full_name":"Hayashi, Makoto","last_name":"Hayashi","first_name":"Makoto"},{"full_name":"Kimura, Kenichi","last_name":"Kimura","first_name":"Kenichi"},{"full_name":"Nakajima, Yu Ichiro","first_name":"Yu Ichiro","last_name":"Nakajima"},{"last_name":"Niwa","first_name":"Ryusuke","full_name":"Niwa, Ryusuke"}],"_id":"21039","pmid":1,"article_processing_charge":"No","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","department":[{"_id":"XiFe"}],"doi":"10.1242/dev.205225","scopus_import":"1","abstract":[{"lang":"eng","text":"Cellular plasticity, the ability of a differentiated cell to adopt another phenotypic identity, is restricted under basal conditions, but can be elicited upon damage. However, the molecular mechanism enabling such plasticity remains largely unexplored. Here, we report damage-induced cellular plasticity of secretory enteroendocrine cells (EEs) in the adult Drosophila midgut. Ionizing radiation induces EE fate conversion and activates stress-responsive programs in EE lineages, accompanied by the induction of the stress-inducible transcription factor Xrp1 and the cytokine gene upd3. Xrp1 and upd3 are both necessary for radiation-induced EE plasticity. Under basal conditions, EE-specific Xrp1 overexpression triggers ectopic expression of progenitor-specific genes, which is necessary for Xrp1 to drive EE plasticity. Our work identifies Xrp1 as a crucial regulator that coordinates damage-induced signaling and transcriptional reprogramming, enabling the reactivation of cellular plasticity in differentiated cells."}],"OA_type":"green","status":"public","article_number":"dev205225","citation":{"chicago":"Qian, Qingyin, HIROKI NAGAI, Yuya Sanaki, Makoto Hayashi, Kenichi Kimura, Yu Ichiro Nakajima, and Ryusuke Niwa. “Xrp1 Drives Damage-Induced Cellular Plasticity of Enteroendocrine Cells in the Adult Drosophila Midgut.” <i>Development</i>. The Company of Biologists, 2026. <a href=\"https://doi.org/10.1242/dev.205225\">https://doi.org/10.1242/dev.205225</a>.","ista":"Qian Q, NAGAI H, Sanaki Y, Hayashi M, Kimura K, Nakajima YI, Niwa R. 2026. Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut. Development. 153(2), dev205225.","apa":"Qian, Q., NAGAI, H., Sanaki, Y., Hayashi, M., Kimura, K., Nakajima, Y. I., &#38; Niwa, R. (2026). Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.205225\">https://doi.org/10.1242/dev.205225</a>","ama":"Qian Q, NAGAI H, Sanaki Y, et al. Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut. <i>Development</i>. 2026;153(2). doi:<a href=\"https://doi.org/10.1242/dev.205225\">10.1242/dev.205225</a>","ieee":"Q. Qian <i>et al.</i>, “Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut,” <i>Development</i>, vol. 153, no. 2. The Company of Biologists, 2026.","mla":"Qian, Qingyin, et al. “Xrp1 Drives Damage-Induced Cellular Plasticity of Enteroendocrine Cells in the Adult Drosophila Midgut.” <i>Development</i>, vol. 153, no. 2, dev205225, The Company of Biologists, 2026, doi:<a href=\"https://doi.org/10.1242/dev.205225\">10.1242/dev.205225</a>.","short":"Q. Qian, H. NAGAI, Y. Sanaki, M. Hayashi, K. Kimura, Y.I. Nakajima, R. Niwa, Development 153 (2026)."},"article_type":"original","oa":1,"day":"15","external_id":{"pmid":["41392708"]},"quality_controlled":"1","oa_version":"Preprint","title":"Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut","type":"journal_article","publication":"Development","publisher":"The Company of Biologists","month":"01","year":"2026","date_updated":"2026-02-12T12:41:18Z","date_published":"2026-01-15T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":153},{"month":"06","year":"2025","date_updated":"2025-09-30T14:07:51Z","license":"https://creativecommons.org/licenses/by/4.0/","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)"},"date_published":"2025-06-27T00:00:00Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":152,"type":"journal_article","PlanS_conform":"1","publication":"Development","publisher":"The Company of Biologists","isi":1,"oa":1,"day":"27","external_id":{"pmid":["40576478"],"isi":["001525252300001"]},"quality_controlled":"1","oa_version":"Published Version","corr_author":"1","title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","status":"public","article_number":"dev204261","article_type":"original","citation":{"ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. The Company of Biologists, 2025.","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, The Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>.","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>"},"file":[{"date_created":"2025-07-23T08:43:01Z","creator":"dernst","relation":"main_file","date_updated":"2025-07-23T08:43:01Z","access_level":"open_access","file_name":"2025_Development_Moriyama.pdf","success":1,"file_id":"20070","checksum":"808d8aa28df79d23fb661838d1fdc1be","content_type":"application/pdf","file_size":25935563}],"department":[{"_id":"CaHe"}],"doi":"10.1242/dev.204261","scopus_import":"1","OA_type":"hybrid","file_date_updated":"2025-07-23T08:43:01Z","abstract":[{"text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.","lang":"eng"}],"_id":"20048","article_processing_charge":"Yes (via OA deal)","pmid":1,"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_created":"2025-07-21T08:10:32Z","OA_place":"publisher","issue":"12","author":[{"first_name":"Yuuta","last_name":"Moriyama","orcid":"0000-0002-2853-8051","id":"addc9b8c-67a0-11f0-b374-a2e094825470","full_name":"Moriyama, Yuuta"},{"full_name":"Mitsui, Toshiyuki","first_name":"Toshiyuki","last_name":"Mitsui"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","intvolume":"       152"},{"ec_funded":1,"abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"file_date_updated":"2024-03-04T07:24:43Z","scopus_import":"1","department":[{"_id":"CaHe"},{"_id":"Bio"}],"doi":"10.1242/dev.202316","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"14926"}]},"_id":"15048","pmid":1,"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"author":[{"last_name":"Schauer","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","full_name":"Schauer, Alexandra"},{"full_name":"Pranjic-Ferscha, Kornelija","first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2024-03-03T23:00:50Z","issue":"4","ddc":["570"],"has_accepted_license":"1","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":"       151","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"volume":151,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-04T12:10:40Z","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)"},"language":[{"iso":"eng"}],"date_published":"2024-02-01T00:00:00Z","month":"02","year":"2024","isi":1,"publisher":"The Company of Biologists","publication":"Development","type":"journal_article","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","corr_author":"1","oa_version":"Published Version","quality_controlled":"1","oa":1,"day":"01","external_id":{"isi":["001170580200001"],"pmid":["38372390"]},"page":"1-18","citation":{"short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>."},"article_type":"original","file":[{"date_updated":"2024-03-04T07:24:43Z","access_level":"open_access","file_name":"2024_Development_Schauer.pdf","file_id":"15050","success":1,"relation":"main_file","creator":"dernst","date_created":"2024-03-04T07:24:43Z","file_size":14839986,"checksum":"6961ea10012bf0d266681f9628bb8f13","content_type":"application/pdf"}],"status":"public"},{"oa_version":"Published Version","quality_controlled":"1","day":"14","external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"oa":1,"title":"Compensation of gene dosage on the mammalian X","article_number":"dev202891","status":"public","file":[{"date_created":"2024-08-28T10:32:16Z","creator":"cchlebak","relation":"main_file","access_level":"open_access","file_name":"2024_Development_Cecalev.pdf","success":1,"file_id":"17464","date_updated":"2024-08-28T10:32:16Z","checksum":"5e428bda0440d3f957c694b315a8f2a9","content_type":"application/pdf","file_size":2085135}],"article_type":"original","citation":{"short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>.","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. The Company of Biologists, 2024.","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891."},"language":[{"iso":"eng"}],"date_published":"2024-08-14T00:00:00Z","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)"},"date_updated":"2025-09-08T08:58:58Z","year":"2024","month":"08","volume":151,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Development","type":"journal_article","isi":1,"publisher":"The Company of Biologists","ddc":["599"],"has_accepted_license":"1","author":[{"first_name":"Daniela","last_name":"Cecalev","full_name":"Cecalev, Daniela"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"},{"last_name":"Galupa","first_name":"Rafael","full_name":"Galupa, Rafael"}],"issue":"15","date_created":"2024-08-25T22:01:07Z","intvolume":"       151","acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","doi":"10.1242/dev.202891","department":[{"_id":"BeVi"}],"file_date_updated":"2024-08-28T10:32:16Z","abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"scopus_import":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"_id":"17458","article_processing_charge":"Yes (in subscription journal)","pmid":1,"publication_status":"published"},{"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"_id":"18621","pmid":1,"article_processing_charge":"No","publication_status":"published","doi":"10.1242/dev.201208","scopus_import":"1","extern":"1","abstract":[{"text":"During neural development, cellular adhesion is crucial for interactions among and between neurons and surrounding tissues. This function is mediated by conserved cell adhesion molecules, which are tightly regulated to allow for coordinated neuronal outgrowth. Here, we show that the proprotein convertase KPC-1 (homolog of mammalian furin) regulates the Menorin adhesion complex during development of PVD dendritic arbors in Caenorhabditis elegans. We found a finely regulated antagonistic balance between PVD-expressed KPC-1 and the epidermally expressed putative cell adhesion molecule MNR-1 (Menorin). Genetically, partial loss of mnr-1 suppressed partial loss of kpc-1, and both loss of kpc-1 and transgenic overexpression of mnr-1 resulted in indistinguishable phenotypes in PVD dendrites. This balance regulated cell-surface localization of the DMA-1 leucine-rich transmembrane receptor in PVD neurons. Lastly, kpc-1 mutants showed increased amounts of MNR-1 and decreased amounts of muscle-derived LECT-2 (Chondromodulin II), which is also part of the Menorin adhesion complex. These observations suggest that KPC-1 in PVD neurons directly or indirectly controls the abundance of proteins of the Menorin adhesion complex from adjacent tissues, thereby providing negative feedback from the dendrite to the instructive cues of surrounding tissues.","lang":"eng"}],"file_date_updated":"2024-12-04T22:12:04Z","OA_type":"hybrid","acknowledgement":"We thank members of the Bülow laboratory for comments on the manuscript and discussions throughout the course of this work; and Ryan Peer and William Corman for their initial help with the modifier genetic screen. We acknowledge the Genomics Core facility and the Advanced Imaging Facility at Albert Einstein College of Medicine for help during these studies. We are grateful to Kang Shen, David Miller and the Caenorhabditis Genetics Center (which is funded by National Institutes of Health Office of Research Infrastructure Programs P40OD0104400) for some of the strains used in this study, and Lhisia Chen for the anti-SAX-7 antibody.\r\nThis work was supported by grants from the National Institutes of Health (F31NS100370 to M.R.; T32GM007288 and F31NS111939 to M.T.; R01NS096672, R21NS081505 and R01NS129992 to H.E.B.; and P30HD071593 to Albert Einstein College of Medicine). N.J.R.-S. was the recipient of a Colciencias-Fulbright Fellowship [funded by Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) and Fulbright Colombia], L.T.H.T. of a Croucher Foundation Fellowship, and H.E.B. of an Irma T. Hirschl Trust/Monique Weill-Caulier Trust research fellowship. Open Access funding provided by Albert Einstein College of Medicine, Yeshiva University. Deposited in PMC for immediate release.","intvolume":"       150","has_accepted_license":"1","ddc":["570"],"issue":"18","OA_place":"publisher","date_created":"2024-12-04T22:02:52Z","author":[{"id":"39831956-E4FE-11E9-85DE-0DC7E5697425","last_name":"Ramirez","first_name":"Nelson","full_name":"Ramirez, Nelson"},{"full_name":"Belalcazar, Helen M.","first_name":"Helen M.","last_name":"Belalcazar"},{"full_name":"Rahman, Maisha","first_name":"Maisha","last_name":"Rahman"},{"first_name":"Meera","last_name":"Trivedi","full_name":"Trivedi, Meera"},{"first_name":"Leo T. H.","last_name":"Tang","full_name":"Tang, Leo T. H."},{"last_name":"Bülow","first_name":"Hannes E.","full_name":"Bülow, Hannes E."}],"type":"journal_article","publication":"Development","publisher":"The Company of Biologists","year":"2023","month":"09","language":[{"iso":"eng"}],"date_published":"2023-09-18T00:00:00Z","date_updated":"2024-12-09T11:43:40Z","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)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":150,"status":"public","file":[{"success":1,"file_name":"dev201208.pdf","file_id":"18624","date_updated":"2024-12-04T22:12:04Z","access_level":"open_access","relation":"main_file","creator":"nramirez","date_created":"2024-12-04T22:12:04Z","file_size":9559527,"checksum":"d2158dc56db50457e6404c4afec4401c","content_type":"application/pdf"}],"article_type":"original","citation":{"chicago":"Ramirez, Nelson, Helen M. Belalcazar, Maisha Rahman, Meera Trivedi, Leo T. H. Tang, and Hannes E. Bülow. “Convertase-Dependent Regulation of Membrane-Tethered and Secreted Ligands Tunes Dendrite Adhesion.” <i>Development</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201208\">https://doi.org/10.1242/dev.201208</a>.","ista":"Ramirez N, Belalcazar HM, Rahman M, Trivedi M, Tang LTH, Bülow HE. 2023. Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion. Development. 150(18).","ama":"Ramirez N, Belalcazar HM, Rahman M, Trivedi M, Tang LTH, Bülow HE. Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion. <i>Development</i>. 2023;150(18). doi:<a href=\"https://doi.org/10.1242/dev.201208\">10.1242/dev.201208</a>","apa":"Ramirez, N., Belalcazar, H. M., Rahman, M., Trivedi, M., Tang, L. T. H., &#38; Bülow, H. E. (2023). Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201208\">https://doi.org/10.1242/dev.201208</a>","ieee":"N. Ramirez, H. M. Belalcazar, M. Rahman, M. Trivedi, L. T. H. Tang, and H. E. Bülow, “Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion,” <i>Development</i>, vol. 150, no. 18. The Company of Biologists, 2023.","short":"N. Ramirez, H.M. Belalcazar, M. Rahman, M. Trivedi, L.T.H. Tang, H.E. Bülow, Development 150 (2023).","mla":"Ramirez, Nelson, et al. “Convertase-Dependent Regulation of Membrane-Tethered and Secreted Ligands Tunes Dendrite Adhesion.” <i>Development</i>, vol. 150, no. 18, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201208\">10.1242/dev.201208</a>."},"day":"18","external_id":{"pmid":["37721334"]},"oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion"},{"publication_status":"published","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_processing_charge":"Yes (via OA deal)","_id":"14774","pmid":1,"keyword":["Developmental Biology","Molecular Biology"],"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"}],"file_date_updated":"2024-01-10T12:41:13Z","doi":"10.1242/dev.201559","department":[{"_id":"AnKi"}],"intvolume":"       150","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.","author":[{"first_name":"Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","last_name":"Harish","full_name":"Harish, Rohit K"},{"first_name":"Mansi","last_name":"Gupta","full_name":"Gupta, Mansi"},{"full_name":"Zöller, Daniela","last_name":"Zöller","first_name":"Daniela"},{"first_name":"Hella","last_name":"Hartmann","full_name":"Hartmann, Hella"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"full_name":"Machate, Anja","last_name":"Machate","first_name":"Anja"},{"full_name":"Hans, Stefan","last_name":"Hans","first_name":"Stefan"},{"full_name":"Brand, Michael","first_name":"Michael","last_name":"Brand"}],"issue":"19","date_created":"2024-01-10T09:18:54Z","ddc":["570"],"has_accepted_license":"1","isi":1,"publisher":"The Company of Biologists","publication":"Development","type":"journal_article","volume":150,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-01T00:00:00Z","language":[{"iso":"eng"}],"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)"},"date_updated":"2024-01-10T12:45:25Z","year":"2023","month":"10","file":[{"file_size":12836306,"checksum":"2d6f52dc33260a9b2352b8f28374ba5f","content_type":"application/pdf","access_level":"open_access","date_updated":"2024-01-10T12:41:13Z","success":1,"file_name":"2023_Development_Harish.pdf","file_id":"14790","relation":"main_file","creator":"dernst","date_created":"2024-01-10T12:41:13Z"}],"citation":{"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>.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","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.","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>","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>.","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."},"article_type":"original","article_number":"dev201559","status":"public","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","oa_version":"Published Version","quality_controlled":"1","day":"01","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"oa":1},{"acknowledgement":"iona intestinalis adults were provided by Dr Yutaka Satou (Kyoto University) and Dr Manabu Yoshida (the University of Tokyo) with support from the National Bio-Resource Project of AMED, Japan. We thank Dr Hidehiko Hashimoto and Dr Yuji Mizotani for technical information about 1P-myosin antibody staining. We thank Dr Kaoru Imai and Dr Yutaka Satou for valuable discussion about Admp and for the DNA construct of Bmp2/4 under the Dlx.b upstream sequence. We thank Ms Maki Kogure for constructing the FUSION360 of the intercalating epidermal cell.\r\nThis work was supported by funding from the Japan Society for the Promotion of Science (JP16H01451, JP21H00440). Open Access funding provided by Keio University: Keio Gijuku Daigaku.","intvolume":"       149","has_accepted_license":"1","ddc":["570"],"issue":"21","date_created":"2023-01-16T09:50:12Z","author":[{"full_name":"Kogure, Yuki S.","last_name":"Kogure","first_name":"Yuki S."},{"last_name":"Muraoka","first_name":"Hiromochi","full_name":"Muraoka, Hiromochi"},{"full_name":"Koizumi, Wataru C.","first_name":"Wataru C.","last_name":"Koizumi"},{"first_name":"Raphaël","last_name":"Gelin-alessi","full_name":"Gelin-alessi, Raphaël"},{"last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","full_name":"Godard, Benoit G"},{"full_name":"Oka, Kotaro","last_name":"Oka","first_name":"Kotaro"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hotta, Kohji","first_name":"Kohji","last_name":"Hotta"}],"keyword":["Developmental Biology","Molecular Biology"],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"article_processing_charge":"No","_id":"12231","pmid":1,"publication_status":"published","doi":"10.1242/dev.200215","department":[{"_id":"CaHe"}],"scopus_import":"1","file_date_updated":"2023-01-27T10:36:50Z","abstract":[{"text":"Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail.","lang":"eng"}],"status":"public","article_number":"dev200215","file":[{"content_type":"application/pdf","checksum":"871b9c58eb79b9e60752de25a46938d6","file_size":9160451,"relation":"main_file","file_id":"12423","success":1,"access_level":"open_access","file_name":"2022_Development_Kogure.pdf","date_updated":"2023-01-27T10:36:50Z","date_created":"2023-01-27T10:36:50Z","creator":"dernst"}],"citation":{"ama":"Kogure YS, Muraoka H, Koizumi WC, et al. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. 2022;149(21). doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>","apa":"Kogure, Y. S., Muraoka, H., Koizumi, W. C., Gelin-alessi, R., Godard, B. G., Oka, K., … Hotta, K. (2022). Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>","ista":"Kogure YS, Muraoka H, Koizumi WC, Gelin-alessi R, Godard BG, Oka K, Heisenberg C-PJ, Hotta K. 2022. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. Development. 149(21), dev200215.","chicago":"Kogure, Yuki S., Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit G Godard, Kotaro Oka, Carl-Philipp J Heisenberg, and Kohji Hotta. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>.","mla":"Kogure, Yuki S., et al. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>, vol. 149, no. 21, dev200215, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>.","short":"Y.S. Kogure, H. Muraoka, W.C. Koizumi, R. Gelin-alessi, B.G. Godard, K. Oka, C.-P.J. Heisenberg, K. Hotta, Development 149 (2022).","ieee":"Y. S. Kogure <i>et al.</i>, “Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona,” <i>Development</i>, vol. 149, no. 21. The Company of Biologists, 2022."},"article_type":"original","external_id":{"pmid":["36227591"],"isi":["000903991700002"]},"day":"01","oa":1,"oa_version":"Published Version","quality_controlled":"1","corr_author":"1","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","type":"journal_article","publication":"Development","publisher":"The Company of Biologists","isi":1,"year":"2022","month":"11","language":[{"iso":"eng"}],"date_published":"2022-11-01T00:00:00Z","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)"},"date_updated":"2024-10-09T21:03:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":149},{"article_number":"dev200474","status":"public","file":[{"checksum":"d7c29b74e9e4032308228cc704a30e88","content_type":"application/pdf","file_size":9348839,"date_created":"2023-01-30T08:35:44Z","creator":"dernst","relation":"main_file","date_updated":"2023-01-30T08:35:44Z","access_level":"open_access","file_id":"12438","success":1,"file_name":"2022_Development_Soto.pdf"}],"article_type":"original","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>.","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.","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>","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>","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).","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>."},"quality_controlled":"1","oa_version":"Published Version","external_id":{"isi":["000918161000003"],"pmid":["36189829"]},"day":"01","oa":1,"title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","publication":"Development","type":"journal_article","isi":1,"publisher":"The Company of Biologists","date_published":"2022-10-01T00:00:00Z","language":[{"iso":"eng"}],"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)"},"date_updated":"2023-08-04T09:41:08Z","year":"2022","month":"10","volume":149,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","intvolume":"       149","ddc":["570"],"has_accepted_license":"1","author":[{"full_name":"Soto, Ximena","first_name":"Ximena","last_name":"Soto"},{"first_name":"Joshua","last_name":"Burton","full_name":"Burton, Joshua"},{"full_name":"Manning, Cerys S.","first_name":"Cerys S.","last_name":"Manning"},{"full_name":"Minchington, Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas"},{"full_name":"Lea, Robert","first_name":"Robert","last_name":"Lea"},{"first_name":"Jessica","last_name":"Lee","full_name":"Lee, Jessica"},{"full_name":"Kursawe, Jochen","first_name":"Jochen","last_name":"Kursawe"},{"first_name":"Magnus","last_name":"Rattray","full_name":"Rattray, Magnus"},{"last_name":"Papalopulu","first_name":"Nancy","full_name":"Papalopulu, Nancy"}],"issue":"19","date_created":"2023-01-16T09:53:17Z","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"_id":"12245","pmid":1,"article_processing_charge":"No","related_material":{"link":[{"relation":"software","url":" https://github.com/burtonjosh/StepwiseMir9"}]},"keyword":["Developmental Biology","Molecular Biology"],"publication_status":"published","doi":"10.1242/dev.200474","department":[{"_id":"AnKi"}],"abstract":[{"lang":"eng","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."}],"file_date_updated":"2023-01-30T08:35:44Z","scopus_import":"1"},{"department":[{"_id":"AnKi"}],"doi":"10.1242/dev.196121","scopus_import":"1","file_date_updated":"2024-04-03T13:58:51Z","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."}],"keyword":["Developmental Biology","Molecular Biology"],"_id":"15262","article_processing_charge":"No","pmid":1,"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_created":"2024-04-03T07:26:41Z","issue":"18","author":[{"full_name":"Vinter, Daisy J.","first_name":"Daisy J.","last_name":"Vinter"},{"full_name":"Hoppe, Caroline","last_name":"Hoppe","first_name":"Caroline"},{"full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington"},{"full_name":"Sutcliffe, Catherine","first_name":"Catherine","last_name":"Sutcliffe"},{"full_name":"Ashe, Hilary L.","last_name":"Ashe","first_name":"Hilary L."}],"intvolume":"       148","month":"09","year":"2021","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)"},"date_updated":"2024-04-03T14:00:33Z","language":[{"iso":"eng"}],"date_published":"2021-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":148,"type":"journal_article","publication":"Development","publisher":"The Company of Biologists","oa":1,"external_id":{"pmid":["33722899 "]},"day":"01","quality_controlled":"1","oa_version":"Published Version","title":"Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo","status":"public","article_number":"dev196121.","citation":{"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>.","short":"D.J. Vinter, C. Hoppe, T. Minchington, C. Sutcliffe, H.L. Ashe, Development 148 (2021).","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>.","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>","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>"},"article_type":"original","file":[{"checksum":"6d0533fe9c712448b3f9feb15e05ec4b","content_type":"application/pdf","file_size":16258500,"relation":"main_file","file_name":"2021_CompanyBiologists_Vinter.pdf","access_level":"open_access","success":1,"file_id":"15290","date_updated":"2024-04-03T13:58:51Z","date_created":"2024-04-03T13:58:51Z","creator":"dernst"}]},{"intvolume":"       148","acknowledgement":"This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months.","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.176065","open_access":"1"}],"author":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"date_created":"2021-03-07T23:01:25Z","issue":"2","article_processing_charge":"No","_id":"9226","pmid":1,"publication_identifier":{"eissn":["1477-9129"]},"publication_status":"published","department":[{"_id":"GaTk"}],"doi":"10.1242/dev.176065","abstract":[{"text":"Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?","lang":"eng"}],"scopus_import":"1","article_number":"dev176065","status":"public","article_type":"original","citation":{"ieee":"G. Tkačik and T. Gregor, “The many bits of positional information,” <i>Development</i>, vol. 148, no. 2. The Company of Biologists, 2021.","short":"G. Tkačik, T. Gregor, Development 148 (2021).","mla":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” <i>Development</i>, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/dev.176065\">10.1242/dev.176065</a>.","ista":"Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065.","chicago":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” <i>Development</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/dev.176065\">https://doi.org/10.1242/dev.176065</a>.","ama":"Tkačik G, Gregor T. The many bits of positional information. <i>Development</i>. 2021;148(2). doi:<a href=\"https://doi.org/10.1242/dev.176065\">10.1242/dev.176065</a>","apa":"Tkačik, G., &#38; Gregor, T. (2021). The many bits of positional information. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176065\">https://doi.org/10.1242/dev.176065</a>"},"quality_controlled":"1","oa_version":"Published Version","oa":1,"external_id":{"isi":["000613906000007"],"pmid":["33526425"]},"day":"01","title":"The many bits of positional information","publication":"Development","type":"journal_article","isi":1,"publisher":"The Company of Biologists","date_updated":"2025-04-14T09:28:43Z","language":[{"iso":"eng"}],"date_published":"2021-02-01T00:00:00Z","month":"02","year":"2021","volume":148,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"volume":146,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-12-04T00:00:00Z","language":[{"iso":"eng"}],"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)"},"date_updated":"2025-04-14T07:27:30Z","year":"2019","month":"12","isi":1,"publisher":"The Company of Biologists","publication":"Development","type":"journal_article","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","corr_author":"1","quality_controlled":"1","oa_version":"Published Version","external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"day":"04","oa":1,"file":[{"content_type":"application/pdf","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","file_size":7797881,"relation":"main_file","file_id":"7177","date_updated":"2020-07-14T12:47:50Z","file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","date_created":"2019-12-13T07:34:06Z","creator":"dernst"}],"article_type":"original","citation":{"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>","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>","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.","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>.","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>.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","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."},"article_number":"dev176297","status":"public","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."}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","scopus_import":"1","doi":"10.1242/dev.176297","department":[{"_id":"AnKi"}],"publication_status":"published","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"_id":"7165","pmid":1,"article_processing_charge":"No","author":[{"last_name":"Guerrero","first_name":"Pilar","full_name":"Guerrero, Pilar"},{"full_name":"Perez-Carrasco, Ruben","last_name":"Perez-Carrasco","first_name":"Ruben"},{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","last_name":"Zagórski"},{"full_name":"Page, David","first_name":"David","last_name":"Page"},{"first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Page, Karen M.","first_name":"Karen M.","last_name":"Page"}],"issue":"23","date_created":"2019-12-10T14:39:50Z","ddc":["570"],"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"intvolume":"       146"},{"quality_controlled":"1","oa_version":"Published Version","oa":1,"external_id":{"isi":["000464583200006"],"pmid":["30910826"]},"day":"04","title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","article_number":"dev171397","status":"public","citation":{"ieee":"T. Stürner <i>et al.</i>, “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” <i>Development</i>, vol. 146, no. 7. The Company of Biologists, 2019.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>.","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>.","ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. 2019;146(7). doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>","apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>"},"article_type":"original","date_updated":"2023-09-07T14:47:00Z","language":[{"iso":"eng"}],"date_published":"2019-04-04T00:00:00Z","month":"04","year":"2019","volume":146,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Development","type":"journal_article","isi":1,"publisher":"The Company of Biologists","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.171397"}],"author":[{"full_name":"Stürner, Tomke","last_name":"Stürner","first_name":"Tomke"},{"first_name":"Anastasia","last_name":"Tatarnikova","full_name":"Tatarnikova, Anastasia"},{"full_name":"Müller, Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"full_name":"Schaffran, Barbara","last_name":"Schaffran","first_name":"Barbara"},{"full_name":"Cuntz, Hermann","first_name":"Hermann","last_name":"Cuntz"},{"last_name":"Zhang","first_name":"Yun","full_name":"Zhang, Yun"},{"full_name":"Nemethova, Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Sven","last_name":"Bogdan","full_name":"Bogdan, Sven"},{"last_name":"Small","first_name":"Vic","full_name":"Small, Vic"},{"full_name":"Tavosanis, Gaia","first_name":"Gaia","last_name":"Tavosanis"}],"date_created":"2020-01-29T16:27:10Z","issue":"7","intvolume":"       146","department":[{"_id":"MiSi"}],"doi":"10.1242/dev.171397","abstract":[{"text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.","lang":"eng"}],"scopus_import":"1","_id":"7404","pmid":1,"article_processing_charge":"No","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"publication_status":"published"},{"status":"public","article_number":"dev175919","citation":{"apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., &#38; Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. 2019;146(17). doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>","ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>.","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” <i>Development</i>, vol. 146, no. 17. The Company of Biologists, 2019."},"article_type":"original","day":"12","external_id":{"pmid":["31391194"],"isi":["000486297400011"]},"oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","type":"journal_article","publication":"Development","publisher":"The Company of Biologists","isi":1,"year":"2019","month":"09","language":[{"iso":"eng"}],"date_published":"2019-09-12T00:00:00Z","date_updated":"2026-04-03T09:45:02Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":146,"project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","intvolume":"       146","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.175919"}],"issue":"17","date_created":"2019-09-22T22:00:36Z","author":[{"full_name":"Zhu, Qiang","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu"},{"full_name":"Gallemi, Marçal","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","last_name":"Gallemi"},{"last_name":"Pospíšil","first_name":"Jiří","full_name":"Pospíšil, Jiří"},{"last_name":"Žádníková","first_name":"Petra","full_name":"Žádníková, Petra"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"publication_identifier":{"eissn":["1477-9129"]},"_id":"6897","article_processing_charge":"No","pmid":1,"publication_status":"published","doi":"10.1242/dev.175919","department":[{"_id":"EvBe"}],"scopus_import":"1","abstract":[{"text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins.","lang":"eng"}],"ec_funded":1},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":134,"month":"11","year":"2007","date_updated":"2021-12-14T08:57:58Z","language":[{"iso":"eng"}],"date_published":"2007-11-15T00:00:00Z","publisher":"The Company of Biologists","type":"journal_article","publication":"Development","title":"Genome-wide analysis of DNA methylation patterns","oa":1,"day":"15","external_id":{"pmid":["17928417"]},"oa_version":"Published Version","quality_controlled":"1","article_type":"review","citation":{"short":"D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.","mla":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007, pp. 3959–65, doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>.","ieee":"D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.","apa":"Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation patterns. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>","ama":"Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. <i>Development</i>. 2007;134(22):3959-3965. doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>","chicago":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>.","ista":"Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965."},"page":"3959-3965","status":"public","scopus_import":"1","extern":"1","abstract":[{"text":"Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.","lang":"eng"}],"department":[{"_id":"DaZi"}],"doi":"10.1242/dev.001131","publication_status":"published","pmid":1,"_id":"9524","article_processing_charge":"No","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"date_created":"2021-06-08T06:29:50Z","issue":"22","author":[{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.001131","open_access":"1"}],"intvolume":"       134"}]