[{"publication":"Nature Immunology","publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"file_date_updated":"2025-07-31T08:00:33Z","pmid":1,"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the Imaging and Optics, Preclinical and Lab Support Facilities. In particular, we thank M. A. Symth and F. G. G. Leite, from the Virus Service Team, who helped generating the lentiviral particles used in this study. We thank all the members of the Sixt group for valuable discussions and feedback, in particular, I. Mayer, for helping with T cell isolation and Z. (P.) Li for providing the Actin–GFP DC line. We are also thankful to J. Mandl and C. Shen for their feedback during the writing of this manuscript. This work was supported by a European Research Council grant ERC-SyG 101071793 to M.S. M.J.A. was supported by an HFSP Postdoctoral Fellowship LTF 177 2021 and A.J.G. by a Lise Meitner Fellowship of the FWF (Austrian Science Fund). Y.F. was supported by the AMED-CREST (JP19gm1310005), the Medical Research Center Initiative for High Depth Omics and CURE:JPMXP1323015486 for MIB, Kyushu University. Open access funding provided by Institute of Science and Technology (IST Austria).","page":"1258–1266","date_created":"2025-07-27T22:01:26Z","status":"public","date_updated":"2026-02-16T11:51:05Z","day":"01","type":"journal_article","abstract":[{"text":"Efficient immune responses rely on the capacity of leukocytes to traverse diverse and complex tissues. To meet such changing environmental conditions, leukocytes usually adopt an ameboid configuration, using their forward-positioned nucleus as a probe to identify and follow the path of least resistance among pre-existing pores. We show that, in dense environments where even the largest pores preclude free passage, leukocytes position their nucleus behind the centrosome and organelles. The local compression imposed on the cell body by its surroundings triggers assembly of a central F-actin pool, located between cell front and nucleus. Central actin pushes outward to transiently dilate a path for organelles and nucleus. Pools of central and front actin are tightly coupled and experimental depletion of the central pool enhances actin accumulation and protrusion formation at the cell front. Although this shifted balance speeds up cells in permissive environments, migration in restrictive environments is impaired, as the unleashed leading edge dissociates from the trapped cell body. Our findings establish an actin regulatory loop that balances path dilation with advancement of the leading edge to maintain cellular coherence.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","language":[{"iso":"eng"}],"scopus_import":"1","volume":26,"project":[{"_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces"},{"name":"Bioelectric patrolling: the role of the local membrane potential in immune cell migration","grant_number":"944-2020","_id":"c092d618-5a5b-11eb-8a69-f92e1e843fc8"}],"external_id":{"isi":["001529134300001"],"pmid":["40664976"]},"doi":"10.1038/s41590-025-02211-w","oa":1,"ddc":["570"],"has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"intvolume":"        26","quality_controlled":"1","_id":"20082","title":"Migrating immune cells globally coordinate protrusive forces","file":[{"date_created":"2025-07-31T08:00:33Z","file_size":13514646,"success":1,"file_id":"20096","creator":"dernst","date_updated":"2025-07-31T08:00:33Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0c725123dca7797c682609bff2c4c5ac","file_name":"2025_NatureImmunology_ReisRodrigues.pdf"}],"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"date_published":"2025-08-01T00:00:00Z","OA_place":"publisher","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","publication_status":"published","year":"2025","corr_author":"1","article_type":"letter_note","PlanS_conform":"1","author":[{"id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues","first_name":"Patricia","full_name":"Dos Reis Rodrigues, Patricia"},{"full_name":"Avellaneda Sarrió, Mario","first_name":"Mario","last_name":"Avellaneda Sarrió","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X"},{"last_name":"Canigova","first_name":"Nikola","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Fukui, Yoshinori","first_name":"Yoshinori","last_name":"Fukui"},{"first_name":"Alba","last_name":"Juanes Garcia","full_name":"Juanes Garcia, Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1009-9652"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"}],"citation":{"short":"P. Dos Reis Rodrigues, M. Avellaneda Sarrió, N. Canigova, F.R. Gärtner, K. Vaahtomeri, M. Riedl, I. de Vries, J. Merrin, R. Hauschild, Y. Fukui, A. Juanes Garcia, M.K. Sixt, Nature Immunology 26 (2025) 1258–1266.","chicago":"Dos Reis Rodrigues, Patricia, Mario Avellaneda Sarrió, Nikola Canigova, Florian R Gärtner, Kari Vaahtomeri, Michael Riedl, Ingrid de Vries, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>.","ista":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, Gärtner FR, Vaahtomeri K, Riedl M, de Vries I, Merrin J, Hauschild R, Fukui Y, Juanes Garcia A, Sixt MK. 2025. Migrating immune cells globally coordinate protrusive forces. Nature Immunology. 26, 1258–1266.","ieee":"P. Dos Reis Rodrigues <i>et al.</i>, “Migrating immune cells globally coordinate protrusive forces,” <i>Nature Immunology</i>, vol. 26. Springer Nature, pp. 1258–1266, 2025.","apa":"Dos Reis Rodrigues, P., Avellaneda Sarrió, M., Canigova, N., Gärtner, F. R., Vaahtomeri, K., Riedl, M., … Sixt, M. K. (2025). Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>","mla":"Dos Reis Rodrigues, Patricia, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>, vol. 26, Springer Nature, 2025, pp. 1258–1266, doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>.","ama":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, et al. Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. 2025;26:1258–1266. doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>"},"month":"08","related_material":{"record":[{"id":"20149","status":"public","relation":"dissertation_contains"}]}},{"author":[{"full_name":"Jain, Kirti","last_name":"Jain","first_name":"Kirti","id":"330F0278-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Römhild, Roderich","first_name":"Roderich","last_name":"Römhild","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","orcid":"0000-0001-9480-5261"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C"}],"related_material":{"record":[{"id":"19626","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:19294","month":"03","citation":{"ama":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Data for “Pulsatile basal gene expression as a fitness determinant in bacteria.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19294\">10.15479/AT:ISTA:19294</a>","mla":"Jain, Kirti, et al. <i>Data for “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19294\">10.15479/AT:ISTA:19294</a>.","apa":"Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet, C. C. (2025). Data for “Pulsatile basal gene expression as a fitness determinant in bacteria.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19294\">https://doi.org/10.15479/AT:ISTA:19294</a>","ieee":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Data for ‘Pulsatile basal gene expression as a fitness determinant in bacteria.’” Institute of Science and Technology Austria, 2025.","ista":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Data for ‘Pulsatile basal gene expression as a fitness determinant in bacteria’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19294\">10.15479/AT:ISTA:19294</a>.","chicago":"Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper Tkačik, and Calin C Guet. “Data for ‘Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19294\">https://doi.org/10.15479/AT:ISTA:19294</a>.","short":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, (2025)."},"year":"2025","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_published":"2025-03-04T00:00:00Z","abstract":[{"lang":"eng","text":"Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of non-functional “promoter leakiness”, merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the non-canonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g. control of costly-to-induce multi-drug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multi-drug resistance is crucial for effective public health measures."}],"OA_place":"repository","OA_type":"gold","corr_author":"1","date_created":"2025-03-04T13:27:21Z","status":"public","type":"research_data","day":"04","file":[{"file_id":"19295","success":1,"file_size":269054,"date_created":"2025-03-04T13:08:52Z","creator":"dernst","date_updated":"2025-03-04T13:08:52Z","access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"Data1.xlsx","checksum":"11a5bab307a4e1e1598a1577d8a2fbb5"},{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","checksum":"3b057894322639f0c1e11fb2e84173e6","file_name":"Data2.xlsx","creator":"dernst","date_created":"2025-03-04T13:08:52Z","file_size":87143,"file_id":"19296","success":1,"access_level":"open_access","date_updated":"2025-03-04T13:08:52Z"},{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","checksum":"a551e1b79a138bb97ab96979aa475b3c","file_name":"Data3.xlsx","creator":"dernst","date_created":"2025-03-04T13:08:52Z","file_size":129101,"success":1,"file_id":"19297","access_level":"open_access","date_updated":"2025-03-04T13:08:52Z"},{"date_created":"2025-03-04T13:08:52Z","file_size":86243,"success":1,"file_id":"19298","creator":"dernst","date_updated":"2025-03-04T13:08:52Z","access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","checksum":"d6909c9bf111f859058082b1a2f970c4","file_name":"Data4.xlsx"},{"file_name":"Data5.xlsx","checksum":"e5725a3a118a3f06846104906c8792c7","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access","date_updated":"2025-03-04T13:08:52Z","creator":"dernst","success":1,"file_id":"19299","date_created":"2025-03-04T13:08:52Z","file_size":26049},{"relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"RawData_2_3.xlsx","checksum":"16763c127049f14bd587dc885677dce1","success":1,"file_id":"19300","date_created":"2025-03-04T13:08:52Z","file_size":7327253,"creator":"dernst","date_updated":"2025-03-04T13:08:52Z","access_level":"open_access"},{"file_name":"Readme.txt","checksum":"2f3e1a368b4e3abc46bf37e02724f0f4","relation":"main_file","content_type":"text/plain","date_updated":"2025-03-05T07:39:38Z","access_level":"open_access","file_id":"19301","success":1,"date_created":"2025-03-05T07:39:38Z","file_size":606,"creator":"dernst"}],"title":"Data for \"Pulsatile basal gene expression as a fitness determinant in bacteria\"","date_updated":"2025-10-15T06:30:54Z","_id":"19294","file_date_updated":"2025-03-05T07:39:38Z","has_accepted_license":"1","ddc":["570"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"CaGu"},{"_id":"Bio"},{"_id":"FyKo"},{"_id":"GaTk"}]},{"intvolume":"        44","quality_controlled":"1","_id":"19404","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","file":[{"checksum":"57e05dd1598c807af0afdb32cec039d3","file_name":"2025_CellReports_Tavano.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-03-17T10:26:54Z","creator":"dernst","date_created":"2025-03-17T10:26:54Z","file_size":9067797,"file_id":"19413","success":1}],"publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"oa":1,"ddc":["570"],"has_accepted_license":"1","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"author":[{"orcid":"0000-0001-9970-7804","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","full_name":"Tavano, Ste","last_name":"Tavano","first_name":"Ste"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","last_name":"Brückner","first_name":"David"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","full_name":"Tasciyan, Saren"},{"first_name":"Xin","last_name":"Tong","full_name":"Tong, Xin","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","last_name":"Kardos","full_name":"Kardos, Roland"},{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"citation":{"ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Elsevier, 2025.","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387."},"issue":"3","month":"03","date_published":"2025-03-25T00:00:00Z","OA_place":"publisher","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","DOAJ_listed":"1","year":"2025","corr_author":"1","article_type":"original","status":"public","date_created":"2025-03-16T23:01:24Z","date_updated":"2025-10-22T07:00:04Z","day":"25","type":"journal_article","publication":"Cell Reports","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"publisher":"Elsevier","isi":1,"file_date_updated":"2025-03-17T10:26:54Z","pmid":1,"acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","volume":44,"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"grant_number":"ALTF 1159-2018","name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration","_id":"269CD5C4-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["001443652700001"],"pmid":["40057955"]},"doi":"10.1016/j.celrep.2025.115387","abstract":[{"lang":"eng","text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"115387","language":[{"iso":"eng"}],"OA_type":"gold","scopus_import":"1"},{"ddc":["570"],"has_accepted_license":"1","oa":1,"department":[{"_id":"CaGu"},{"_id":"Bio"},{"_id":"FyKo"},{"_id":"GaTk"}],"quality_controlled":"1","intvolume":"       122","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2025_PNAS_Jain.pdf","checksum":"115a687f40009660eb4b38b4f6559d41","creator":"dernst","file_id":"19888","success":1,"file_size":2949523,"date_created":"2025-06-24T07:27:43Z","access_level":"open_access","date_updated":"2025-06-24T07:27:43Z"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"19626","title":"Pulsatile basal gene expression as a fitness determinant in bacteria","publication_status":"published","oa_version":"Published Version","year":"2025","date_published":"2025-04-15T00:00:00Z","OA_place":"publisher","article_type":"original","corr_author":"1","author":[{"full_name":"Jain, Kirti","last_name":"Jain","first_name":"Kirti","id":"330F0278-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva"},{"orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich","last_name":"Römhild","first_name":"Roderich"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"19294","status":"public","relation":"research_data"}]},"issue":"15","citation":{"ama":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(15). doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>","ieee":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Pulsatile basal gene expression as a fitness determinant in bacteria,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of Sciences, 2025.","apa":"Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet, C. C. (2025). Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>","mla":"Jain, Kirti, et al. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15, e2413709122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>.","short":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper Tkačik, and Calin C Guet. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>.","ista":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Pulsatile basal gene expression as a fitness determinant in bacteria. Proceedings of the National Academy of Sciences. 122(15), e2413709122."},"month":"04","isi":1,"file_date_updated":"2025-06-24T07:27:43Z","publication":"Proceedings of the National Academy of Sciences","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"National Academy of Sciences","pmid":1,"acknowledgement":"K.J. thanks B. Wu, I. Tomanek, K. Tomasek for detailed discussions on the manuscript, all other members from the Guet laboratory for valuable feedback, R. Chait, & Imaging and Optics Facility, Institute of Science and Technology Austria for helping with microscopy, Dr. Sudha Rao and Dr. Raja Mugasimangalam, Genotypic Technology India for allowing time off to address the revisions. K.J. acknowledges Institute of Science and Technology fellowship IC1006FELL02, R.H. was supported in part by Chan Zuckerberg Initiative and Donor Advised-Fund grant 2020-225401 (https://doi.org/10.37921/120055ratwvi), O.O.B. acknowledges Fonds Zur Förderung der Wissenschaftlichen Forschung (FWF) Grant ESP253-B, R.R. acknowledges FWF Grant 10.55776/ESP219, C.C.G. acknowledges FWF I5127-B.","status":"public","date_created":"2025-04-27T22:02:13Z","day":"15","type":"journal_article","date_updated":"2025-10-15T06:30:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of nonfunctional “promoter leakiness,” merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the noncanonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g., control of costly-to-induce multidrug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multidrug resistance is crucial for effective public health measures.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","article_number":"e2413709122","language":[{"iso":"eng"}],"OA_type":"hybrid","volume":122,"external_id":{"pmid":["40193613"],"isi":["001471235200001"]},"doi":"10.1073/pnas.2413709122","project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"},{"grant_number":"E219","name":"Non-canonical antibiotic interactions","_id":"bd6f94d1-d553-11ed-ba76-ae9f07250f74"},{"_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"}]},{"publication_identifier":{"eissn":["2375-2548"]},"file":[{"date_updated":"2025-05-12T07:46:10Z","access_level":"open_access","file_id":"19679","success":1,"date_created":"2025-05-12T07:46:10Z","file_size":2707050,"creator":"dernst","file_name":"2025_ScienceAdvance_Schmitt.pdf","checksum":"e8ba22922fa5b23ccfcce8865f57226c","relation":"main_file","content_type":"application/pdf"}],"title":"Protecting centrosomes from fracturing enables efficient cell navigation","_id":"19663","quality_controlled":"1","intvolume":"        11","department":[{"_id":"Bio"},{"_id":"NanoFab"}],"has_accepted_license":"1","ddc":["570"],"oa":1,"month":"04","citation":{"ama":"Schmitt MT, Kroll J, Ruiz-Fernandez MJA, et al. Protecting centrosomes from fracturing enables efficient cell navigation. <i>Science Advances</i>. 2025;11(17). doi:<a href=\"https://doi.org/10.1126/sciadv.adx4047\">10.1126/sciadv.adx4047</a>","apa":"Schmitt, M. T., Kroll, J., Ruiz-Fernandez, M. J. A., Hauschild, R., Ghosh, S., Kameritsch, P., … Renkawitz, J. (2025). Protecting centrosomes from fracturing enables efficient cell navigation. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adx4047\">https://doi.org/10.1126/sciadv.adx4047</a>","ieee":"M. T. Schmitt <i>et al.</i>, “Protecting centrosomes from fracturing enables efficient cell navigation,” <i>Science Advances</i>, vol. 11, no. 17. AAAS, 2025.","mla":"Schmitt, Madeleine T., et al. “Protecting Centrosomes from Fracturing Enables Efficient Cell Navigation.” <i>Science Advances</i>, vol. 11, no. 17, eadx4047, AAAS, 2025, doi:<a href=\"https://doi.org/10.1126/sciadv.adx4047\">10.1126/sciadv.adx4047</a>.","chicago":"Schmitt, Madeleine T., Janina Kroll, Mauricio J.A. Ruiz-Fernandez, Robert Hauschild, Shaunak Ghosh, Petra Kameritsch, Jack Merrin, et al. “Protecting Centrosomes from Fracturing Enables Efficient Cell Navigation.” <i>Science Advances</i>. AAAS, 2025. <a href=\"https://doi.org/10.1126/sciadv.adx4047\">https://doi.org/10.1126/sciadv.adx4047</a>.","short":"M.T. Schmitt, J. Kroll, M.J.A. Ruiz-Fernandez, R. Hauschild, S. Ghosh, P. Kameritsch, J. Merrin, J. Schmid, K. Stefanowski, A.W. Thomae, J. Cheng, G.N. Öztan, P. Konopka, G.C. Ortega, T. Penz, L. Bach, D. Baumjohann, C. Bock, T. Straub, F. Meissner, E. Kiermaier, J. Renkawitz, Science Advances 11 (2025).","ista":"Schmitt MT, Kroll J, Ruiz-Fernandez MJA, Hauschild R, Ghosh S, Kameritsch P, Merrin J, Schmid J, Stefanowski K, Thomae AW, Cheng J, Öztan GN, Konopka P, Ortega GC, Penz T, Bach L, Baumjohann D, Bock C, Straub T, Meissner F, Kiermaier E, Renkawitz J. 2025. Protecting centrosomes from fracturing enables efficient cell navigation. Science Advances. 11(17), eadx4047."},"issue":"17","author":[{"first_name":"Madeleine T.","last_name":"Schmitt","full_name":"Schmitt, Madeleine T."},{"last_name":"Kroll","first_name":"Janina","full_name":"Kroll, Janina"},{"first_name":"Mauricio J.A.","last_name":"Ruiz-Fernandez","full_name":"Ruiz-Fernandez, Mauricio J.A."},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"last_name":"Ghosh","first_name":"Shaunak","full_name":"Ghosh, Shaunak"},{"full_name":"Kameritsch, Petra","last_name":"Kameritsch","first_name":"Petra"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"Schmid","first_name":"Johanna","full_name":"Schmid, Johanna"},{"last_name":"Stefanowski","first_name":"Kasia","full_name":"Stefanowski, Kasia"},{"last_name":"Thomae","first_name":"Andreas W.","full_name":"Thomae, Andreas W."},{"full_name":"Cheng, Jingyuan","last_name":"Cheng","first_name":"Jingyuan"},{"first_name":"Gamze Naz","last_name":"Öztan","full_name":"Öztan, Gamze Naz"},{"full_name":"Konopka, Peter","last_name":"Konopka","first_name":"Peter"},{"first_name":"Germán Camargo","last_name":"Ortega","full_name":"Ortega, Germán Camargo"},{"last_name":"Penz","first_name":"Thomas","full_name":"Penz, Thomas"},{"last_name":"Bach","first_name":"Luisa","full_name":"Bach, Luisa"},{"last_name":"Baumjohann","first_name":"Dirk","full_name":"Baumjohann, Dirk"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Tobias","last_name":"Straub","full_name":"Straub, Tobias"},{"first_name":"Felix","last_name":"Meissner","full_name":"Meissner, Felix"},{"first_name":"Eva","last_name":"Kiermaier","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz"}],"article_type":"original","year":"2025","oa_version":"Published Version","publication_status":"published","DOAJ_listed":"1","OA_place":"publisher","date_published":"2025-04-25T00:00:00Z","type":"journal_article","day":"25","date_updated":"2025-09-30T12:26:21Z","status":"public","date_created":"2025-05-11T22:02:38Z","acknowledgement":"We thank L. Pelkmans and D. Dormann for providing Dyrk3-EGFP plasmids; M. Heuzé for providing a RFP-Pericentrin plasmid; T. Balla for providing a PH-Akt-GFP plasmid; E. Snaar-Jagalska for providing a pLenti-V6.3 Ultra-Chili plasmid; T. Tang for providing CEP120 a plasmid; D. Trono for providing pMD2.G and psSPAX2 plasmids; M. Sixt for providing EB3-mCherry and EMTB-mCherry plasmids as well as 3T3 fibroblasts, Lifeact-GFP Hoxb8 cells, and LX293 cells; M. Duggan for RNA isolation from migrating DCs; M. Schuster from the Biomedical Sequencing Facility at CeMM; J. Schwarz for providing Jurkat T cells; M. Götz for initial transcriptome analysis; M. Götz and F. Merino for discussion and sharing reagents; F. Gärtner for discussions and support; M. Benjamin Braun for critical reading of the manuscript; and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support.\r\nThis work was supported by Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (J.R.); German Research Foundation grant “CRC914, project A12” (J.R); German Research Foundation grant “SPP2332, project 492014049” (J.R.); LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (J.R.); Medical & Clinician Scientist Program (MCSP) LMU Munich (J.K.); Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany’s Excellence Strategy – EXC2151 – 390873048 (D.B.); Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) Grossgeräteantrag 457838313 and under Germany’s Excellence Strategy – EXC 2151 – 390873048 (E.K.); Ministry of Innovation, Science and Research of North-Rhine-Westphalia (fellowship AZ: 421-8.03.03.02-137069) (E.K.); TRA Life and Health (University of Bonn) as part of the Excellence Strategy of the federal and state governments (E.K.); and CZI grant DAF2020-225401 and grant (DOI https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (R.H.).","pmid":1,"isi":1,"file_date_updated":"2025-05-12T07:46:10Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"AAAS","publication":"Science Advances","doi":"10.1126/sciadv.adx4047","external_id":{"pmid":["40279414"],"isi":["001476113400016"]},"project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"}],"volume":11,"scopus_import":"1","language":[{"iso":"eng"}],"OA_type":"gold","article_number":"eadx4047","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","abstract":[{"text":"The centrosome is a microtubule orchestrator, nucleating and anchoring microtubules that grow radially and exert forces on cargos. At the same time, mechanical stresses from the microenvironment and cellular shape changes compress and bend microtubules. Yet, centrosomes are membraneless organelles, raising the question of how centrosomes withstand mechanical forces. Here, we discover that centrosomes can deform and even fracture. We reveal that centrosomes experience deformations during navigational pathfinding within motile cells. Coherence of the centrosome is maintained by Dyrk3 and cNAP1, preventing fracturing by forces. While cells can compensate for the depletion of centriolar-based centrosomes, the fracturing of centrosomes impedes cellular function by generating coexisting microtubule organizing centers that compete during path navigation and thereby cause cellular entanglement in the microenvironment. Our findings show that cells actively maintain the integrity of the centrosome to withstand mechanical forces. These results suggest that centrosome stability preservation is fundamental, given that almost all cells in multicellular organisms experience forces.","lang":"eng"}]},{"publication":"Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","ec_funded":1,"file_date_updated":"2025-07-03T06:55:20Z","isi":1,"pmid":1,"acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","page":"398-410","status":"public","date_created":"2025-05-18T22:02:51Z","date_updated":"2026-01-05T14:11:56Z","day":"12","type":"journal_article","abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"OA_type":"hybrid","scopus_import":"1","volume":642,"project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"external_id":{"pmid":["40335689"],"isi":["001483477000001"]},"doi":"10.1038/s41586-025-08985-1","oa":1,"ddc":["570"],"has_accepted_license":"1","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"intvolume":"       642","quality_controlled":"1","_id":"19704","title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","file":[{"access_level":"open_access","date_updated":"2025-07-03T06:55:20Z","creator":"dernst","date_created":"2025-07-03T06:55:20Z","file_size":133201290,"success":1,"file_id":"19959","checksum":"ebc99d7108e728f46db0a009292675ef","file_name":"2025_Nature_Tavakoli.pdf","content_type":"application/pdf","relation":"main_file"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"OA_place":"publisher","date_published":"2025-06-12T00:00:00Z","publication_status":"published","oa_version":"Published Version","year":"2025","corr_author":"1","article_type":"original","PlanS_conform":"1","author":[{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854"},{"full_name":"Lyudchik, Julia","first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Januszewski, Michał","last_name":"Januszewski","first_name":"Michał"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","first_name":"Vitali","last_name":"Vistunou"},{"full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer","first_name":"Jakob"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","first_name":"Caroline"},{"full_name":"Oliveira, Bárbara","last_name":"Oliveira","first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"},{"full_name":"Jain, Viren","last_name":"Jain","first_name":"Viren"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"citation":{"short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>"},"month":"06","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"18677"},{"status":"public","relation":"research_data","id":"18697"}]}},{"date_created":"2025-12-28T23:01:27Z","status":"public","date_updated":"2025-12-29T09:23:58Z","type":"journal_article","day":"04","publisher":"Elsevier","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Developmental Cell","acknowledgement":"The authors would like to acknowledge the Super Resolution Light Microcopy and Nanoscopy (SLN) Facility of ICFO for their support with imaging experiments, Johann Osmond (Nanofabrication laboratory, ICFO) for the design and production of molds for generating confinement coverslip, Merche Rivas for cell culture of immune cells and further support from the CRG Core Facilities for Genomics and Advanced Light Microscopy. We would like to thank Michael Sixt for discussions on this work and the Quidant, Ruprecht, and Wieser lab members for critical reading of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Nanofabrication Facility (NFF). C.A. acknowledges the funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no 847517 and V.V. from the ICFOstepstone – PhD Programme funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no 665884. S.W. acknowledges support through the Spanish Ministry of Economy and Competitiveness via MINECO’s Plan Nacional (BFU2017-86296-P). V.R. acknowledges funding from the European Union’s HORIZON-EIC-2021-PATHFINDEROPEN program under grant agreement no. 101046620 and European Union's Horizon Europe program under the grant agreement no. 101072123. E.K. acknowledges funding by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048 and by the TRA Life and Health (University of Bonn) as part of the Excellence Strategy of the federal and state governments.","pmid":1,"doi":"10.1016/j.devcel.2025.10.006","external_id":{"pmid":["41192429"]},"acknowledged_ssus":[{"_id":"NanoFab"}],"article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Effective immune responses rely on the efficient migration of leukocytes. Yet, how temperature regulates migration dynamics at the single-cell level has remained poorly understood. Using zebrafish embryos and mouse tissue explants, we found that temperature positively regulates leukocyte migration speed, exploration, and arrival frequencies to wounds and lymph vessels. Complementary 2D and 3D cultures revealed that this thermokinetic control of cell migration is conserved across immune cell types, independently of the 3D tissue environment. By applying precise (sub-)cellular temperature modulation, we identified a rapid and reversible thermo-response that depends on myosin II activity. Small physiological increases in temperature (1°C –2°C), as present during fever-like conditions, profoundly increased immune responses by accelerating arrival times at lymphatic vessels and tissue wounds. These findings identify myosin-II-dependent actomyosin contractility as a critical mechanical structure regulating single-cell thermo-adaptability, with physiological implications for tuning the speed of immune responses in vivo.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"OA_type":"hybrid","scopus_import":"1","quality_controlled":"1","title":"Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses","_id":"20859","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"oa":1,"has_accepted_license":"1","ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2025.10.006"}],"department":[{"_id":"Bio"},{"_id":"NanoFab"}],"author":[{"last_name":"Company-Garrido","first_name":"Iván","full_name":"Company-Garrido, Iván"},{"last_name":"Zurita Carpio","first_name":"Alberto","full_name":"Zurita Carpio, Alberto"},{"full_name":"Colomer-Rosell, Mariona","first_name":"Mariona","last_name":"Colomer-Rosell"},{"full_name":"Ciraulo, Bernard","first_name":"Bernard","last_name":"Ciraulo"},{"full_name":"Molkenbur, Ronja","first_name":"Ronja","last_name":"Molkenbur"},{"last_name":"Lanzerstorfer","first_name":"Peter","full_name":"Lanzerstorfer, Peter"},{"full_name":"Pezzano, Fabio","last_name":"Pezzano","first_name":"Fabio"},{"full_name":"Agazzi, Costanza","last_name":"Agazzi","first_name":"Costanza"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Saumey","last_name":"Jain","full_name":"Jain, Saumey"},{"first_name":"Jeroen M.","last_name":"Jacques","full_name":"Jacques, Jeroen M."},{"first_name":"Valeria","last_name":"Venturini","full_name":"Venturini, Valeria"},{"first_name":"Christian","last_name":"Knapp","full_name":"Knapp, Christian"},{"first_name":"Yufei","last_name":"Xie","full_name":"Xie, Yufei"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"last_name":"Weghuber","first_name":"Julian","full_name":"Weghuber, Julian"},{"full_name":"Schaaf, Marcel","last_name":"Schaaf","first_name":"Marcel"},{"full_name":"Quidant, Romain","last_name":"Quidant","first_name":"Romain"},{"full_name":"Kiermaier, Eva","first_name":"Eva","last_name":"Kiermaier","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ortega Arroyo, Jaime","last_name":"Ortega Arroyo","first_name":"Jaime"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser"}],"PlanS_conform":"1","month":"11","citation":{"apa":"Company-Garrido, I., Zurita Carpio, A., Colomer-Rosell, M., Ciraulo, B., Molkenbur, R., Lanzerstorfer, P., … Wieser, S. (2025). Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.10.006\">https://doi.org/10.1016/j.devcel.2025.10.006</a>","ieee":"I. Company-Garrido <i>et al.</i>, “Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses,” <i>Developmental Cell</i>. Elsevier, 2025.","mla":"Company-Garrido, Iván, et al. “Myosin II Regulates Cellular Thermo-Adaptability and the Efficiency of Immune Responses.” <i>Developmental Cell</i>, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.10.006\">10.1016/j.devcel.2025.10.006</a>.","ama":"Company-Garrido I, Zurita Carpio A, Colomer-Rosell M, et al. Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses. <i>Developmental Cell</i>. 2025. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.10.006\">10.1016/j.devcel.2025.10.006</a>","chicago":"Company-Garrido, Iván, Alberto Zurita Carpio, Mariona Colomer-Rosell, Bernard Ciraulo, Ronja Molkenbur, Peter Lanzerstorfer, Fabio Pezzano, et al. “Myosin II Regulates Cellular Thermo-Adaptability and the Efficiency of Immune Responses.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.10.006\">https://doi.org/10.1016/j.devcel.2025.10.006</a>.","short":"I. Company-Garrido, A. Zurita Carpio, M. Colomer-Rosell, B. Ciraulo, R. Molkenbur, P. Lanzerstorfer, F. Pezzano, C. Agazzi, R. Hauschild, S. Jain, J.M. Jacques, V. Venturini, C. Knapp, Y. Xie, J. Merrin, J. Weghuber, M. Schaaf, R. Quidant, E. Kiermaier, J. Ortega Arroyo, V. Ruprecht, S. Wieser, Developmental Cell (2025).","ista":"Company-Garrido I, Zurita Carpio A, Colomer-Rosell M, Ciraulo B, Molkenbur R, Lanzerstorfer P, Pezzano F, Agazzi C, Hauschild R, Jain S, Jacques JM, Venturini V, Knapp C, Xie Y, Merrin J, Weghuber J, Schaaf M, Quidant R, Kiermaier E, Ortega Arroyo J, Ruprecht V, Wieser S. 2025. Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses. Developmental Cell."},"date_published":"2025-11-04T00:00:00Z","OA_place":"publisher","year":"2025","oa_version":"Published Version","publication_status":"epub_ahead","article_type":"original"},{"OA_type":"closed access","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2025-10-24T00:00:00Z","abstract":[{"text":"RNA sequencing (RNA-seq) methodologies have evolved rapidly, offering powerful tools to study gene expression, transcriptome dynamics, and molecular mechanisms in various biological contexts. However, the complexity of these approaches poses challenges in data interpretation, sensitivity, and applicability. This chapter provides a comprehensive overview of RNA-seq methodologies, highlighting their advantages, limitations, and applications, particularly in cardiovascular research. Bulk RNA sequencing enables high-throughput gene expression profiling but lacks the resolution to capture cellular heterogeneity and spatial context. Direct RNA sequencing preserves native RNA modifications, offering insights into post-transcriptional regulation, though it remains technically challenging. Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) bridge these gaps by resolving transcriptomic complexity at the cellular level and within tissue architecture, providing crucial insights into disease mechanisms such as atherosclerosis. By summarizing the strengths and limitations of these methodologies, this chapter aims to guide researchers in selecting the most suitable transcriptomic approach for their studies, ultimately advancing precision medicine and biomarker discovery in cardiovascular disease.","lang":"eng"}],"article_processing_charge":"No","oa_version":"None","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","citation":{"ama":"Stopa V, Sopić M, Li G, et al. Essentials of transcriptomic methods: Navigating through RNA sequencing and beyond. In: Devaux Y, Sopic M, eds. <i>Transcriptomics in Atherosclerosis</i>. Elsevier; 2025:131-172. doi:<a href=\"https://doi.org/10.1016/b978-0-443-33064-3.00016-5\">10.1016/b978-0-443-33064-3.00016-5</a>","mla":"Stopa, Victoria, et al. “Essentials of Transcriptomic Methods: Navigating through RNA Sequencing and Beyond.” <i>Transcriptomics in Atherosclerosis</i>, edited by Yvan Devaux and Miron Sopic, Elsevier, 2025, pp. 131–72, doi:<a href=\"https://doi.org/10.1016/b978-0-443-33064-3.00016-5\">10.1016/b978-0-443-33064-3.00016-5</a>.","apa":"Stopa, V., Sopić, M., Li, G., Sluimer, J., Basílio, J., van der Laan, S. W., … Hochreiter, B. (2025). Essentials of transcriptomic methods: Navigating through RNA sequencing and beyond. In Y. Devaux &#38; M. Sopic (Eds.), <i>Transcriptomics in Atherosclerosis</i> (pp. 131–172). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-443-33064-3.00016-5\">https://doi.org/10.1016/b978-0-443-33064-3.00016-5</a>","ieee":"V. Stopa <i>et al.</i>, “Essentials of transcriptomic methods: Navigating through RNA sequencing and beyond,” in <i>Transcriptomics in Atherosclerosis</i>, Y. Devaux and M. Sopic, Eds. Elsevier, 2025, pp. 131–172.","ista":"Stopa V, Sopić M, Li G, Sluimer J, Basílio J, van der Laan SW, Kreil DP, Devaux Y, Hochreiter B. 2025.Essentials of transcriptomic methods: Navigating through RNA sequencing and beyond. In: Transcriptomics in Atherosclerosis. , 131–172.","chicago":"Stopa, Victoria, Miron Sopić, Guanliang Li, Judith Sluimer, José Basílio, Sander W. van der Laan, David P. Kreil, Yvan Devaux, and Bernhard Hochreiter. “Essentials of Transcriptomic Methods: Navigating through RNA Sequencing and Beyond.” In <i>Transcriptomics in Atherosclerosis</i>, edited by Yvan Devaux and Miron Sopic, 131–72. Elsevier, 2025. <a href=\"https://doi.org/10.1016/b978-0-443-33064-3.00016-5\">https://doi.org/10.1016/b978-0-443-33064-3.00016-5</a>.","short":"V. Stopa, M. Sopić, G. Li, J. Sluimer, J. Basílio, S.W. van der Laan, D.P. Kreil, Y. Devaux, B. Hochreiter, in:, Y. Devaux, M. Sopic (Eds.), Transcriptomics in Atherosclerosis, Elsevier, 2025, pp. 131–172."},"month":"10","doi":"10.1016/b978-0-443-33064-3.00016-5","editor":[{"full_name":"Devaux, Yvan","last_name":"Devaux","first_name":"Yvan"},{"last_name":"Sopic","first_name":"Miron","full_name":"Sopic, Miron"}],"author":[{"full_name":"Stopa, Victoria","last_name":"Stopa","first_name":"Victoria"},{"full_name":"Sopić, Miron","first_name":"Miron","last_name":"Sopić"},{"last_name":"Li","first_name":"Guanliang","full_name":"Li, Guanliang"},{"full_name":"Sluimer, Judith","last_name":"Sluimer","first_name":"Judith"},{"full_name":"Basílio, José","last_name":"Basílio","first_name":"José"},{"first_name":"Sander W.","last_name":"van der Laan","full_name":"van der Laan, Sander W."},{"full_name":"Kreil, David P.","first_name":"David P.","last_name":"Kreil"},{"first_name":"Yvan","last_name":"Devaux","full_name":"Devaux, Yvan"},{"first_name":"Bernhard","last_name":"Hochreiter","full_name":"Hochreiter, Bernhard","id":"e6cab3de-17f6-11ed-9210-c1e42e045e9d"}],"department":[{"_id":"Bio"}],"page":"131-172","publication":"Transcriptomics in Atherosclerosis","publisher":"Elsevier","_id":"20870","title":"Essentials of transcriptomic methods: Navigating through RNA sequencing and beyond","date_updated":"2026-01-05T11:49:54Z","day":"24","type":"book_chapter","publication_identifier":{"isbn":["9780443330643"]},"date_created":"2025-12-29T12:16:22Z","status":"public","quality_controlled":"1"},{"_id":"17468","title":"Marcus kinetics control singlet and triplet oxygen evolving from superoxide","file":[{"access_level":"open_access","date_updated":"2025-10-20T10:26:13Z","creator":"dernst","file_id":"20500","success":1,"file_size":3809247,"date_created":"2025-10-20T10:26:13Z","file_name":"2025_Nature_Mondal.pdf","checksum":"b507ddd23df0388aa65d04dc9b00fe3d","content_type":"application/pdf","relation":"main_file"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"intvolume":"       646","quality_controlled":"1","department":[{"_id":"StFr"},{"_id":"Bio"}],"oa":1,"ddc":["540"],"has_accepted_license":"1","issue":"8085","citation":{"short":"S. Mondal, H.T.K. Nguyen, R. Hauschild, S.A. Freunberger, Nature 646 (2025) 601–605.","chicago":"Mondal, Soumyadip, Huyen T.K. Nguyen, Robert Hauschild, and Stefan Alexander Freunberger. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>.","ista":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. 2025. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. 646(8085), 601–605.","ieee":"S. Mondal, H. T. K. Nguyen, R. Hauschild, and S. A. Freunberger, “Marcus kinetics control singlet and triplet oxygen evolving from superoxide,” <i>Nature</i>, vol. 646, no. 8085. Springer Nature, pp. 601–605, 2025.","apa":"Mondal, S., Nguyen, H. T. K., Hauschild, R., &#38; Freunberger, S. A. (2025). Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>","mla":"Mondal, Soumyadip, et al. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>, vol. 646, no. 8085, Springer Nature, 2025, pp. 601–605, doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>.","ama":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. 2025;646(8085):601–605. doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>"},"month":"10","PlanS_conform":"1","author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","first_name":"Soumyadip","last_name":"Mondal"},{"full_name":"Nguyen, Huyen T.K.","first_name":"Huyen T.K.","last_name":"Nguyen"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"corr_author":"1","article_type":"original","OA_place":"publisher","date_published":"2025-10-16T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2025","date_updated":"2025-11-27T13:20:38Z","day":"16","type":"journal_article","status":"public","date_created":"2024-08-29T10:40:23Z","pmid":1,"acknowledgement":"S.A.F. thanks the Institute of Science and Technology Austria (ISTA) for the support. The Scientific Service Units of ISTA supported this research through resources provided by the Imaging and Optics Facility, the Lab Support Facility, the Miba Machine Shop and Scientific Computing. This research was partly funded by the Austrian Science Fund (FWF) (10.55776/P37169 and 10.55776/COE5). For open access purposes, the author has applied for a CC BY public copyright licence to any author-accepted manuscript version arising from this submission. R.H. acknowledges funding through CZI grant DAF2020-225401 (10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (10.13039/100014989). H.T.K.N. acknowledges funding by the European Commission Erasmus Mundus Joint Masters programme. We thank M. Sixt and M. Chinon for the discussions about O-redox in life and R. Jethwa for proofreading. Open access funding was provided by ISTA.","page":"601–605","publication":"Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","file_date_updated":"2025-10-20T10:26:13Z","isi":1,"project":[{"name":"Singlet oxygen in non-aqueous oxygen redox chemistry","grant_number":"P37169","_id":"8df062be-16d5-11f0-9cad-f559b6612c7e"},{"grant_number":"CZI01","name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473"}],"external_id":{"pmid":["41044415"],"isi":["001586378900001"]},"doi":"10.1038/s41586-025-09587-7","volume":646,"language":[{"iso":"eng"}],"OA_type":"hybrid","scopus_import":"1","abstract":[{"text":"Oxygen redox chemistry is central to life1 and many human-made technologies, such as in energy storage2,3,4. The large energy gain from oxygen redox reactions is often connected with the occurrence of harmful reactive oxygen species3,5,6. Key species are superoxide and the highly reactive singlet oxygen3,4,5,6,7, which may evolve from superoxide. However, the factors determining the formation of singlet oxygen, rather than the relatively unreactive triplet oxygen, are unknown. Here we report that the release of triplet or singlet oxygen is governed by individual Marcus normal and inverted region behaviour. We found that as the driving force for the reaction increases, the initially dominant evolution of triplet oxygen slows down, and singlet oxygen evolution becomes predominant with higher maximum kinetics. This behaviour also applies to the widely observed superoxide disproportionation, in which one superoxide is oxidized by another, in both non-aqueous and aqueous systems, with Lewis and Brønsted acidity controlling the driving forces. Singlet oxygen yields governed by these conditions are relevant, for example, in batteries or cellular organelles in which superoxide forms. Our findings suggest ways to understand and control spin states and kinetics in oxygen redox chemistry, with implications for fields, including life sciences, pure chemistry and energy storage.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":42,"external_id":{"isi":["001065254200001"],"pmid":["37653226"]},"doi":"10.1038/s41587-023-01911-8","project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","language":[{"iso":"eng"}],"OA_type":"hybrid","date_created":"2023-09-03T22:01:15Z","status":"public","day":"01","type":"journal_article","date_updated":"2025-04-23T07:34:17Z","isi":1,"file_date_updated":"2025-01-09T07:48:01Z","publication":"Nature Biotechnology","ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","page":"1051-1064","pmid":1,"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","author":[{"full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korinkova","first_name":"Hana","full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","full_name":"Watson, Jake"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino"},{"full_name":"Roessler, Karl","first_name":"Karl","last_name":"Roessler"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"full_name":"Höftberger, Romana","first_name":"Romana","last_name":"Höftberger"},{"last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"deleted","relation":"dissertation_contains","id":"18660"},{"id":"18674","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"13126"}],"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}]},"citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064."},"month":"07","oa_version":"Published Version","publication_status":"published","year":"2024","OA_place":"publisher","date_published":"2024-07-01T00:00:00Z","article_type":"original","corr_author":"1","quality_controlled":"1","intvolume":"        42","file":[{"checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","file_name":"2024_NatureBiotech_Michalska.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T07:48:01Z","creator":"dernst","file_size":26065165,"date_created":"2025-01-09T07:48:01Z","success":1,"file_id":"18784"}],"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"_id":"14257","title":"Imaging brain tissue architecture across millimeter to nanometer scales","ddc":["570"],"has_accepted_license":"1","oa":1,"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}]},{"volume":248,"doi":"10.1039/d3fd00088e","external_id":{"pmid":["37750344"],"isi":["001070423500001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"status":"public","date_created":"2023-05-22T06:53:34Z","type":"journal_article","day":"01","date_updated":"2025-12-04T09:13:49Z","isi":1,"file_date_updated":"2024-07-16T07:46:39Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (3.0)"},"publisher":"Royal Society of Chemistry","publication":"Faraday Discussions","page":"175-189","pmid":1,"author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","last_name":"Mondal","first_name":"Soumyadip"},{"orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","last_name":"Jethwa"},{"id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","full_name":"Pant, Bhargavi","last_name":"Pant","first_name":"Bhargavi"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"}],"keyword":["Physical and Theoretical Chemistry"],"related_material":{"record":[{"id":"20607","status":"public","relation":"dissertation_contains"}]},"month":"01","citation":{"chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>.","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions 248 (2024) 175–189.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2024. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 248, 175–189.","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. 2024;248:175-189. doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 175–189, 2024.","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., &#38; Freunberger, S. A. (2024). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 175–89, doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>."},"year":"2024","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/3.0/","publication_status":"published","date_published":"2024-01-01T00:00:00Z","article_type":"original","corr_author":"1","quality_controlled":"1","intvolume":"       248","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"file":[{"creator":"dernst","file_id":"17249","success":1,"file_size":1303733,"date_created":"2024-07-16T07:46:39Z","access_level":"open_access","date_updated":"2024-07-16T07:46:39Z","content_type":"application/pdf","relation":"main_file","file_name":"2024_FaradayDiscussions_Mondal.pdf","checksum":"6515a227ed3e8942496fe6a1feeffd18"}],"title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","_id":"13044","has_accepted_license":"1","ddc":["540"],"oa":1,"department":[{"_id":"StFr"},{"_id":"Bio"}]},{"acknowledgement":"We would like to thank the members of the Sweeney Lab (especially Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion, and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their scientific insight and mentorship during the conception of this project. This\r\nproject would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA). In addition, we thank our funding sources for providing the resources to do these\r\nexperiments: FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS 5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.); NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities (ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472 (Z.H.); and Project A.L.S. (S.B-M.). ","main_file_link":[{"url":"https://doi.org/10.1101/2024.09.20.614050","open_access":"1"}],"department":[{"_id":"LoSw"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"publication":"bioRxiv","oa":1,"date_updated":"2025-05-14T11:40:13Z","title":"Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis","_id":"19520","type":"preprint","day":"27","status":"public","date_created":"2025-04-07T08:48:28Z","corr_author":"1","OA_type":"green","language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species."}],"date_published":"2024-09-27T00:00:00Z","OA_place":"repository","year":"2024","publication_status":"submitted","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","citation":{"ama":"Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>","apa":"Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R., Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>","ieee":"D. Vijatovic <i>et al.</i>, “Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis,” <i>bioRxiv</i>. .","mla":"Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>.","short":"D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.).","chicago":"Vijatovic, David, Florina Alexandra  Toma, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.09.20.614050\">https://doi.org/10.1101/2024.09.20.614050</a>.","ista":"Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv, <a href=\"https://doi.org/10.1101/2024.09.20.614050\">10.1101/2024.09.20.614050</a>."},"project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis"},{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551"},{"grant_number":"CZI01","name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473"}],"doi":"10.1101/2024.09.20.614050","author":[{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David","full_name":"Vijatovic, David"},{"last_name":"Toma","first_name":"Florina Alexandra ","full_name":"Toma, Florina Alexandra ","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e"},{"orcid":"0009-0008-0158-4032","id":"a8144562-32c9-11ee-b5ce-d9800628bda2","last_name":"Harrington","first_name":"Zoe P","full_name":"Harrington, Zoe P"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trevisan, Alexandra J.","last_name":"Trevisan","first_name":"Alexandra J."},{"full_name":"Chapman, Phillip","last_name":"Chapman","first_name":"Phillip"},{"first_name":"Mara","last_name":"Julseth","full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"first_name":"Mariano I.","last_name":"Gabitto","full_name":"Gabitto, Mariano I."},{"full_name":"Dasen, Jeremy S.","first_name":"Jeremy S.","last_name":"Dasen"},{"full_name":"Bikoff, Jay B.","first_name":"Jay B.","last_name":"Bikoff"},{"orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"}]},{"month":"02","citation":{"mla":"Hauschild, Robert. <i>Matlab Script for Analysis of Clone Dispersal</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","short":"R. Hauschild, (2024)."},"doi":"10.15479/AT:ISTA:14926","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15048"}]},"author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"}],"corr_author":"1","date_published":"2024-02-02T00:00:00Z","year":"2024","license":"https://opensource.org/licenses/MIT","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-09-04T12:10:39Z","title":"Matlab script for analysis of clone dispersal","_id":"14926","type":"software","day":"02","file":[{"relation":"main_file","content_type":"application/octet-stream","file_name":"README.md","checksum":"df7f358ae19a176cf710c0a802ce31b1","success":1,"file_id":"14927","file_size":736,"date_created":"2024-02-02T14:40:31Z","creator":"rhauschild","date_updated":"2024-02-02T14:40:31Z","access_level":"open_access"},{"date_updated":"2024-02-02T14:40:31Z","access_level":"open_access","file_size":3543,"date_created":"2024-02-02T14:40:31Z","file_id":"14928","success":1,"creator":"rhauschild","checksum":"10194cc11619eccd8f4b24472e465b7f","file_name":"Supplementary_file_1.zip","relation":"main_file","content_type":"application/x-zip-compressed"}],"status":"public","date_created":"2024-02-02T14:42:26Z","department":[{"_id":"Bio"}],"tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2024-02-02T14:40:31Z","has_accepted_license":"1","ddc":["570"]},{"date_created":"2024-03-03T23:00:50Z","status":"public","day":"01","type":"journal_article","date_updated":"2025-09-04T12:10:40Z","isi":1,"file_date_updated":"2024-03-04T07:24:43Z","publication":"Development","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"The Company of Biologists","ec_funded":1,"page":"1-18","pmid":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. ","volume":151,"external_id":{"pmid":["38372390"],"isi":["001170580200001"]},"doi":"10.1242/dev.202316","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       151","file":[{"access_level":"open_access","date_updated":"2024-03-04T07:24:43Z","creator":"dernst","date_created":"2024-03-04T07:24:43Z","file_size":14839986,"success":1,"file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","file_name":"2024_Development_Schauer.pdf","content_type":"application/pdf","relation":"main_file"}],"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"_id":"15048","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","ddc":["570"],"has_accepted_license":"1","oa":1,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"author":[{"full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"related_material":{"record":[{"id":"14926","relation":"research_data","status":"public"}]},"issue":"4","citation":{"short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 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>.","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.","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>","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>","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>."},"month":"02","oa_version":"Published Version","publication_status":"published","year":"2024","date_published":"2024-02-01T00:00:00Z","article_type":"original","corr_author":"1"},{"intvolume":"       223","quality_controlled":"1","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","_id":"15146","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"file":[{"success":1,"file_id":"15188","date_created":"2024-03-25T12:52:04Z","file_size":11907016,"creator":"dernst","date_updated":"2024-03-25T12:52:04Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2024_JCB_Zens.pdf","checksum":"90d1984a93660735e506c2a304bc3f73"}],"oa":1,"has_accepted_license":"1","ddc":["570"],"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","last_name":"Zens","first_name":"Bettina","full_name":"Zens, Bettina"},{"full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","first_name":"Jesse","last_name":"Hansen"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler"},{"orcid":"0000-0003-3904-947X","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"full_name":"Alanko, Jonna H","first_name":"Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"month":"03","issue":"6","citation":{"chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>"},"date_published":"2024-03-20T00:00:00Z","year":"2024","oa_version":"Published Version","publication_status":"published","corr_author":"1","article_type":"original","status":"public","date_created":"2024-03-21T06:45:51Z","date_updated":"2025-09-04T13:17:16Z","type":"journal_article","day":"20","publisher":"Rockefeller University Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication":"Journal of Cell Biology","file_date_updated":"2024-03-25T12:52:04Z","isi":1,"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","pmid":1,"volume":223,"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ visual proteomics and structure determination","grant_number":"CZI01"}],"doi":"10.1083/jcb.202309125","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"article_number":"e202309125","scopus_import":"1"},{"volume":631,"doi":"10.1038/s41586-024-07671-y","external_id":{"isi":["001281636500020"],"pmid":["38987596"]},"project":[{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"status":"public","date_created":"2024-07-21T22:01:02Z","type":"journal_article","day":"18","date_updated":"2025-09-08T08:14:25Z","file_date_updated":"2024-07-22T06:16:11Z","isi":1,"ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","publication":"Nature","page":"645-653","acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","pmid":1,"author":[{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R"},{"full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold","first_name":"Hellen"},{"first_name":"Susanne","last_name":"Stutte","full_name":"Stutte, Susanne"},{"full_name":"Fu, Wenwen","first_name":"Wenwen","last_name":"Fu"},{"first_name":"Jutta","last_name":"Weitz","full_name":"Weitz, Jutta"},{"full_name":"Dueck, Anne","last_name":"Dueck","first_name":"Anne"},{"first_name":"Bhavishya","last_name":"Nelakuditi","full_name":"Nelakuditi, Bhavishya"},{"first_name":"Valeria","last_name":"Fumagalli","full_name":"Fumagalli, Valeria"},{"full_name":"Van Den Heuvel, Dominic","first_name":"Dominic","last_name":"Van Den Heuvel"},{"last_name":"Belz","first_name":"Larissa","full_name":"Belz, Larissa"},{"full_name":"Sobirova, Gulnoza","first_name":"Gulnoza","last_name":"Sobirova"},{"last_name":"Zhang","first_name":"Zhe","full_name":"Zhang, Zhe"},{"full_name":"Titova, Anna","first_name":"Anna","last_name":"Titova"},{"full_name":"Navarro, Alejandro Martinez","first_name":"Alejandro Martinez","last_name":"Navarro"},{"last_name":"Pekayvaz","first_name":"Kami","full_name":"Pekayvaz, Kami"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"last_name":"Von Baumgarten","first_name":"Louisa","full_name":"Von Baumgarten, Louisa"},{"full_name":"Kranich, Jan","first_name":"Jan","last_name":"Kranich"},{"last_name":"Straub","first_name":"Tobias","full_name":"Straub, Tobias"},{"last_name":"Popper","first_name":"Bastian","full_name":"Popper, Bastian"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann"},{"full_name":"Guo, Chenglong","last_name":"Guo","first_name":"Chenglong"},{"full_name":"Piontek, Guido","first_name":"Guido","last_name":"Piontek"},{"full_name":"Von Stillfried, Saskia","last_name":"Von Stillfried","first_name":"Saskia"},{"full_name":"Boor, Peter","last_name":"Boor","first_name":"Peter"},{"full_name":"Colonna, Marco","first_name":"Marco","last_name":"Colonna"},{"first_name":"Sebastian","last_name":"Clauß","full_name":"Clauß, Sebastian"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"first_name":"Thomas","last_name":"Brocker","full_name":"Brocker, Thomas"},{"full_name":"Walzog, Barbara","first_name":"Barbara","last_name":"Walzog"},{"first_name":"Christoph","last_name":"Scheiermann","full_name":"Scheiermann, Christoph"},{"full_name":"Aird, William C.","last_name":"Aird","first_name":"William C."},{"full_name":"Nerlov, Claus","last_name":"Nerlov","first_name":"Claus"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"full_name":"Petzold, Tobias","last_name":"Petzold","first_name":"Tobias"},{"last_name":"Engelhardt","first_name":"Stefan","full_name":"Engelhardt, Stefan"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martina","last_name":"Rudelius","full_name":"Rudelius, Martina"},{"full_name":"Oostendorp, Robert A.J.","last_name":"Oostendorp","first_name":"Robert A.J."},{"full_name":"Iannacone, Matteo","last_name":"Iannacone","first_name":"Matteo"},{"last_name":"Heinig","first_name":"Matthias","full_name":"Heinig, Matthias"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"}],"related_material":{"link":[{"url":"https://github.com/heiniglab/gaertner_megakaryocytes","relation":"software"}]},"month":"07","citation":{"chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>.","short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653.","ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653.","ieee":"F. R. Gärtner <i>et al.</i>, “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” <i>Nature</i>, vol. 631. Springer Nature, pp. 645–653, 2024.","apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>, vol. 631, Springer Nature, 2024, pp. 645–53, doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>.","ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. 2024;631:645-653. doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>"},"year":"2024","publication_status":"published","oa_version":"Published Version","date_published":"2024-07-18T00:00:00Z","article_type":"original","corr_author":"1","quality_controlled":"1","intvolume":"       631","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"file":[{"file_name":"2024_Nature_Gaertner.pdf","checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2024-07-22T06:16:11Z","creator":"dernst","success":1,"file_id":"17286","date_created":"2024-07-22T06:16:11Z","file_size":15704819}],"title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","_id":"17284","has_accepted_license":"1","ddc":["570"],"oa":1,"department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}]},{"author":[{"full_name":"Méhes, Elod","first_name":"Elod","last_name":"Méhes"},{"full_name":"Mones, Enys","last_name":"Mones","first_name":"Enys"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"full_name":"Zsigmond, Áron","first_name":"Áron","last_name":"Zsigmond"},{"full_name":"Biri-Kovács, Beáta","first_name":"Beáta","last_name":"Biri-Kovács"},{"last_name":"Nyitray","first_name":"László","full_name":"Nyitray, László"},{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"}],"month":"08","citation":{"ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>, vol. 6, 817, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>","ieee":"E. Méhes <i>et al.</i>, “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” <i>Communications Biology</i>, vol. 6. Springer Nature, 2023.","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>."},"date_published":"2023-08-04T00:00:00Z","year":"2023","oa_version":"Published Version","publication_status":"published","article_type":"original","intvolume":"         6","quality_controlled":"1","title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","_id":"14041","publication_identifier":{"eissn":["2399-3642"]},"file":[{"date_updated":"2023-08-14T07:17:36Z","access_level":"open_access","date_created":"2023-08-14T07:17:36Z","file_size":10181997,"success":1,"file_id":"14045","creator":"dernst","checksum":"1f9324f736bdbb76426b07736651c4cd","file_name":"2023_CommBiology_Mehes.pdf","relation":"main_file","content_type":"application/pdf"}],"oa":1,"has_accepted_license":"1","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"volume":6,"doi":"10.1038/s42003-023-05181-7","external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_number":"817","scopus_import":"1","date_created":"2023-08-13T22:01:13Z","status":"public","date_updated":"2023-12-13T12:07:33Z","type":"journal_article","day":"04","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","publication":"Communications Biology","isi":1,"file_date_updated":"2023-08-14T07:17:36Z","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","pmid":1},{"volume":5,"doi":"10.1038/s42255-023-00766-2","external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"article_processing_charge":"No","abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2023-03-23T12:58:43Z","status":"public","date_updated":"2023-11-28T07:31:33Z","type":"journal_article","day":"20","publisher":"Springer Nature","publication":"Nature Metabolism","isi":1,"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","pmid":1,"page":"495-515","author":[{"full_name":"Cikes, Domagoj","first_name":"Domagoj","last_name":"Cikes"},{"full_name":"Elsayad, Kareem","first_name":"Kareem","last_name":"Elsayad"},{"last_name":"Sezgin","first_name":"Erdinc","full_name":"Sezgin, Erdinc"},{"last_name":"Koitai","first_name":"Erika","full_name":"Koitai, Erika"},{"full_name":"Ferenc, Torma","first_name":"Torma","last_name":"Ferenc"},{"full_name":"Orthofer, Michael","first_name":"Michael","last_name":"Orthofer"},{"first_name":"Rebecca","last_name":"Yarwood","full_name":"Yarwood, Rebecca"},{"full_name":"Heinz, Leonhard X.","first_name":"Leonhard X.","last_name":"Heinz"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser","last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser"},{"first_name":"Adrian","last_name":"Taylor","full_name":"Taylor, Adrian"},{"full_name":"Grapentine, Sophie","first_name":"Sophie","last_name":"Grapentine"},{"full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi","first_name":"Fathiya"},{"full_name":"Abot, Anne","last_name":"Abot","first_name":"Anne"},{"first_name":"Adelheid","last_name":"Weidinger","full_name":"Weidinger, Adelheid"},{"last_name":"Kutchukian","first_name":"Candice","full_name":"Kutchukian, Candice"},{"full_name":"Sanchez, Colline","last_name":"Sanchez","first_name":"Colline"},{"full_name":"Cronin, Shane J. F.","last_name":"Cronin","first_name":"Shane J. F."},{"first_name":"Maria","last_name":"Novatchkova","full_name":"Novatchkova, Maria"},{"full_name":"Kavirayani, Anoop","last_name":"Kavirayani","first_name":"Anoop"},{"last_name":"Schuetz","first_name":"Thomas","full_name":"Schuetz, Thomas"},{"full_name":"Haubner, Bernhard","first_name":"Bernhard","last_name":"Haubner"},{"full_name":"Haas, Lisa","last_name":"Haas","first_name":"Lisa"},{"last_name":"Hagelkruys","first_name":"Astrid","full_name":"Hagelkruys, Astrid"},{"last_name":"Jackowski","first_name":"Suzanne","full_name":"Jackowski, Suzanne"},{"first_name":"Andrey","last_name":"Kozlov","full_name":"Kozlov, Andrey"},{"first_name":"Vincent","last_name":"Jacquemond","full_name":"Jacquemond, Vincent"},{"first_name":"Claude","last_name":"Knauf","full_name":"Knauf, Claude"},{"last_name":"Superti-Furga","first_name":"Giulio","full_name":"Superti-Furga, Giulio"},{"first_name":"Eric","last_name":"Rullman","full_name":"Rullman, Eric"},{"first_name":"Thomas","last_name":"Gustafsson","full_name":"Gustafsson, Thomas"},{"first_name":"John","last_name":"McDermot","full_name":"McDermot, John"},{"full_name":"Lowe, Martin","last_name":"Lowe","first_name":"Martin"},{"last_name":"Radak","first_name":"Zsolt","full_name":"Radak, Zsolt"},{"full_name":"Chamberlain, Jeffrey S.","last_name":"Chamberlain","first_name":"Jeffrey S."},{"last_name":"Bakovic","first_name":"Marica","full_name":"Bakovic, Marica"},{"first_name":"Siddharth","last_name":"Banka","full_name":"Banka, Siddharth"},{"full_name":"Penninger, Josef M.","first_name":"Josef M.","last_name":"Penninger"}],"keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"month":"03","citation":{"ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515."},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-023-00791-1"}]},"date_published":"2023-03-20T00:00:00Z","year":"2023","oa_version":"Preprint","publication_status":"published","article_type":"original","intvolume":"         5","quality_controlled":"1","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","_id":"12747","publication_identifier":{"issn":["2522-5812"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"department":[{"_id":"Bio"}]},{"quality_controlled":"1","intvolume":"        58","file":[{"file_name":"2023_DevelopmentalCell_Huljev.pdf","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","relation":"main_file","content_type":"application/pdf","date_updated":"2023-04-17T07:41:25Z","access_level":"open_access","file_id":"12842","success":1,"file_size":7925886,"date_created":"2023-04-17T07:41:25Z","creator":"dernst"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"_id":"12830","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","ddc":["570"],"has_accepted_license":"1","oa":1,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"},{"first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","first_name":"Diana C"},{"first_name":"Friedrich","last_name":"Preusser","full_name":"Preusser, Friedrich"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene","last_name":"Steccari","first_name":"Irene"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik","first_name":"Suyash","full_name":"Naik, Suyash"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"issue":"7","citation":{"ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. 2023;58(7):582-596.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>","ieee":"K. Huljev <i>et al.</i>, “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” <i>Developmental Cell</i>, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7."},"month":"04","publication_status":"published","oa_version":"Published Version","year":"2023","date_published":"2023-04-10T00:00:00Z","article_type":"original","corr_author":"1","status":"public","date_created":"2023-04-16T22:01:07Z","day":"10","type":"journal_article","date_updated":"2025-04-23T08:51:34Z","isi":1,"file_date_updated":"2023-04-17T07:41:25Z","publication":"Developmental Cell","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","ec_funded":1,"page":"582-596.e7","pmid":1,"acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","volume":58,"external_id":{"pmid":["36931269"],"isi":["000982111800001"]},"doi":"10.1016/j.devcel.2023.02.016","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","language":[{"iso":"eng"}]},{"publication":"Scientific Reports","publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-05-22T07:57:37Z","isi":1,"pmid":1,"acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","status":"public","date_created":"2023-05-19T11:12:25Z","date_updated":"2025-04-23T08:56:48Z","day":"17","type":"journal_article","abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"7959","language":[{"iso":"eng"}],"scopus_import":"1","volume":13,"external_id":{"pmid":["37198326"],"isi":["000995271600104"]},"doi":"10.1038/s41598-023-35162-z","oa":1,"ddc":["570"],"has_accepted_license":"1","department":[{"_id":"Bio"}],"intvolume":"        13","quality_controlled":"1","_id":"13033","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2023_ScientificReports_Zavadakova.pdf","checksum":"8c1b769693ff4288df8376e59ad1176d","success":1,"file_id":"13047","file_size":3055077,"date_created":"2023-05-22T07:57:37Z","creator":"dernst","date_updated":"2023-05-22T07:57:37Z","access_level":"open_access"}],"publication_identifier":{"issn":["2045-2322"]},"date_published":"2023-05-17T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2023","article_type":"original","keyword":["Multidisciplinary"],"author":[{"last_name":"Zavadakova","first_name":"Anna","full_name":"Zavadakova, Anna"},{"last_name":"Vistejnova","first_name":"Lucie","full_name":"Vistejnova, Lucie"},{"id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova","first_name":"Tereza","full_name":"Belinova, Tereza"},{"full_name":"Tichanek, Filip","last_name":"Tichanek","first_name":"Filip"},{"full_name":"Bilikova, Dagmar","first_name":"Dagmar","last_name":"Bilikova"},{"full_name":"Mouton, Peter R.","last_name":"Mouton","first_name":"Peter R."}],"issue":"1","citation":{"mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023)."},"month":"05","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]}}]