[{"file":[{"creator":"dernst","checksum":"1ca6f0822c1cbd430686d5e2a4f96401","file_id":"20872","file_size":12564806,"date_created":"2025-12-29T13:45:05Z","content_type":"application/pdf","file_name":"2025_DevelopmentalCell_McLaren.pdf","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2025-12-29T13:45:05Z"}],"title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.devcel.2025.04.010","status":"public","ec_funded":1,"ddc":["570"],"OA_type":"hybrid","type":"journal_article","PlanS_conform":"1","OA_place":"publisher","oa":1,"has_accepted_license":"1","file_date_updated":"2025-12-29T13:45:05Z","article_processing_charge":"Yes (in subscription journal)","page":"2237-2247.e4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","abstract":[{"lang":"eng","text":"An enlarged brain underlies the complex central nervous system of vertebrates. The dramatic expansion of the brain that diverges its shape from the spinal cord follows neural tube closure during embryonic development. Here, we show that this differential deformation is encoded by a pre-pattern of tissue material properties in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting in a thinning versus a resisting response to increasing lumen pressure, respectively. The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain cells to the spinal cord can locally create an expanded brain-like morphology in some cases. Our findings raise questions in vertebrate head evolution and suggest a general role of mechanical pre-patterning in sculpting epithelial tubes."}],"doi":"10.1016/j.devcel.2025.04.010","date_published":"2025-09-08T00:00:00Z","day":"08","author":[{"last_name":"Mclaren","first_name":"Susannah B.P.","full_name":"Mclaren, Susannah B.P."},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","full_name":"Xue, Shi-lei"},{"first_name":"Siyuan","last_name":"Ding","full_name":"Ding, Siyuan"},{"full_name":"Winkel, Alexander K.","last_name":"Winkel","first_name":"Alexander K."},{"first_name":"Oscar","last_name":"Baldwin","full_name":"Baldwin, Oscar"},{"full_name":"Dwarakacherla, Shreya","last_name":"Dwarakacherla","first_name":"Shreya"},{"last_name":"Franze","first_name":"Kristian","full_name":"Franze, Kristian"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Fengzhu","last_name":"Xiong","full_name":"Xiong, Fengzhu"}],"date_updated":"2026-10-20T08:25:00Z","date_created":"2025-05-18T22:02:50Z","year":"2025","citation":{"apa":"Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla, S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>","ama":"Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. 2025;60(17):2237-2247.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>","ista":"Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. Developmental Cell. 60(17), 2237–2247.e4.","mla":"Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>, vol. 60, no. 17, Cell Press, 2025, p. 2237–2247.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>.","ieee":"S. B. P. Mclaren <i>et al.</i>, “Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord,” <i>Developmental Cell</i>, vol. 60, no. 17. Cell Press, p. 2237–2247.e4, 2025.","short":"S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla, K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.","chicago":"Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel, Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>."},"publication":"Developmental Cell","quality_controlled":"1","issue":"17","pmid":1,"intvolume":"        60","volume":60,"article_type":"original","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"09","oa_version":"Published Version","publisher":"Cell Press","external_id":{"isi":["001570502100005"],"pmid":["40347948"]},"acknowledgement":"We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum, I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi, and Xiong labs for technical assistance and constructive feedback. We thank Ryan Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.; an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an ERC Starting Grant (851288) to E.H.","_id":"19703","department":[{"_id":"EdHa"}]},{"title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","file":[{"file_size":32104588,"file_id":"20875","checksum":"b944de5fbd7455f58e1ff338ad352239","creator":"dernst","date_updated":"2025-12-29T14:15:25Z","relation":"main_file","success":1,"access_level":"open_access","file_name":"2025_Cell_Zhang.pdf","content_type":"application/pdf","date_created":"2025-12-29T14:15:25Z"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.cell.2025.07.002","status":"public","ddc":["570"],"OA_type":"hybrid","type":"journal_article","PlanS_conform":"1","OA_place":"publisher","oa":1,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2025-12-29T14:15:25Z","page":"5862-5877.e23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism.","lang":"eng"}],"scopus_import":"1","doi":"10.1016/j.cell.2025.07.002","date_published":"2025-10-16T00:00:00Z","day":"16","author":[{"first_name":"Zhiying","last_name":"Zhang","full_name":"Zhang, Zhiying"},{"first_name":"Thomas C.","last_name":"Todeschini","full_name":"Todeschini, Thomas C."},{"full_name":"Wu, Yi","last_name":"Wu","first_name":"Yi"},{"first_name":"Roman","last_name":"Kogay","full_name":"Kogay, Roman"},{"full_name":"Naji, Ameena","last_name":"Naji","first_name":"Ameena"},{"full_name":"Cardenas Rodriguez, Joaquin","first_name":"Joaquin","last_name":"Cardenas Rodriguez"},{"full_name":"Mondi, Rupavidhya","last_name":"Mondi","first_name":"Rupavidhya"},{"last_name":"Kaganovich","first_name":"Daniel","full_name":"Kaganovich, Daniel"},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."},{"full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","last_name":"Bravo"},{"first_name":"Marianna","last_name":"Teplova","full_name":"Teplova, Marianna"},{"full_name":"Amen, Triana","first_name":"Triana","last_name":"Amen"},{"full_name":"Koonin, Eugene","last_name":"Koonin","first_name":"Eugene"},{"full_name":"Patel, Dinshaw J.","first_name":"Dinshaw J.","last_name":"Patel"},{"last_name":"Nobrega","first_name":"Franklin L.","full_name":"Nobrega, Franklin L."}],"date_updated":"2026-10-20T08:23:33Z","date_created":"2025-08-07T05:00:04Z","year":"2025","citation":{"apa":"Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>","ista":"Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ, Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 188(21), 5862–5877.e23.","ama":"Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. 2025;188(21):5862-5877.e23. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>","short":"Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez, R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin, D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23.","ieee":"Z. Zhang <i>et al.</i>, “Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites,” <i>Cell</i>, vol. 188, no. 21. Cell Press, p. 5862–5877.e23, 2025.","mla":"Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>, vol. 188, no. 21, Cell Press, 2025, p. 5862–5877.e23, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>.","chicago":"Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>."},"publication":"Cell","quality_controlled":"1","issue":"21","pmid":1,"intvolume":"       188","volume":188,"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"article_type":"original","month":"10","oa_version":"Published Version","publisher":"Cell Press","external_id":{"pmid":["40730155"],"isi":["001603560700005"]},"acknowledgement":"We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of Southampton. This work was supported by Royal Society grant RGS\\R2\\222312 to F.L.N.; Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.; Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P. In addition to MSKCC cryo-EM resources, some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and Simons Foundation (SF349247) and NY State Assembly grants. This research used NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II, operated for the DOE Office of Science by Brookhaven National Laboratory under contract no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the NIH, the National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program of the NIH (National Library of Medicine).","_id":"20143","department":[{"_id":"JaBr"}]},{"date_updated":"2026-10-20T08:25:34Z","author":[{"full_name":"Najjar, Hadil","first_name":"Hadil","last_name":"Najjar"},{"full_name":"Weiß, Sarah","first_name":"Sarah","last_name":"Weiß"},{"first_name":"Ferdinand","id":"b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e","last_name":"Horvath","full_name":"Horvath, Ferdinand"},{"last_name":"Hopl","first_name":"Valentina","full_name":"Hopl, Valentina"},{"full_name":"Tiffner, Adéla","first_name":"Adéla","last_name":"Tiffner"},{"full_name":"Höbarth, Lorenz","first_name":"Lorenz","last_name":"Höbarth"},{"full_name":"Söllner, Julia","first_name":"Julia","last_name":"Söllner"},{"full_name":"Fröhlich, Maximilian","last_name":"Fröhlich","first_name":"Maximilian"},{"last_name":"Prantl","first_name":"Magdalena","full_name":"Prantl, Magdalena"},{"full_name":"Müller, Nora","last_name":"Müller","first_name":"Nora"},{"first_name":"Yuliia","last_name":"Nazarenko","full_name":"Nazarenko, Yuliia"},{"first_name":"Selina","last_name":"Harant","full_name":"Harant, Selina"},{"full_name":"Weissenböck, Lukas","first_name":"Lukas","last_name":"Weissenböck"},{"full_name":"Grabmayr, Herwig","last_name":"Grabmayr","first_name":"Herwig"},{"full_name":"Sallinger, Matthias","first_name":"Matthias","last_name":"Sallinger"},{"first_name":"Lena","last_name":"Maltan","full_name":"Maltan, Lena"},{"full_name":"Echefu, Linda V.","first_name":"Linda V.","last_name":"Echefu"},{"full_name":"Radiskovic, Tamara","last_name":"Radiskovic","first_name":"Tamara"},{"full_name":"Leopold, Melanie","last_name":"Leopold","first_name":"Melanie"},{"full_name":"Lindinger, Sonja","first_name":"Sonja","last_name":"Lindinger"},{"full_name":"Humer, Christina","first_name":"Christina","last_name":"Humer"},{"full_name":"Höglinger, Carmen","first_name":"Carmen","last_name":"Höglinger"},{"full_name":"Krobath, Heinrich","first_name":"Heinrich","last_name":"Krobath"},{"full_name":"Renger, Thomas","first_name":"Thomas","last_name":"Renger"},{"full_name":"Derler, Isabella","last_name":"Derler","first_name":"Isabella"}],"publication":"Cell Reports Physical Science","year":"2025","date_created":"2025-06-15T22:01:31Z","citation":{"mla":"Najjar, Hadil, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>, vol. 6, no. 6, 102623, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>.","ieee":"H. Najjar <i>et al.</i>, “STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening,” <i>Cell Reports Physical Science</i>, vol. 6, no. 6. Cell Press, 2025.","short":"H. Najjar, S. Weiß, F. Horvath, V. Hopl, A. Tiffner, L. Höbarth, J. Söllner, M. Fröhlich, M. Prantl, N. Müller, Y. Nazarenko, S. Harant, L. Weissenböck, H. Grabmayr, M. Sallinger, L. Maltan, L.V. Echefu, T. Radiskovic, M. Leopold, S. Lindinger, C. Humer, C. Höglinger, H. Krobath, T. Renger, I. Derler, Cell Reports Physical Science 6 (2025).","chicago":"Najjar, Hadil, Sarah Weiß, Ferdinand Horvath, Valentina Hopl, Adéla Tiffner, Lorenz Höbarth, Julia Söllner, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>.","apa":"Najjar, H., Weiß, S., Horvath, F., Hopl, V., Tiffner, A., Höbarth, L., … Derler, I. (2025). STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>","ista":"Najjar H, Weiß S, Horvath F, Hopl V, Tiffner A, Höbarth L, Söllner J, Fröhlich M, Prantl M, Müller N, Nazarenko Y, Harant S, Weissenböck L, Grabmayr H, Sallinger M, Maltan L, Echefu LV, Radiskovic T, Leopold M, Lindinger S, Humer C, Höglinger C, Krobath H, Renger T, Derler I. 2025. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science. 6(6), 102623.","ama":"Najjar H, Weiß S, Horvath F, et al. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. 2025;6(6). doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>"},"doi":"10.1016/j.xcrp.2025.102623","day":"18","date_published":"2025-06-18T00:00:00Z","DOAJ_listed":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"The Ca2+-release-activated Ca2+ (CRAC) channel Orai1 is activated by interaction with the Ca2+ sensor Stromal Interaction Molecule 1 (STIM1). Owing to the lack of structurally resolved Orai1/STIM1 complexes, the impact of their coupling on individual Orai1 transmembrane domain (TM) movements is unclear. This study investigates STIM1-independent and STIM1-dependent Orai1-TM dynamics using photocrosslinking unnatural amino acids (UAAs) at each individual TM position. We primarily identify CRAC-channel-like currents directly after UAA incorporation or additional UV-light irradiation at TM3 sites that interface with non-pore-lining TMs. Using UAAs combined with conventional site-directed mutagenesis and molecular dynamics simulations, we discover that pore opening involves a widening of interfaces formed by TM3 with non-pore-lining TMs. Orai1 mutants with a UAA in TM3 exhibit weaker STIM1-induced activation after UV exposure, possibly caused by a restricted widening of non-pore-lining TM interfaces. We demonstrate that photocrosslinking UAAs are excellent tools for improving our understanding of key determinants and ion channel dynamics modulating pore opening."}],"external_id":{"isi":["001516570500009"]},"oa_version":"Published Version","month":"06","publisher":"Cell Press","_id":"19846","department":[{"_id":"AnSa"}],"acknowledgement":"We thank S. Buchegger for excellent technical assistance. This research was funded by the Austrian Science Fund (FWF) projects https://doi.org/10.55776/P32851, https://doi.org/10.55776/P35900, and https://doi.org/10.55776/P36202 to I.D. and https://doi.org/10.55776/PAT6871323 to A.T. N.M. is funded within the DOC program of the OeAW (Austrian Academy of Science). For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","issue":"6","article_number":"102623","quality_controlled":"1","volume":6,"publication_identifier":{"eissn":["2666-3864"]},"article_type":"original","intvolume":"         6","status":"public","OA_type":"gold","type":"journal_article","ddc":["570"],"file":[{"date_created":"2025-06-23T10:20:22Z","content_type":"application/pdf","file_name":"2025_CellReportsPhysicalScience_Najjar.pdf","access_level":"open_access","date_updated":"2025-06-23T10:20:22Z","success":1,"relation":"main_file","creator":"dernst","checksum":"37ff7c396f966d0ec363e4691d63d402","file_id":"19868","file_size":9771117}],"title":"STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.xcrp.2025.102623","isi":1,"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2025-06-23T10:20:22Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"OA_place":"publisher"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"Vacuolar acidification is crucial for the homeostasis of intracellular pH and the recycling of proteins and nutrients in cells, thereby playing important roles in various physiological processes related to vacuolar function. The key factors regulating vacuolar acidification and underlying mechanisms remain unclear. Here, we report that Arabidopsis phospholipase Dζ2 (PLDζ2) promotes the acidification of the vacuolar lumen to stimulate autophagic degradation under phosphorus deficiency. The pldζ2 mutant massively accumulates autophagic structures while exhibiting premature leaf senescence under nutrient starvation. Impaired autophagic flux, lytic vacuole morphology, and lytic degradation in pldζ2 indicate that PLDζ2 regulates autophagy by affecting the vacuolar function. PLDζ2 locates in both tonoplast and cytoplasm. Genetic, structural, and biochemical studies demonstrate that PLDζ2 directly interacts with vacuolar-type ATPase (V-ATPase) subunit D (VATD) to promote vacuolar acidification and autophagy under phosphorus starvation. These findings reveal the importance of V-ATPase and vacuolar pH in autophagic activity and provide clues in elucidating the regulatory mechanism of vacuolar acidification."}],"doi":"10.1016/j.celrep.2025.116024","date_published":"2025-07-22T00:00:00Z","day":"22","year":"2025","date_created":"2025-07-20T22:02:01Z","citation":{"chicago":"Guan, Bin, Ke Xuan Xie, Xin Qiao Du, Yu Xuan Bai, Peng Chao Hao, Wen Hui Lin, Jiří Friml, and Hong Wei Xue. “Arabidopsis Phospholipase Dζ2 Facilitates Vacuolar Acidification and Autophagy under Phosphorus Starvation by Interacting with VATD.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116024\">https://doi.org/10.1016/j.celrep.2025.116024</a>.","mla":"Guan, Bin, et al. “Arabidopsis Phospholipase Dζ2 Facilitates Vacuolar Acidification and Autophagy under Phosphorus Starvation by Interacting with VATD.” <i>Cell Reports</i>, vol. 44, no. 7, 116024, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116024\">10.1016/j.celrep.2025.116024</a>.","short":"B. Guan, K.X. Xie, X.Q. Du, Y.X. Bai, P.C. Hao, W.H. Lin, J. Friml, H.W. Xue, Cell Reports 44 (2025).","ieee":"B. Guan <i>et al.</i>, “Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD,” <i>Cell Reports</i>, vol. 44, no. 7. Cell Press, 2025.","ama":"Guan B, Xie KX, Du XQ, et al. Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. <i>Cell Reports</i>. 2025;44(7). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116024\">10.1016/j.celrep.2025.116024</a>","ista":"Guan B, Xie KX, Du XQ, Bai YX, Hao PC, Lin WH, Friml J, Xue HW. 2025. Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. Cell Reports. 44(7), 116024.","apa":"Guan, B., Xie, K. X., Du, X. Q., Bai, Y. X., Hao, P. C., Lin, W. H., … Xue, H. W. (2025). Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.116024\">https://doi.org/10.1016/j.celrep.2025.116024</a>"},"publication":"Cell Reports","author":[{"full_name":"Guan, Bin","last_name":"Guan","first_name":"Bin","id":"56aad729-cca2-11ed-a45a-9b4138991a48"},{"first_name":"Ke Xuan","last_name":"Xie","full_name":"Xie, Ke Xuan"},{"full_name":"Du, Xin Qiao","last_name":"Du","first_name":"Xin Qiao"},{"first_name":"Yu Xuan","last_name":"Bai","full_name":"Bai, Yu Xuan"},{"full_name":"Hao, Peng Chao","first_name":"Peng Chao","last_name":"Hao"},{"last_name":"Lin","first_name":"Wen Hui","full_name":"Lin, Wen Hui"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong Wei","first_name":"Hong Wei","last_name":"Xue"}],"date_updated":"2026-10-20T08:22:53Z","intvolume":"        44","volume":44,"publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"article_type":"original","quality_controlled":"1","issue":"7","article_number":"116024","pmid":1,"acknowledgement":"The study was supported by National Natural Science Foundation of China (NSFC, 92354301, 32230011, 32200274, and 91954206). The computations were run on the Siyuan-1 cluster supported by the Center for High-Performance Computing at Shanghai Jiao Tong University.","_id":"20029","department":[{"_id":"JiFr"}],"month":"07","oa_version":"Published Version","publisher":"Cell Press","external_id":{"pmid":["40668679"],"isi":["001533244800001"]},"isi":1,"fulldoi":"https://doi.org/10.1016/j.celrep.2025.116024","title":"Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD","file":[{"checksum":"ee03deee47a084b0295251dc49470ad4","creator":"dernst","file_id":"20067","file_size":37708120,"file_name":"2025_CellReports_Guan.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-07-22T08:52:17Z","success":1,"date_updated":"2025-07-22T08:52:17Z","relation":"main_file"}],"publication_status":"published","ddc":["580"],"OA_type":"hybrid","type":"journal_article","status":"public","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2025-07-22T08:52:17Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)"},{"DOAJ_listed":"1","date_published":"2025-07-24T00:00:00Z","day":"24","doi":"10.1016/j.celrep.2025.116056","abstract":[{"text":"Auxin regulates various aspects of plant growth and development by modulating the transcription of target genes through the degradation of auxin/indole-3-acetic acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1), a positive regulator of proteasome activity, has been implicated in auxin-mediated proteasome suppression; however, the mechanism by which auxin modulates PTRE1 function remains unclear. Here, we demonstrate that auxin promotes the interaction between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis, ultimately resulting in suppressed auxin-mediated transcriptional regulation. Our findings uncover a previously uncharacterized regulatory axis in auxin signaling that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which fine-tunes Aux/IAA protein homeostasis and auxin responses.","lang":"eng"}],"scopus_import":"1","date_updated":"2026-10-20T08:23:15Z","author":[{"first_name":"Faqing","last_name":"Xu","full_name":"Xu, Faqing"},{"last_name":"Yu","first_name":"Yongqiang","full_name":"Yu, Yongqiang"},{"full_name":"Guan, Bin","first_name":"Bin","id":"56aad729-cca2-11ed-a45a-9b4138991a48","last_name":"Guan"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Xu, Zhihong","first_name":"Zhihong","last_name":"Xu"},{"first_name":"Hongwei","last_name":"Xue","full_name":"Xue, Hongwei"}],"publication":"Cell Reports","citation":{"mla":"Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>, vol. 44, no. 8, 116056, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>.","ieee":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis,” <i>Cell Reports</i>, vol. 44, no. 8. Cell Press, 2025.","short":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).","chicago":"Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>.","apa":"Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., &#38; Xue, H. (2025). Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>","ama":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>","ista":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. Cell Reports. 44(8), 116056."},"date_created":"2025-08-04T13:39:11Z","year":"2025","issue":"8","pmid":1,"article_number":"116056","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["2211-1247"]},"volume":44,"intvolume":"        44","external_id":{"isi":["001542038500001"],"pmid":["40714631"]},"publisher":"Cell Press","month":"07","oa_version":"Published Version","department":[{"_id":"JiFr"}],"_id":"20116","acknowledgement":"The study was supported by the National Natural Science Foundation of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai Jiao Tong University) for kind help with the laser confocal microscope observation and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional mutants.","publication_status":"published","title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","file":[{"creator":"dernst","checksum":"3c43e040a4a7a65ec67ae1d2bb81261a","file_size":24178018,"file_id":"20120","date_created":"2025-08-05T06:15:09Z","content_type":"application/pdf","file_name":"2025_CellReports_Xu.pdf","access_level":"open_access","relation":"main_file","date_updated":"2025-08-05T06:15:09Z","success":1}],"fulldoi":"https://doi.org/10.1016/j.celrep.2025.116056","isi":1,"status":"public","type":"journal_article","OA_type":"gold","ddc":["580"],"OA_place":"publisher","file_date_updated":"2025-08-05T06:15:09Z","has_accepted_license":"1","article_processing_charge":"Yes","oa":1,"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":85,"article_type":"original","publication_identifier":{"issn":["1097-2765"]},"intvolume":"        85","issue":"15","quality_controlled":"1","_id":"20374","department":[{"_id":"AlMi"}],"acknowledgement":"We thank M. Schütz for laboratory management, organization, and assistance with manuscript editing. We are grateful to all Thomä and Schübeler lab members. We thank Ulrich Hassiepen from Novartis for his support and insightful discussions on the kinetic analysis. This work was supported by funding from the European Research Council (ERC), under the European Union’s H2020 research program (NucEM, grant no. 884331); the Swiss National Science Foundation (SNF, grant no. 310030_301206 and 310030_214852); Krebsforschung (KFS, grant no. KFS-5933-08-2023); Novartis Research Foundation (to N.H.T.); the Novartis Freenovation (grant no. FN23-0000000514 to C.R.S.); the National Health and Medical Research Council CJ Martin Fellowship (APP1148380); the EU Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant (grant no. 748760); the South Australian immunoGENomics Cancer Institute grant funding from the Australian Government; and the Sylvia and Charles Viertel Charitable Foundation Senior Medical Research Fellowship (to L.I.).","oa_version":"Published Version","month":"08","publisher":"Cell Press","doi":"10.1016/j.molcel.2025.06.027","day":"07","date_published":"2025-08-07T00:00:00Z","scopus_import":"1","abstract":[{"text":"Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However, it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors. In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring inaccessible chromatin. We examined the interaction of chromatin-bound p53 with co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct motif locations on the nucleosome (super-helical location [SHL]−5.7 and SHL+5.9), the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered interaction domains of co-factors and TFs govern compatibility between co-factors, TFs, and chromatin.","lang":"eng"}],"publication":"Molecular Cell","year":"2025","date_created":"2025-09-23T08:56:13Z","citation":{"chicago":"Chakraborty, Deyasini, Colby R. Sandate, Luke Isbel, Georg Kempf, Joscha Weiss, Simone Cavadini, Lukas Kater, et al. “Nucleosomes Specify Co-Factor Access to P53.” <i>Molecular Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">https://doi.org/10.1016/j.molcel.2025.06.027</a>.","short":"D. Chakraborty, C.R. Sandate, L. Isbel, G. Kempf, J. Weiss, S. Cavadini, L. Kater, J. Seebacher, Z. Kozicka, L. Stoos, R.S. Grand, D. Schübeler, A.K. Michael, N.H. Thomä, Molecular Cell 85 (2025) 2919–2936.e12.","ieee":"D. Chakraborty <i>et al.</i>, “Nucleosomes specify co-factor access to p53,” <i>Molecular Cell</i>, vol. 85, no. 15. Cell Press, p. 2919–2936.e12, 2025.","mla":"Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.” <i>Molecular Cell</i>, vol. 85, no. 15, Cell Press, 2025, p. 2919–2936.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">10.1016/j.molcel.2025.06.027</a>.","ista":"Chakraborty D, Sandate CR, Isbel L, Kempf G, Weiss J, Cavadini S, Kater L, Seebacher J, Kozicka Z, Stoos L, Grand RS, Schübeler D, Michael AK, Thomä NH. 2025. Nucleosomes specify co-factor access to p53. Molecular Cell. 85(15), 2919–2936.e12.","ama":"Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access to p53. <i>Molecular Cell</i>. 2025;85(15):2919-2936.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">10.1016/j.molcel.2025.06.027</a>","apa":"Chakraborty, D., Sandate, C. R., Isbel, L., Kempf, G., Weiss, J., Cavadini, S., … Thomä, N. H. (2025). Nucleosomes specify co-factor access to p53. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">https://doi.org/10.1016/j.molcel.2025.06.027</a>"},"date_updated":"2026-10-20T08:50:29Z","author":[{"last_name":"Chakraborty","first_name":"Deyasini","full_name":"Chakraborty, Deyasini"},{"last_name":"Sandate","first_name":"Colby R.","full_name":"Sandate, Colby R."},{"first_name":"Luke","last_name":"Isbel","full_name":"Isbel, Luke"},{"last_name":"Kempf","first_name":"Georg","full_name":"Kempf, Georg"},{"full_name":"Weiss, Joscha","last_name":"Weiss","first_name":"Joscha"},{"first_name":"Simone","last_name":"Cavadini","full_name":"Cavadini, Simone"},{"first_name":"Lukas","last_name":"Kater","full_name":"Kater, Lukas"},{"full_name":"Seebacher, Jan","last_name":"Seebacher","first_name":"Jan"},{"last_name":"Kozicka","first_name":"Zuzanna","full_name":"Kozicka, Zuzanna"},{"last_name":"Stoos","first_name":"Lisa","full_name":"Stoos, Lisa"},{"last_name":"Grand","first_name":"Ralph S.","full_name":"Grand, Ralph S."},{"last_name":"Schübeler","first_name":"Dirk","full_name":"Schübeler, Dirk"},{"orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia"},{"first_name":"Nicolas H.","last_name":"Thomä","full_name":"Thomä, Nicolas H."}],"OA_place":"publisher","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2919-2936.e12","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2025-09-24T07:54:03Z","oa":1,"fulldoi":"https://doi.org/10.1016/j.molcel.2025.06.027","title":"Nucleosomes specify co-factor access to p53","file":[{"success":1,"date_updated":"2025-09-24T07:54:03Z","relation":"main_file","access_level":"open_access","file_name":"2025_MolecularCell_Chakraborty.pdf","content_type":"application/pdf","date_created":"2025-09-24T07:54:03Z","file_id":"20386","file_size":41813494,"checksum":"e60390ca629b350af3221d4718ca6534","creator":"dernst"}],"publication_status":"published","OA_type":"hybrid","type":"journal_article","ddc":["570"],"status":"public"},{"corr_author":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1137-1139","language":[{"iso":"eng"}],"title":"Unlocking plant regeneration: The role for glutathione","publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.devcel.2025.03.012","status":"public","OA_type":"closed access","type":"journal_article","quality_controlled":"1","pmid":1,"issue":"8","intvolume":"        60","volume":60,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"article_type":"letter_note","oa_version":"None","month":"04","publisher":"Cell Press","external_id":{"pmid":["40262524"],"isi":["001477400800001"]},"_id":"19594","department":[{"_id":"EvBe"}],"abstract":[{"text":"In this issue of Developmental Cell, Lee et al. identify a pivotal role for glutathione (GSH) in plant regeneration, a vital biological process enabling plants to regrow tissues and organs after injury. Applying single-cell RNA sequencing (scRNA-seq) and live imaging, the authors demonstrate that GSH, released upon tissue damage, accelerates cell-cycle transitions, particularly shortening the G1 phase, thereby facilitating efficient organ regeneration.","lang":"eng"}],"scopus_import":"1","doi":"10.1016/j.devcel.2025.03.012","day":"21","date_published":"2025-04-21T00:00:00Z","author":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"date_updated":"2026-10-20T08:24:38Z","year":"2025","date_created":"2025-04-20T22:01:28Z","citation":{"short":"E. Benková, Developmental Cell 60 (2025) 1137–1139.","ieee":"E. Benková, “Unlocking plant regeneration: The role for glutathione,” <i>Developmental Cell</i>, vol. 60, no. 8. Cell Press, pp. 1137–1139, 2025.","mla":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>, vol. 60, no. 8, Cell Press, 2025, pp. 1137–39, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>.","chicago":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>.","apa":"Benková, E. (2025). Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>","ama":"Benková E. Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. 2025;60(8):1137-1139. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>","ista":"Benková E. 2025. Unlocking plant regeneration: The role for glutathione. Developmental Cell. 60(8), 1137–1139."},"publication":"Developmental Cell"},{"publication_status":"published","file":[{"success":1,"relation":"main_file","date_updated":"2025-06-10T07:24:46Z","date_created":"2025-06-10T07:24:46Z","content_type":"application/pdf","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","access_level":"open_access","file_id":"19802","file_size":7238179,"creator":"dernst","checksum":"4018c833f25a3ad3b57e3577fed70334"}],"project":[{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","fulldoi":"https://doi.org/10.1016/j.bpr.2025.100211","status":"public","ec_funded":1,"ddc":["570"],"type":"journal_article","OA_type":"gold","corr_author":"1","OA_place":"publisher","related_material":{"record":[{"id":"20206","status":"public","relation":"dissertation_contains"},{"status":"public","id":"22744","relation":"dissertation_contains"}]},"oa":1,"file_date_updated":"2025-06-10T07:24:46Z","has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.","lang":"eng"}],"scopus_import":"1","DOAJ_listed":"1","date_published":"2025-06-11T00:00:00Z","day":"11","doi":"10.1016/j.bpr.2025.100211","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"author":[{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501"},{"id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","first_name":"Nikolai","last_name":"Semenov","full_name":"Semenov, Nikolai"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Javoor, Manjunath","orcid":"0000-0003-2311-2112","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","last_name":"Javoor"},{"last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina"},{"last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie"},{"last_name":"Tavakoli","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba"},{"full_name":"Suplata, Marek","last_name":"Suplata","id":"EE8452B8-C26A-11E9-B157-E80CE6697425","first_name":"Marek"},{"last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"},{"last_name":"Wartak","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","first_name":"Andreas","full_name":"Wartak, Andreas"},{"last_name":"Schur","first_name":"Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian Km"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-20T08:55:34Z","citation":{"mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Cell Press, 2025.","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211."},"date_created":"2025-06-08T22:01:22Z","year":"2025","publication":"Biophysical Reports","quality_controlled":"1","issue":"2","article_number":"100211","intvolume":"         5","article_type":"original","publication_identifier":{"eissn":["2667-0747"]},"volume":5,"publisher":"Cell Press","oa_version":"Published Version","month":"06","acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work 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 (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"_id":"19795"},{"OA_place":"publisher","related_material":{"link":[{"url":"https://github.com/marioni-group/Metabolic_trait","relation":"software"}]},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2025-01-08T09:26:42Z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"106-115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts","file":[{"creator":"dernst","checksum":"891d120554f07da2c35d38388c29a690","file_size":2266488,"file_id":"18776","content_type":"application/pdf","date_created":"2025-01-08T09:26:42Z","access_level":"open_access","file_name":"2025_AJHG_Smith.pdf","relation":"main_file","date_updated":"2025-01-08T09:26:42Z","success":1}],"isi":1,"fulldoi":"https://doi.org/10.1016/j.ajhg.2024.11.012","status":"public","ddc":["570"],"type":"journal_article","OA_type":"hybrid","quality_controlled":"1","issue":"1","pmid":1,"intvolume":"       112","article_type":"original","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"volume":112,"publisher":"Cell Press","oa_version":"Published Version","month":"01","external_id":{"pmid":["39706196"],"isi":["001412498600001"]},"department":[{"_id":"MaRo"}],"_id":"18754","scopus_import":"1","abstract":[{"lang":"eng","text":"Exploring the molecular correlates of metabolic health measures may identify their shared and unique biological processes and pathways. Molecular proxies of these traits may also provide a more objective approach to their measurement. Here, DNA methylation (DNAm) data were used in epigenome-wide association studies (EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000 volunteers from the Generation Scotland (GS) cohort. We observed a maximum of 12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression EWAS. By contrast, a joint and conditional Bayesian penalized regression approach yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936 [LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance in the measured traits, respectively. The corresponding results in LBC1936 were 14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat, where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05). Accounting for the correlation structure across the methylome can vastly affect the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly applicable across populations and can reflect differences in cognition."}],"day":"02","date_published":"2025-01-02T00:00:00Z","doi":"10.1016/j.ajhg.2024.11.012","author":[{"full_name":"Smith, Hannah M.","last_name":"Smith","first_name":"Hannah M."},{"full_name":"Ng, Hong Kiat","last_name":"Ng","first_name":"Hong Kiat"},{"full_name":"Moodie, Joanna E.","last_name":"Moodie","first_name":"Joanna E."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"full_name":"Mccartney, Daniel L.","first_name":"Daniel L.","last_name":"Mccartney"},{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"full_name":"Redmond, Paul","first_name":"Paul","last_name":"Redmond"},{"full_name":"Taylor, Adele","last_name":"Taylor","first_name":"Adele"},{"full_name":"Page, Danielle","first_name":"Danielle","last_name":"Page"},{"full_name":"Corley, Janie","last_name":"Corley","first_name":"Janie"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"full_name":"Tay, Darwin","last_name":"Tay","first_name":"Darwin"},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Chambers, John C.","first_name":"John C.","last_name":"Chambers"},{"last_name":"Loh","first_name":"Marie","full_name":"Loh, Marie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"},{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."}],"date_updated":"2026-10-20T08:53:52Z","citation":{"ista":"Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A, Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal of Human Genetics. 112(1), 106–115.","ama":"Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. 2025;112(1):106-115. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>","apa":"Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu, E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>","chicago":"Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>.","mla":"Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>, vol. 112, no. 1, Cell Press, 2025, pp. 106–15, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>.","short":"H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu, A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J. Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni, R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.","ieee":"H. M. Smith <i>et al.</i>, “DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts,” <i>American Journal of Human Genetics</i>, vol. 112, no. 1. Cell Press, pp. 106–115, 2025."},"year":"2025","date_created":"2025-01-05T23:01:56Z","publication":"American Journal of Human Genetics"},{"article_number":"116080","issue":"8","quality_controlled":"1","volume":44,"article_type":"original","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"intvolume":"        44","external_id":{"isi":["001544472300002"]},"month":"08","oa_version":"Published Version","publisher":"Cell Press","_id":"20099","department":[{"_id":"PeJo"}],"acknowledgement":"We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically reading an earlier version of the manuscript. We also thank Florian Marr and Christina Altmutter for excellent technical assistance, Alois Schlögl for programming and data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.) and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).","doi":"10.1016/j.celrep.2025.116080","DOAJ_listed":"1","day":"01","date_published":"2025-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3."}],"scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_updated":"2026-10-20T08:55:57Z","author":[{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Vargas Barroso, Victor M","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"}],"publication":"Cell Reports","date_created":"2025-08-03T22:01:30Z","year":"2025","citation":{"ama":"Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>","ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","apa":"Watson, J., Vargas Barroso, V. M., &#38; Jonas, P. M. (2025). Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>","chicago":"Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>.","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).","ieee":"J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes information flow through hippocampal CA3,” <i>Cell Reports</i>, vol. 44, no. 8. Cell Press, 2025.","mla":"Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>, vol. 44, no. 8, 116080, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>."},"PlanS_conform":"1","OA_place":"publisher","corr_author":"1","article_processing_charge":"Yes","file_date_updated":"2025-08-04T06:53:07Z","has_accepted_license":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"name":"Neuronal circuits in health and disease (Jonas)","_id":"0a6c8641-b036-11f1-bacf-e4eec62b5bb4","grant_number":"COE16"}],"title":"Cell-specific wiring routes information flow through hippocampal CA3","file":[{"success":1,"date_updated":"2025-08-04T06:53:07Z","relation":"main_file","access_level":"open_access","file_name":"2025_CellReports_Watson.pdf","content_type":"application/pdf","date_created":"2025-08-04T06:53:07Z","file_size":27695214,"file_id":"20106","checksum":"556ff9760661ecd23949d75031043b1f","creator":"dernst"}],"publication_status":"published","fulldoi":"https://doi.org/10.1016/j.celrep.2025.116080","isi":1,"status":"public","OA_type":"gold","type":"journal_article","ddc":["570"],"ec_funded":1},{"publication_identifier":{"issn":["2663-337X"]},"_id":"20206","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"acknowledgement":"The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. ","oa_version":"Published Version","month":"08","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"doi":"10.15479/AT-ISTA-20206","day":"25","date_published":"2025-08-25T00:00:00Z","abstract":[{"text":"The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n","lang":"eng"}],"supervisor":[{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"date_created":"2025-08-22T08:12:55Z","year":"2025","citation":{"chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>.","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","mla":"Vorlaufer, Jakob. <i>Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>.","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria.","ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>","apa":"Vorlaufer, J. (2025). <i>Construction of a cryo-super-resolution microscope to guide in situ structure analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>"},"date_updated":"2026-10-20T08:55:33Z","author":[{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer"}],"OA_place":"publisher","corr_author":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"107","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"file_date_updated":"2025-08-25T13:49:56Z","article_processing_charge":"No","has_accepted_license":"1","oa":1,"related_material":{"record":[{"id":"19795","status":"public","relation":"part_of_dissertation"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-20206","title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","file":[{"checksum":"191db3367c19c9b32b65f4bc3a7c19de","creator":"jvorlauf","file_id":"20228","file_size":39735535,"access_level":"closed","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","date_created":"2025-08-25T13:49:55Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-08-25T13:49:55Z","relation":"source_file"},{"file_size":10947446,"file_id":"20229","checksum":"104400e6036921569610230c1d4899dc","creator":"jvorlauf","relation":"main_file","success":1,"date_updated":"2025-08-25T13:49:56Z","access_level":"open_access","file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","content_type":"application/pdf","date_created":"2025-08-25T13:49:56Z"}],"project":[{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"}],"publication_status":"published","type":"dissertation","ddc":["621","535"],"degree_awarded":"PhD","status":"public"},{"day":"07","date_published":"2025-05-07T00:00:00Z","doi":"10.1016/j.neuron.2025.02.025","scopus_import":"1","abstract":[{"lang":"eng","text":"Hippocampal reactivation of waking neuronal assemblies in sleep is a key initial step of systems consolidation. Nevertheless, it is unclear whether reactivated assemblies are static or whether they reorganize gradually over prolonged sleep. We tracked reactivated CA1 assembly patterns over ∼20 h of sleep/rest periods and related them to assemblies seen before or after in a spatial learning paradigm using rats. We found that reactivated assembly patterns were gradually transformed and started to resemble those seen in the subsequent recall session. Periods of rapid eye movement (REM) sleep and non-REM (NREM) had antagonistic roles: whereas NREM accelerated the assembly drift, REM countered it. Moreover, only a subset of rate-changing pyramidal cells contributed to the drift, whereas stable-firing-rate cells maintained unaltered reactivation patterns. Our data suggest that prolonged sleep promotes the spontaneous reorganization of spatial assemblies, which can contribute to daily cognitive map changes or encoding new learning situations."}],"date_updated":"2026-10-20T08:54:27Z","author":[{"full_name":"Bollmann, Lars","last_name":"Bollmann","first_name":"Lars","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","full_name":"Baracskay, Peter"},{"full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"publication":"Neuron","citation":{"chicago":"Bollmann, Lars, Peter Baracskay, Federico Stella, and Jozsef L Csicsvari. “Sleep Stages Antagonistically Modulate Reactivation Drift.” <i>Neuron</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">https://doi.org/10.1016/j.neuron.2025.02.025</a>.","short":"L. Bollmann, P. Baracskay, F. Stella, J.L. Csicsvari, Neuron 113 (2025) 1446–1459.e6.","ieee":"L. Bollmann, P. Baracskay, F. Stella, and J. L. Csicsvari, “Sleep stages antagonistically modulate reactivation drift,” <i>Neuron</i>, vol. 113, no. 9. Cell Press, p. 1446–1459.e6, 2025.","mla":"Bollmann, Lars, et al. “Sleep Stages Antagonistically Modulate Reactivation Drift.” <i>Neuron</i>, vol. 113, no. 9, Cell Press, 2025, p. 1446–1459.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">10.1016/j.neuron.2025.02.025</a>.","ama":"Bollmann L, Baracskay P, Stella F, Csicsvari JL. Sleep stages antagonistically modulate reactivation drift. <i>Neuron</i>. 2025;113(9):1446-1459.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">10.1016/j.neuron.2025.02.025</a>","ista":"Bollmann L, Baracskay P, Stella F, Csicsvari JL. 2025. Sleep stages antagonistically modulate reactivation drift. Neuron. 113(9), 1446–1459.e6.","apa":"Bollmann, L., Baracskay, P., Stella, F., &#38; Csicsvari, J. L. (2025). Sleep stages antagonistically modulate reactivation drift. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">https://doi.org/10.1016/j.neuron.2025.02.025</a>"},"year":"2025","date_created":"2025-04-06T22:01:32Z","pmid":1,"issue":"9","quality_controlled":"1","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"article_type":"original","volume":113,"intvolume":"       113","external_id":{"isi":["001510440400001"],"pmid":["40132588"]},"publisher":"Cell Press","oa_version":"Published Version","month":"05","department":[{"_id":"JoCs"}],"_id":"19506","acknowledgement":"We thank Andrea Cumpelik, Lisa Genzel, and Freya Ólafsdóttir for comments on an earlier version of the manuscript. This work was supported by the European Research Council (281511) and Austrian Science Fund (FWF I3713).","publication_status":"published","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511"},{"call_identifier":"FWF","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425","grant_number":"I 3713-B27"}],"file":[{"content_type":"application/pdf","date_created":"2025-08-05T12:43:44Z","access_level":"open_access","file_name":"2025_Neuron_Bollmann.pdf","date_updated":"2025-08-05T12:43:44Z","success":1,"relation":"main_file","creator":"dernst","checksum":"5e57852a45a78a751dd3a5e807bf015f","file_id":"20133","file_size":27047730}],"title":"Sleep stages antagonistically modulate reactivation drift","fulldoi":"https://doi.org/10.1016/j.neuron.2025.02.025","isi":1,"status":"public","type":"journal_article","OA_type":"hybrid","ddc":["570"],"ec_funded":1,"PlanS_conform":"1","corr_author":"1","OA_place":"publisher","file_date_updated":"2025-08-05T12:43:44Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/","relation":"press_release","description":"News on ISTA website"}]},"oa":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1446-1459.e6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"820-827.e4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/paloha/faket/"}]},"file_date_updated":"2025-08-05T12:15:13Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","OA_place":"publisher","corr_author":"1","PlanS_conform":"1","ddc":["570"],"OA_type":"hybrid","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1016/j.str.2025.01.020","file":[{"file_size":4367530,"file_id":"20130","creator":"dernst","checksum":"f346bc357a66a88cca3d0eb95793fb73","success":1,"relation":"main_file","date_updated":"2025-08-05T12:15:13Z","date_created":"2025-08-05T12:15:13Z","content_type":"application/pdf","access_level":"open_access","file_name":"2025_Structure_Harar.pdf"}],"title":"FakET: Simulating cryo-electron tomograms with neural style transfer","publication_status":"published","acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","_id":"19443","department":[{"_id":"AlMi"}],"oa_version":"Published Version","month":"04","publisher":"Cell Press","external_id":{"pmid":["39947174"],"isi":["001463196100001"]},"intvolume":"        33","volume":33,"publication_identifier":{"issn":["0969-2126"],"eissn":["1878-4186"]},"article_type":"original","quality_controlled":"1","issue":"4","pmid":1,"year":"2025","date_created":"2025-03-23T23:01:27Z","citation":{"chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Cell Press, p. 820–827.e4, 2025.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Cell Press, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.","ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4. doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>","apa":"Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>"},"publication":"Structure","author":[{"full_name":"Harar, Pavol","orcid":"0000-0001-5206-1794","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","first_name":"Pavol","last_name":"Harar"},{"last_name":"Herrmann","first_name":"Lukas","full_name":"Herrmann, Lukas"},{"last_name":"Grohs","first_name":"Philipp","full_name":"Grohs, Philipp"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"}],"date_updated":"2026-10-20T08:54:10Z","scopus_import":"1","abstract":[{"text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.","lang":"eng"}],"doi":"10.1016/j.str.2025.01.020","date_published":"2025-04-03T00:00:00Z","day":"03"},{"date_updated":"2026-10-20T08:54:50Z","author":[{"full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"Hetzer"},{"full_name":"Toda, Tomohisa","last_name":"Toda","first_name":"Tomohisa"}],"publication":"Trends in Neurosciences","citation":{"short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.","ieee":"M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” <i>Trends in Neurosciences</i>, vol. 48, no. 9. Cell Press, pp. 645–654, 2025.","mla":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>, vol. 48, no. 9, Cell Press, 2025, pp. 645–54, doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>.","chicago":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>.","apa":"Hetzer, M., &#38; Toda, T. (2025). Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>","ama":"Hetzer M, Toda T. Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. 2025;48(9):645-654. doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>","ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 645–654."},"date_created":"2025-08-10T22:01:29Z","year":"2025","date_published":"2025-09-01T00:00:00Z","day":"01","doi":"10.1016/j.tins.2025.07.004","scopus_import":"1","abstract":[{"text":"In long-lived mammals, including humans, brain cell homeostasis is critical for maintaining brain function throughout life. Most neurons are generated during development and must maintain their cellular identity and plasticity to preserve brain function. Although extensive studies indicate the importance of recycling and regenerating cellular molecules to maintain cellular homeostasis, recent evidence has shown that some proteins and RNAs do not turn over for months and even years. We propose that these long-lived cellular molecules may be the basis for maintaining brain function in the long term, but also a potential convergent target of brain aging. We highlight key discoveries and challenges, and propose potential directions to unravel the mystery of brain cell longevity.","lang":"eng"}],"external_id":{"pmid":["40744775"],"isi":["001568965400001"]},"publisher":"Cell Press","month":"09","oa_version":"Published Version","department":[{"_id":"MaHe"}],"_id":"20154","acknowledgement":"The work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872 – T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG, 101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank Dr Laura J. Harrison for editing assistance.","pmid":1,"issue":"9","quality_controlled":"1","publication_identifier":{"issn":["0166-2236"],"eissn":["1878-108X"]},"article_type":"original","volume":48,"intvolume":"        48","status":"public","type":"journal_article","OA_type":"hybrid","ddc":["570"],"publication_status":"published","title":"Long-lived cellular molecules in the brain","file":[{"creator":"dernst","checksum":"90942491b499f70b0bf48b8aec2e7387","file_id":"20873","file_size":327847,"content_type":"application/pdf","date_created":"2025-12-29T13:47:27Z","file_name":"2025_TrendsNeurosciences_Hetzer.pdf","access_level":"open_access","success":1,"date_updated":"2025-12-29T13:47:27Z","relation":"main_file"}],"fulldoi":"https://doi.org/10.1016/j.tins.2025.07.004","isi":1,"has_accepted_license":"1","file_date_updated":"2025-12-29T13:47:27Z","article_processing_charge":"Yes (in subscription journal)","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"page":"645-654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","corr_author":"1","OA_place":"publisher"},{"scopus_import":"1","abstract":[{"text":"Animal cells migrating up chemotactic gradients often show speed oscillations. A new study describes a molecular circuit that switches zebrafish germ cells between phases of straight runs, tumbling and directional reorientation.","lang":"eng"}],"date_published":"2025-09-22T00:00:00Z","day":"22","doi":"10.1016/j.cub.2025.08.016","author":[{"last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang","full_name":"Li, Ziqiang"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"date_updated":"2026-10-20T08:55:09Z","citation":{"chicago":"LI, ZIQIANG, and Michael K Sixt. “Cell Migration: How Animal Cells Run and Tumble.” <i>Current Biology</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">https://doi.org/10.1016/j.cub.2025.08.016</a>.","mla":"LI, ZIQIANG, and Michael K. Sixt. “Cell Migration: How Animal Cells Run and Tumble.” <i>Current Biology</i>, vol. 35, no. 18, Cell Press, 2025, pp. R890–92, doi:<a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">10.1016/j.cub.2025.08.016</a>.","ieee":"Z. LI and M. K. Sixt, “Cell migration: How animal cells run and tumble,” <i>Current Biology</i>, vol. 35, no. 18. Cell Press, pp. R890–R892, 2025.","short":"Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892.","ama":"LI Z, Sixt MK. Cell migration: How animal cells run and tumble. <i>Current Biology</i>. 2025;35(18):R890-R892. doi:<a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">10.1016/j.cub.2025.08.016</a>","ista":"LI Z, Sixt MK. 2025. Cell migration: How animal cells run and tumble. Current Biology. 35(18), R890–R892.","apa":"LI, Z., &#38; Sixt, M. K. (2025). Cell migration: How animal cells run and tumble. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">https://doi.org/10.1016/j.cub.2025.08.016</a>"},"date_created":"2025-10-05T22:01:35Z","year":"2025","publication":"Current Biology","quality_controlled":"1","pmid":1,"issue":"18","intvolume":"        35","publication_identifier":{"eissn":["1879-0445"]},"article_type":"letter_note","volume":35,"publisher":"Cell Press","oa_version":"None","month":"09","external_id":{"pmid":["40987270"],"isi":["001592664700001"]},"department":[{"_id":"MiSi"}],"_id":"20427","publication_status":"published","title":"Cell migration: How animal cells run and tumble","isi":1,"fulldoi":"https://doi.org/10.1016/j.cub.2025.08.016","status":"public","type":"journal_article","OA_type":"closed access","corr_author":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"R890-R892"},{"pmid":1,"issue":"5","quality_controlled":"1","volume":60,"researchdata_availability":"yes","article_type":"original","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"intvolume":"        60","external_id":{"isi":["001444798600001"],"pmid":["39603234"]},"oa_version":"Published Version","month":"03","publisher":"Cell Press","_id":"15016","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"acknowledgement":"We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).","doi":"10.1016/j.devcel.2024.10.025","date_published":"2025-03-10T00:00:00Z","day":"10","scopus_import":"1","abstract":[{"lang":"eng","text":"Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution."}],"das_tickbox":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"date_updated":"2026-10-20T08:56:33Z","author":[{"first_name":"Eliza C.B.","last_name":"Jaeger","full_name":"Jaeger, Eliza C.B."},{"full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941","first_name":"David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic"},{"full_name":"Deryckere, Astrid","first_name":"Astrid","last_name":"Deryckere"},{"first_name":"Nikol","last_name":"Zorin","full_name":"Zorin, Nikol"},{"last_name":"Nguyen","first_name":"Akemi L.","full_name":"Nguyen, Akemi L."},{"orcid":"0009-0002-3999-3735","full_name":"Ivanian, Georgiy","last_name":"Ivanian","first_name":"Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05"},{"full_name":"Woych, Jamie","first_name":"Jamie","last_name":"Woych"},{"full_name":"Arnold, Rebecca C","first_name":"Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f","last_name":"Arnold"},{"full_name":"Ortega Gurrola, Alonso","first_name":"Alonso","last_name":"Ortega Gurrola"},{"last_name":"Shvartsman","first_name":"Arik","full_name":"Shvartsman, Arik"},{"last_name":"Barbieri","id":"a9492887-8972-11ed-ae7b-bfae10998254","first_name":"Francesca","full_name":"Barbieri, Francesca"},{"full_name":"Toma, Florina-Alexandra","last_name":"Toma","first_name":"Florina-Alexandra","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5"},{"full_name":"Gorbsky, Gary J.","last_name":"Gorbsky","first_name":"Gary J."},{"full_name":"Horb, Marko E.","first_name":"Marko E.","last_name":"Horb"},{"first_name":"Hollis T.","last_name":"Cline","full_name":"Cline, Hollis T."},{"full_name":"Shay, Timothy F.","first_name":"Timothy F.","last_name":"Shay"},{"first_name":"Darcy B.","last_name":"Kelley","full_name":"Kelley, Darcy B."},{"first_name":"Ayako","last_name":"Yamaguchi","full_name":"Yamaguchi, Ayako"},{"full_name":"Shein-Idelson, Mark","first_name":"Mark","last_name":"Shein-Idelson"},{"full_name":"Tosches, Maria Antonietta","first_name":"Maria Antonietta","last_name":"Tosches"},{"orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"publication":"Developmental Cell","date_created":"2024-02-20T09:20:32Z","year":"2025","citation":{"apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. 2025;60(5):794-812.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>Developmental Cell</i>, vol. 60, no. 5. Cell Press, p. 794–812.e6, 2025.","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>, vol. 60, no. 5, Cell Press, 2025, p. 794–812.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>.","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>."},"supplementarymaterial":"yes","OA_place":"publisher","corr_author":"1","file_date_updated":"2025-06-04T05:43:27Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"22667"},{"status":"public","id":"22803","relation":"research_data"}]},"dataavailabilitystatement":"FAMD RStudio code and raw data used for analysis of post-metamorphic P. waltl injection outcomes are available via Dryad repository: https://doi.org/10.5061/dryad.mpg4f4r89. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","page":"794-812.e6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"project":[{"grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis"},{"name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","grant_number":"F7814","name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity"}],"file":[{"relation":"main_file","success":1,"date_updated":"2025-06-04T05:43:27Z","access_level":"open_access","file_name":"2025_DevelopmentalCell_Jaeger.pdf","content_type":"application/pdf","date_created":"2025-06-04T05:43:27Z","file_id":"19790","file_size":11936258,"checksum":"a83a4cb58f5941096d3ad91ca0172594","creator":"dernst"}],"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.025","isi":1,"status":"public","OA_type":"hybrid","type":"journal_article","ddc":["570"]},{"OA_type":"gold","type":"journal_article","ddc":["580"],"status":"public","fulldoi":"https://doi.org/10.1016/j.xplc.2024.101181","isi":1,"title":"Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1","file":[{"file_size":4443183,"file_id":"19575","creator":"dernst","checksum":"7b0e4511e43cc0da06730c3edb7c1167","relation":"main_file","success":1,"date_updated":"2025-04-16T09:02:05Z","content_type":"application/pdf","date_created":"2025-04-16T09:02:05Z","file_name":"2025_PlantComm_Wei.pdf","access_level":"open_access"}],"publication_status":"published","dataavailabilitystatement":"The ABCB1 structures in the substrate-unbound state, BL-bound state, and ATP plus BL-bound state have been deposited in the Protein Data Bank under accession codes 8ZPX, 8ZPZ, and 8ZQ4, respectively. The corresponding cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under accession codes EMD-60366, EMD-60369, and EMD-60370, respectively.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2025-04-16T09:02:05Z","article_processing_charge":"Yes","has_accepted_license":"1","oa":1,"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","supplementarymaterial":"yes","publication":"Plant Communications","date_created":"2024-12-04T11:21:16Z","year":"2025","citation":{"apa":"Wei, H., Zhu, H., Ying, W., Janssens, H., Kvasnica, M., Winne, J., … Sun, L. (2025). Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. <i>Plant Communications</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">https://doi.org/10.1016/j.xplc.2024.101181</a>","ama":"Wei H, Zhu H, Ying W, et al. Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. <i>Plant Communications</i>. 2025;6(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">10.1016/j.xplc.2024.101181</a>","ista":"Wei H, Zhu H, Ying W, Janssens H, Kvasnica M, Winne J, Gao Y, Friml J, Ma Q, Tan S, Liu X, Russinova E, Sun L. 2025. Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications. 6(1), 101181.","mla":"Wei, H., et al. “Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC Transporter ABCB1.” <i>Plant Communications</i>, vol. 6, no. 1, 101181, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">10.1016/j.xplc.2024.101181</a>.","short":"H. Wei, H. Zhu, W. Ying, H. Janssens, M. Kvasnica, J. Winne, Y. Gao, J. Friml, Q. Ma, S. Tan, X. Liu, E. Russinova, L. Sun, Plant Communications 6 (2025).","ieee":"H. Wei <i>et al.</i>, “Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1,” <i>Plant Communications</i>, vol. 6, no. 1. Cell Press, 2025.","chicago":"Wei, H, H Zhu, W Ying, H Janssens, M Kvasnica, JM Winne, Y Gao, et al. “Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC Transporter ABCB1.” <i>Plant Communications</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">https://doi.org/10.1016/j.xplc.2024.101181</a>."},"date_updated":"2026-10-20T08:56:15Z","author":[{"first_name":"H","last_name":"Wei","full_name":"Wei, H"},{"first_name":"H","last_name":"Zhu","full_name":"Zhu, H"},{"first_name":"W","last_name":"Ying","full_name":"Ying, W"},{"full_name":"Janssens, H","last_name":"Janssens","first_name":"H"},{"full_name":"Kvasnica, M","first_name":"M","last_name":"Kvasnica"},{"last_name":"Winne","first_name":"JM","full_name":"Winne, JM"},{"last_name":"Gao","first_name":"Y","full_name":"Gao, Y"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Q","last_name":"Ma","full_name":"Ma, Q"},{"last_name":"Tan","first_name":"S","full_name":"Tan, S"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"first_name":"E","last_name":"Russinova","full_name":"Russinova, E"},{"full_name":"Sun, L","last_name":"Sun","first_name":"L"}],"das_tickbox":"1","doi":"10.1016/j.xplc.2024.101181","DOAJ_listed":"1","date_published":"2025-01-13T00:00:00Z","day":"13","abstract":[{"lang":"eng","text":"Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signalling initiation, which requires binding of BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure, BL was bound to the hydrophobic cavity formed by the transmembrane domain, and triggered local conformational changes. Together, our data provide additional insights into the ABC transporter-mediated BR export."}],"scopus_import":"1","_id":"18619","department":[{"_id":"JiFr"}],"acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We thank Yaowei Wang, Yongming Luo, and Nemanja Vukašinović (VIB-UGhent, Belgium) for useful discussions and technical support. L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation. No conflict of interest is declared.","external_id":{"pmid":["39497419"],"isi":["001416757300001"]},"oa_version":"Published Version","month":"01","publisher":"Cell Press","researchdata_availability":"yes","volume":6,"article_type":"original","publication_identifier":{"issn":["2590-3462"]},"intvolume":"         6","issue":"1","pmid":1,"article_number":"101181","quality_controlled":"1"},{"OA_type":"hybrid","type":"journal_article","ddc":["580"],"ec_funded":1,"status":"public","fulldoi":"https://doi.org/10.1093/plcell/koaf006","isi":1,"file":[{"file_size":53904111,"file_id":"20092","checksum":"9d3f8218ff37a29f29c48a7bbe831bd3","creator":"dernst","success":1,"date_updated":"2025-07-31T07:03:43Z","relation":"main_file","access_level":"open_access","file_name":"2025_PlantCell_Gallei.pdf","content_type":"application/pdf","date_created":"2025-07-31T07:03:43Z"}],"title":"Super-resolution expansion microscopy in plant roots","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"269B5B22-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-07-31T07:03:43Z","oa":1,"related_material":{"record":[{"id":"18837","status":"public","relation":"research_data"},{"relation":"earlier_version","id":"18689","status":"public"}]},"OA_place":"publisher","corr_author":"1","PlanS_conform":"1","publication":"The Plant Cell","date_created":"2025-02-05T06:52:06Z","year":"2025","citation":{"chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>.","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots. The Plant Cell. 37(4), koaf006.","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>"},"date_updated":"2026-10-20T09:19:12Z","author":[{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","last_name":"Inumella","full_name":"Inumella, Syamala","orcid":"0009-0002-5890-120X"},{"last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","last_name":"Tavakoli"},{"last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","last_name":"Vorlaufer"},{"last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"M-Shop"}],"doi":"10.1093/plcell/koaf006","day":"01","date_published":"2025-04-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. ","lang":"eng"}],"_id":"19003","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis project has received funding from the European Research Council under the Horizon 2020 Framework Programme (grant agreement No 742985, J.F.). It has also received funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018). M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship no. 26137. The project has further received funding from the Austrian Science Fund, via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship from the Human Frontier Science Program (LT000557/2018). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","external_id":{"isi":["001462763100001"],"pmid":["39792900"]},"month":"04","oa_version":"Published Version","publisher":"Oxford University Press","volume":37,"article_type":"original","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"intvolume":"        37","article_number":"koaf006","issue":"4","pmid":1,"quality_controlled":"1"},{"related_material":{"record":[{"status":"public","id":"22770","relation":"research_data"}]},"oa":1,"article_processing_charge":"Yes","file_date_updated":"2025-10-13T07:54:51Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"The training sets, training scripts, MD input files, and trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit; see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided with this paper. Source data are provided with this paper.","PlanS_conform":"1","supplementarymaterial":"no","corr_author":"1","OA_place":"publisher","status":"public","ddc":["000"],"type":"journal_article","OA_type":"gold","publication_status":"published","title":"Machine learning of charges and long-range interactions from energies and forces","file":[{"file_size":4907055,"file_id":"20460","creator":"dernst","checksum":"34b6005d349bbff85839c4e51d6c8725","date_updated":"2025-10-13T07:54:51Z","success":1,"relation":"main_file","date_created":"2025-10-13T07:54:51Z","content_type":"application/pdf","file_name":"2025_NatureComm_King.pdf","access_level":"open_access"}],"isi":1,"fulldoi":"https://doi.org/10.1038/s41467-025-63852-x","publisher":"Springer Nature","month":"10","oa_version":"Published Version","external_id":{"isi":["001586620700015"],"pmid":["41034200"]},"acknowledgement":"We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq) dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq) dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.","department":[{"_id":"BiCh"}],"_id":"20452","quality_controlled":"1","pmid":1,"article_number":"8763","intvolume":"        16","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","volume":16,"researchdata_availability":"no","author":[{"first_name":"Daniel S.","last_name":"King","full_name":"King, Daniel S."},{"full_name":"Kim, Dongjin","first_name":"Dongjin","last_name":"Kim"},{"first_name":"Peichen","last_name":"Zhong","full_name":"Zhong, Peichen"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"date_updated":"2026-10-20T09:48:07Z","citation":{"ama":"King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>","ista":"King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range interactions from energies and forces. Nature Communications. 16, 8763.","apa":"King, D. S., Kim, D., Zhong, P., &#38; Cheng, B. (2025). Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>","chicago":"King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>.","mla":"King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>, vol. 16, 8763, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>.","ieee":"D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and long-range interactions from energies and forces,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025)."},"date_created":"2025-10-12T22:01:25Z","year":"2025","publication":"Nature Communications","abstract":[{"lang":"eng","text":"Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges."}],"scopus_import":"1","day":"01","date_published":"2025-10-01T00:00:00Z","DOAJ_listed":"1","doi":"10.1038/s41467-025-63852-x","das_tickbox":"1"},{"arxiv":1,"fulldoi":"https://doi.org/10.1371/journal.pcbi.1012868","isi":1,"publication_status":"published","title":"Colonization times in Moran process on graphs","file":[{"file_name":"2025_PloSCompBio_Kopfova.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-05-19T07:45:31Z","success":1,"date_updated":"2025-05-19T07:45:31Z","relation":"main_file","checksum":"73e35151eebd5064972c5a07ffdf2b69","creator":"dernst","file_id":"19709","file_size":6805943}],"type":"journal_article","OA_type":"gold","ddc":["000"],"status":"public","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"e1012868","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2025-05-19T07:45:31Z","oa":1,"day":"01","date_published":"2025-05-01T00:00:00Z","DOAJ_listed":"1","doi":"10.1371/journal.pcbi.1012868","scopus_import":"1","abstract":[{"lang":"eng","text":"Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process."}],"publication":"PLoS Computational Biology","citation":{"chicago":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>. Public Library of Science, 2025. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>.","mla":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>, vol. 21, no. 5, Public Library of Science, 2025, p. e1012868, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>.","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.","ieee":"L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,” <i>PLoS Computational Biology</i>, vol. 21, no. 5. Public Library of Science, p. e1012868, 2025.","ama":"Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. 2025;21(5):e1012868. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>","ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS Computational Biology. 21(5), e1012868.","apa":"Kopfová, L., &#38; Tkadlec, J. (2025). Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>"},"year":"2025","date_created":"2025-05-18T22:02:50Z","date_updated":"2026-10-20T09:45:59Z","author":[{"full_name":"Kopfová, Lenka","first_name":"Lenka","id":"17691681-50b9-11ef-ad56-edf4cacb21b0","last_name":"Kopfová"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","publication_identifier":{"eissn":["1553-7358"]},"volume":21,"intvolume":"        21","issue":"5","quality_controlled":"1","department":[{"_id":"GradSch"}],"_id":"19702","external_id":{"arxiv":["2410.09476"],"isi":["001481670600002"]},"publisher":"Public Library of Science","month":"05","oa_version":"Published Version"}]