[{"doi":"10.15479/AT-ISTA-20741","day":"09","file_date_updated":"2025-12-10T13:09:58Z","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"}],"abstract":[{"lang":"eng","text":"Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. \r\n\r\nFirstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. \r\n\r\nNext, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. \r\n\r\nFinally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. "}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","month":"12","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-073-2"]},"has_accepted_license":"1","article_processing_charge":"No","file":[{"access_level":"closed","file_size":142876975,"checksum":"a3643d07e93134b2490a566b02a4517d","date_updated":"2025-12-10T13:09:58Z","file_id":"20774","file_name":"2025_marko_kojic_thesis.docx","creator":"mkojic","date_created":"2025-12-10T13:09:58Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"creator":"mkojic","access_level":"open_access","checksum":"0a096f0af6ccc3a8329d5bb8797ad533","date_updated":"2025-12-10T13:09:38Z","file_id":"20775","file_name":"2025_marko_kojic_thesis.pdf","file_size":8597045,"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-12-10T13:09:38Z"}],"degree_awarded":"PhD","year":"2025","_id":"20741","status":"public","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"15118"}]},"date_published":"2025-12-09T00:00:00Z","OA_place":"publisher","title":"Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-20741","citation":{"ama":"Kojic M. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>","apa":"Kojic, M. (2025). <i>Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>","ista":"Kojic M. 2025. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria.","ieee":"M. Kojic, “Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria,” Institute of Science and Technology Austria, 2025.","mla":"Kojic, Marko. <i>Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20741\">10.15479/AT-ISTA-20741</a>.","short":"M. Kojic, Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria, Institute of Science and Technology Austria, 2025.","chicago":"Kojic, Marko. “Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20741\">https://doi.org/10.15479/AT-ISTA-20741</a>."},"date_created":"2025-12-09T13:08:11Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-16T10:35:47Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"license":"https://creativecommons.org/licenses/by/4.0/","oa":1,"author":[{"id":"73e7ecd4-dc85-11ea-9058-88a16394b160","full_name":"Kojic, Marko","first_name":"Marko","orcid":"0000-0001-7244-8128","last_name":"Kojic"}],"ddc":["572"]},{"title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","OA_place":"publisher","OA_type":"gold","type":"dissertation","related_material":{"record":[{"status":"public","id":"12788","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9903","status":"public"},{"relation":"part_of_dissertation","id":"19425","status":"public"},{"id":"14851","status":"public","relation":"part_of_dissertation"},{"id":"15004","status":"public","relation":"part_of_dissertation"}]},"status":"public","date_published":"2025-03-13T00:00:00Z","_id":"19393","degree_awarded":"PhD","year":"2025","file":[{"content_type":"application/pdf","date_created":"2025-03-12T12:56:46Z","relation":"main_file","success":1,"access_level":"open_access","file_name":"thesis_final.pdf","date_updated":"2025-03-12T12:56:46Z","checksum":"d3ab25782c7ea38ce9910e57d25f6733","file_id":"19394","file_size":10625143,"creator":"vkarle"},{"creator":"vkarle","date_updated":"2025-03-20T08:02:35Z","file_name":"thesis.zip","checksum":"3ccfb0aeba4d860d71e18347913034e4","file_id":"19400","file_size":23119202,"access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2025-03-13T13:15:10Z"}],"month":"03","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"eissn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","abstract":[{"lang":"eng","text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies."}],"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko"}],"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19393","day":"13","file_date_updated":"2025-03-20T08:02:35Z","author":[{"last_name":"Karle","orcid":"0000-0002-6963-0129","first_name":"Volker","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"}],"ddc":["530"],"oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-16T12:16:52Z","alternative_title":["ISTA Thesis"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"date_created":"2025-03-12T13:04:59Z","publisher":"Institute of Science and Technology Austria","corr_author":"1","page":"192","citation":{"short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025.","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>.","mla":"Karle, Volker. <i>Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>.","ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025.","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>","apa":"Karle, V. (2025). <i>Non-equilibrium topological phases with periodically driven molecules and quantum rotors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19393"},{"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.).","date_published":"2025-01-23T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","id":"18688","status":"public"}]},"type":"journal_article","status":"public","_id":"18879","year":"2025","file":[{"creator":"dernst","access_level":"open_access","file_name":"2025_Cell_Watson.pdf","file_id":"18884","date_updated":"2025-01-27T08:46:33Z","checksum":"d5a818edc32d249cdf75e1bb5b70a4b7","file_size":14082343,"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-01-27T08:46:33Z"}],"scopus_import":"1","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","OA_place":"publisher","OA_type":"hybrid","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. "}],"issue":"2","publication":"Cell","volume":188,"file_date_updated":"2025-01-27T08:46:33Z","doi":"10.1016/j.cell.2024.11.022","day":"23","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"month":"01","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635"},{"grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"call_identifier":"FWF","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"},{"name":"Synaptic networks of human brain","_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e","grant_number":"PAT 4178023"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:20:04Z","department":[{"_id":"JoDa"},{"_id":"PeJo"},{"_id":"GradSch"}],"ddc":["570"],"author":[{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson"},{"last_name":"Vargas Barroso","first_name":"Victor M","full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morse","full_name":"Morse, Rebecca","first_name":"Rebecca","id":"ceb89ae7-dc8d-11ea-abe3-da3301d0eab4"},{"orcid":"0000-0002-9280-8597","first_name":"Andrea C","full_name":"Navas Olivé, Andrea C","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","last_name":"Navas Olivé"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"first_name":"Matthias","full_name":"Tomschik, Matthias","last_name":"Tomschik"},{"last_name":"Rössler","full_name":"Rössler, Karl","first_name":"Karl"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M"}],"oa":1,"ec_funded":1,"citation":{"ama":"Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. 2025;188(2):501-514.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>","apa":"Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>","ieee":"J. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>Cell</i>, vol. 188, no. 2. Cell Press, p. 501–514.e18, 2025.","ista":"Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18.","mla":"Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>, vol. 188, no. 2, Cell Press, 2025, p. 501–514.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>.","chicago":"Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>.","short":"J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18."},"fulldoi":"https://doi.org/10.1016/j.cell.2024.11.022","external_id":{"pmid":["39667938"],"isi":["001408395600001"]},"page":"501-514.e18","corr_author":"1","intvolume":"       188","article_type":"original","isi":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"publisher":"Cell Press","date_created":"2025-01-26T23:01:49Z"},{"oa":1,"ddc":["570"],"author":[{"last_name":"Tavano","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9970-7804","full_name":"Tavano, Ste","first_name":"Ste"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","first_name":"David","last_name":"Brückner"},{"last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","first_name":"Saren"},{"last_name":"Tong","full_name":"Tong, Xin","first_name":"Xin","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425"},{"first_name":"Roland","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos"},{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer"},{"first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:20:45Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Cell Press","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_created":"2025-03-16T23:01:24Z","DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"        44","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1016/j.celrep.2025.115387","citation":{"short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>.","ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Cell Press, 2025.","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387.","ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>"},"external_id":{"isi":["001443652700001"],"pmid":["40057955"]},"corr_author":"1","OA_type":"gold","scopus_import":"1","OA_place":"publisher","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","year":"2025","file":[{"creator":"dernst","file_size":9067797,"file_name":"2025_CellReports_Tavano.pdf","checksum":"57e05dd1598c807af0afdb32cec039d3","file_id":"19413","date_updated":"2025-03-17T10:26:54Z","access_level":"open_access","success":1,"relation":"main_file","date_created":"2025-03-17T10:26:54Z","content_type":"application/pdf"}],"article_number":"115387","_id":"19404","date_published":"2025-03-25T00:00:00Z","acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","status":"public","type":"journal_article","publication_status":"published","pmid":1,"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"grant_number":"ALTF 1159-2018","_id":"269CD5C4-B435-11E9-9278-68D0E5697425","name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"article_processing_charge":"Yes","has_accepted_license":"1","quality_controlled":"1","month":"03","publication":"Cell Reports","file_date_updated":"2025-03-17T10:26:54Z","volume":44,"issue":"3","doi":"10.1016/j.celrep.2025.115387","day":"25","oa_version":"Published Version","abstract":[{"text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation.","lang":"eng"}]},{"OA_type":"hybrid","OA_place":"publisher","title":"Extensive N4 cytosine methylation is essential for Marchantia sperm function","scopus_import":"1","year":"2025","file":[{"access_level":"open_access","date_updated":"2025-12-29T13:40:32Z","checksum":"0dcc2feb368dfe7c4890093366b2dacb","file_id":"20871","file_name":"2025_Cell_Walker.pdf","file_size":11622960,"creator":"dernst","content_type":"application/pdf","date_created":"2025-12-29T13:40:32Z","relation":"main_file","success":1}],"_id":"19602","status":"public","type":"journal_article","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/","relation":"press_release"}]},"date_published":"2025-05-29T00:00:00Z","acknowledgement":"We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the High Performance Computing resources provided by the ISTA Scientific Computing Facility and Norwich BioScience Institute Partnership Computing Infrastructure. This work was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111 to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship (S.X.), and ISTA core funding (Y.Y. and X.F.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"804981","_id":"bdb51a6e-d553-11ed-ba76-c2025f3d5725","name":"Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants"}],"quality_controlled":"1","month":"05","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"29","doi":"10.1016/j.cell.2025.03.014","volume":188,"file_date_updated":"2025-12-29T13:40:32Z","publication":"Cell","issue":"11","abstract":[{"text":"N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications.","lang":"eng"}],"PlanS_conform":"1","oa_version":"Published Version","ec_funded":1,"oa":1,"author":[{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"last_name":"Liu","full_name":"Liu, Yalin","first_name":"Yalin"},{"id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan","first_name":"Shujuan","last_name":"Xu"},{"id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","orcid":"0000-0002-9919-7282","first_name":"Yiming","full_name":"Yu, Yiming","last_name":"Yu"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"id":"fec73395-8b60-11ed-b69e-927fda99c743","full_name":"Ouyang, Weizhi","first_name":"Weizhi","last_name":"Ouyang"},{"full_name":"Tálas, Judit","first_name":"Judit","last_name":"Tálas"},{"last_name":"Dolan","first_name":"Liam","full_name":"Dolan, Liam"},{"last_name":"Nakajima","full_name":"Nakajima, Keiji","first_name":"Keiji"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"}],"ddc":["570"],"date_updated":"2026-10-20T08:22:21Z","language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"date_created":"2025-04-20T22:01:28Z","publisher":"Cell Press","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"article_type":"original","intvolume":"       188","corr_author":"1","page":"2890-2906.e14","external_id":{"isi":["001504744800006"],"pmid":["40209706"]},"fulldoi":"https://doi.org/10.1016/j.cell.2025.03.014","citation":{"ieee":"J. Walker <i>et al.</i>, “Extensive N4 cytosine methylation is essential for Marchantia sperm function,” <i>Cell</i>, vol. 188, no. 11. Cell Press, p. 2890–2906.e14, 2025.","ista":"Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 188(11), 2890–2906.e14.","ama":"Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. 2025;188(11):2890-2906.e14. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>","apa":"Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025). Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>","chicago":"Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers, Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>.","short":"J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas, L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14.","mla":"Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>, vol. 188, no. 11, Cell Press, 2025, p. 2890–2906.e14, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>."}},{"intvolume":"        60","article_type":"original","isi":1,"citation":{"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.","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.","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>","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>.","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>."},"fulldoi":"https://doi.org/10.1016/j.devcel.2025.04.010","external_id":{"isi":["001570502100005"],"pmid":["40347948"]},"page":"2237-2247.e4","publisher":"Cell Press","date_created":"2025-05-18T22:02:50Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:25:00Z","oa":1,"ec_funded":1,"ddc":["570"],"author":[{"last_name":"Mclaren","first_name":"Susannah B.P.","full_name":"Mclaren, Susannah B.P."},{"last_name":"Xue","full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Siyuan","full_name":"Ding, Siyuan","last_name":"Ding"},{"last_name":"Winkel","full_name":"Winkel, Alexander K.","first_name":"Alexander K."},{"last_name":"Baldwin","full_name":"Baldwin, Oscar","first_name":"Oscar"},{"full_name":"Dwarakacherla, Shreya","first_name":"Shreya","last_name":"Dwarakacherla"},{"full_name":"Franze, Kristian","first_name":"Kristian","last_name":"Franze"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Xiong","full_name":"Xiong, Fengzhu","first_name":"Fengzhu"}],"issue":"17","publication":"Developmental Cell","file_date_updated":"2025-12-29T13:45:05Z","volume":60,"day":"08","doi":"10.1016/j.devcel.2025.04.010","PlanS_conform":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"pmid":1,"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"09","quality_controlled":"1","_id":"19703","file":[{"creator":"dernst","date_updated":"2025-12-29T13:45:05Z","checksum":"1ca6f0822c1cbd430686d5e2a4f96401","file_name":"2025_DevelopmentalCell_McLaren.pdf","file_id":"20872","file_size":12564806,"access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2025-12-29T13:45:05Z"}],"year":"2025","date_published":"2025-09-08T00:00:00Z","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.","type":"journal_article","status":"public","OA_type":"hybrid","scopus_import":"1","title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","OA_place":"publisher"},{"oa":1,"ddc":["570"],"author":[{"first_name":"Zhiying","full_name":"Zhang, Zhiying","last_name":"Zhang"},{"first_name":"Thomas C.","full_name":"Todeschini, Thomas C.","last_name":"Todeschini"},{"last_name":"Wu","full_name":"Wu, Yi","first_name":"Yi"},{"first_name":"Roman","full_name":"Kogay, Roman","last_name":"Kogay"},{"first_name":"Ameena","full_name":"Naji, Ameena","last_name":"Naji"},{"first_name":"Joaquin","full_name":"Cardenas Rodriguez, Joaquin","last_name":"Cardenas Rodriguez"},{"first_name":"Rupavidhya","full_name":"Mondi, Rupavidhya","last_name":"Mondi"},{"last_name":"Kaganovich","full_name":"Kaganovich, Daniel","first_name":"Daniel"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"first_name":"Marianna","full_name":"Teplova, Marianna","last_name":"Teplova"},{"first_name":"Triana","full_name":"Amen, Triana","last_name":"Amen"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"},{"last_name":"Patel","first_name":"Dinshaw J.","full_name":"Patel, Dinshaw J."},{"first_name":"Franklin L.","full_name":"Nobrega, Franklin L.","last_name":"Nobrega"}],"date_updated":"2026-10-20T08:23:33Z","department":[{"_id":"JaBr"}],"language":[{"iso":"eng"}],"publisher":"Cell Press","date_created":"2025-08-07T05:00:04Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       188","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1016/j.cell.2025.07.002","citation":{"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.","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.","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>","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>","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.","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>.","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>."},"external_id":{"pmid":["40730155"],"isi":["001603560700005"]},"page":"5862-5877.e23","OA_type":"hybrid","scopus_import":"1","OA_place":"publisher","title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","file":[{"file_size":32104588,"file_id":"20875","file_name":"2025_Cell_Zhang.pdf","checksum":"b944de5fbd7455f58e1ff338ad352239","date_updated":"2025-12-29T14:15:25Z","access_level":"open_access","creator":"dernst","date_created":"2025-12-29T14:15:25Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"year":"2025","_id":"20143","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).","date_published":"2025-10-16T00:00:00Z","status":"public","type":"journal_article","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","month":"10","publication":"Cell","file_date_updated":"2025-12-29T14:15:25Z","volume":188,"issue":"21","doi":"10.1016/j.cell.2025.07.002","day":"16","oa_version":"Published Version","PlanS_conform":"1","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"}]},{"oa":1,"author":[{"full_name":"Najjar, Hadil","first_name":"Hadil","last_name":"Najjar"},{"full_name":"Weiß, Sarah","first_name":"Sarah","last_name":"Weiß"},{"id":"b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e","full_name":"Horvath, Ferdinand","first_name":"Ferdinand","last_name":"Horvath"},{"last_name":"Hopl","first_name":"Valentina","full_name":"Hopl, Valentina"},{"last_name":"Tiffner","first_name":"Adéla","full_name":"Tiffner, Adéla"},{"last_name":"Höbarth","first_name":"Lorenz","full_name":"Höbarth, Lorenz"},{"first_name":"Julia","full_name":"Söllner, Julia","last_name":"Söllner"},{"first_name":"Maximilian","full_name":"Fröhlich, Maximilian","last_name":"Fröhlich"},{"last_name":"Prantl","first_name":"Magdalena","full_name":"Prantl, Magdalena"},{"full_name":"Müller, Nora","first_name":"Nora","last_name":"Müller"},{"last_name":"Nazarenko","full_name":"Nazarenko, Yuliia","first_name":"Yuliia"},{"last_name":"Harant","first_name":"Selina","full_name":"Harant, Selina"},{"full_name":"Weissenböck, Lukas","first_name":"Lukas","last_name":"Weissenböck"},{"last_name":"Grabmayr","full_name":"Grabmayr, Herwig","first_name":"Herwig"},{"full_name":"Sallinger, Matthias","first_name":"Matthias","last_name":"Sallinger"},{"last_name":"Maltan","first_name":"Lena","full_name":"Maltan, Lena"},{"first_name":"Linda V.","full_name":"Echefu, Linda V.","last_name":"Echefu"},{"first_name":"Tamara","full_name":"Radiskovic, Tamara","last_name":"Radiskovic"},{"full_name":"Leopold, Melanie","first_name":"Melanie","last_name":"Leopold"},{"first_name":"Sonja","full_name":"Lindinger, Sonja","last_name":"Lindinger"},{"last_name":"Humer","first_name":"Christina","full_name":"Humer, Christina"},{"first_name":"Carmen","full_name":"Höglinger, Carmen","last_name":"Höglinger"},{"first_name":"Heinrich","full_name":"Krobath, Heinrich","last_name":"Krobath"},{"last_name":"Renger","first_name":"Thomas","full_name":"Renger, Thomas"},{"first_name":"Isabella","full_name":"Derler, Isabella","last_name":"Derler"}],"ddc":["570"],"department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:25:34Z","DOAJ_listed":"1","date_created":"2025-06-15T22:01:31Z","publisher":"Cell Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","isi":1,"intvolume":"         6","external_id":{"isi":["001516570500009"]},"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>.","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>","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>","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.","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."},"fulldoi":"https://doi.org/10.1016/j.xcrp.2025.102623","OA_type":"gold","title":"STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening","OA_place":"publisher","scopus_import":"1","_id":"19846","article_number":"102623","year":"2025","file":[{"access_level":"open_access","file_size":9771117,"file_id":"19868","file_name":"2025_CellReportsPhysicalScience_Najjar.pdf","date_updated":"2025-06-23T10:20:22Z","checksum":"37ff7c396f966d0ec363e4691d63d402","creator":"dernst","date_created":"2025-06-23T10:20:22Z","content_type":"application/pdf","relation":"main_file","success":1}],"type":"journal_article","status":"public","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.","date_published":"2025-06-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"06","quality_controlled":"1","article_processing_charge":"Yes","has_accepted_license":"1","publication_identifier":{"eissn":["2666-3864"]},"day":"18","doi":"10.1016/j.xcrp.2025.102623","issue":"6","file_date_updated":"2025-06-23T10:20:22Z","publication":"Cell Reports Physical Science","volume":6,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"oa":1,"ddc":["580"],"author":[{"last_name":"Guan","id":"56aad729-cca2-11ed-a45a-9b4138991a48","first_name":"Bin","full_name":"Guan, Bin"},{"full_name":"Xie, Ke Xuan","first_name":"Ke Xuan","last_name":"Xie"},{"first_name":"Xin Qiao","full_name":"Du, Xin Qiao","last_name":"Du"},{"last_name":"Bai","first_name":"Yu Xuan","full_name":"Bai, Yu Xuan"},{"last_name":"Hao","full_name":"Hao, Peng Chao","first_name":"Peng Chao"},{"last_name":"Lin","first_name":"Wen Hui","full_name":"Lin, Wen Hui"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Xue","first_name":"Hong Wei","full_name":"Xue, Hong Wei"}],"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"date_updated":"2026-10-20T08:22:53Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","publisher":"Cell Press","date_created":"2025-07-20T22:02:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"intvolume":"        44","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1016/j.celrep.2025.116024","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>.","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).","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>.","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.","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.","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>","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>"},"external_id":{"isi":["001533244800001"],"pmid":["40668679"]},"OA_type":"hybrid","scopus_import":"1","OA_place":"publisher","title":"Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD","file":[{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-07-22T08:52:17Z","creator":"dernst","access_level":"open_access","file_name":"2025_CellReports_Guan.pdf","date_updated":"2025-07-22T08:52:17Z","checksum":"ee03deee47a084b0295251dc49470ad4","file_id":"20067","file_size":37708120}],"year":"2025","_id":"20029","article_number":"116024","date_published":"2025-07-22T00:00:00Z","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.","status":"public","type":"journal_article","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","quality_controlled":"1","month":"07","publication":"Cell Reports","file_date_updated":"2025-07-22T08:52:17Z","volume":44,"issue":"7","day":"22","doi":"10.1016/j.celrep.2025.116024","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","doi":"10.1016/j.celrep.2025.116056","day":"24","issue":"8","volume":44,"publication":"Cell Reports","file_date_updated":"2025-08-05T06:15:09Z","month":"07","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"Yes","publication_identifier":{"eissn":["2211-1247"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","pmid":1,"type":"journal_article","status":"public","date_published":"2025-07-24T00:00:00Z","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.","_id":"20116","article_number":"116056","file":[{"file_size":24178018,"checksum":"3c43e040a4a7a65ec67ae1d2bb81261a","date_updated":"2025-08-05T06:15:09Z","file_name":"2025_CellReports_Xu.pdf","file_id":"20120","access_level":"open_access","creator":"dernst","date_created":"2025-08-05T06:15:09Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"year":"2025","title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","OA_place":"publisher","scopus_import":"1","OA_type":"gold","external_id":{"pmid":["40714631"],"isi":["001542038500001"]},"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>.","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.","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."},"fulldoi":"https://doi.org/10.1016/j.celrep.2025.116056","article_type":"original","isi":1,"intvolume":"        44","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"date_created":"2025-08-04T13:39:11Z","DOAJ_listed":"1","publisher":"Cell Press","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"date_updated":"2026-10-20T08:23:15Z","author":[{"first_name":"Faqing","full_name":"Xu, Faqing","last_name":"Xu"},{"last_name":"Yu","first_name":"Yongqiang","full_name":"Yu, Yongqiang"},{"last_name":"Guan","id":"56aad729-cca2-11ed-a45a-9b4138991a48","full_name":"Guan, Bin","first_name":"Bin"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"first_name":"Zhihong","full_name":"Xu, Zhihong","last_name":"Xu"},{"first_name":"Hongwei","full_name":"Xue, Hongwei","last_name":"Xue"}],"ddc":["580"],"oa":1},{"page":"2919-2936.e12","fulldoi":"https://doi.org/10.1016/j.molcel.2025.06.027","citation":{"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.","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.","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>","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>","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.","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>.","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>."},"article_type":"original","intvolume":"        85","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2025-09-23T08:56:13Z","publisher":"Cell Press","date_updated":"2026-10-20T08:50:29Z","department":[{"_id":"AlMi"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Deyasini","full_name":"Chakraborty, Deyasini","last_name":"Chakraborty"},{"last_name":"Sandate","full_name":"Sandate, Colby R.","first_name":"Colby R."},{"last_name":"Isbel","first_name":"Luke","full_name":"Isbel, Luke"},{"last_name":"Kempf","full_name":"Kempf, Georg","first_name":"Georg"},{"first_name":"Joscha","full_name":"Weiss, Joscha","last_name":"Weiss"},{"last_name":"Cavadini","full_name":"Cavadini, Simone","first_name":"Simone"},{"full_name":"Kater, Lukas","first_name":"Lukas","last_name":"Kater"},{"full_name":"Seebacher, Jan","first_name":"Jan","last_name":"Seebacher"},{"full_name":"Kozicka, Zuzanna","first_name":"Zuzanna","last_name":"Kozicka"},{"first_name":"Lisa","full_name":"Stoos, Lisa","last_name":"Stoos"},{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"first_name":"Dirk","full_name":"Schübeler, Dirk","last_name":"Schübeler"},{"first_name":"Alicia","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Thomä, Nicolas H.","first_name":"Nicolas H.","last_name":"Thomä"}],"ddc":["570"],"oa":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"}],"PlanS_conform":"1","oa_version":"Published Version","doi":"10.1016/j.molcel.2025.06.027","day":"07","volume":85,"file_date_updated":"2025-09-24T07:54:03Z","publication":"Molecular Cell","issue":"15","quality_controlled":"1","month":"08","publication_identifier":{"issn":["1097-2765"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","type":"journal_article","date_published":"2025-08-07T00:00:00Z","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.).","year":"2025","file":[{"creator":"dernst","access_level":"open_access","file_size":41813494,"file_id":"20386","file_name":"2025_MolecularCell_Chakraborty.pdf","checksum":"e60390ca629b350af3221d4718ca6534","date_updated":"2025-09-24T07:54:03Z","relation":"main_file","success":1,"date_created":"2025-09-24T07:54:03Z","content_type":"application/pdf"}],"_id":"20374","OA_place":"publisher","title":"Nucleosomes specify co-factor access to p53","scopus_import":"1","OA_type":"hybrid"},{"department":[{"_id":"EvBe"}],"date_updated":"2026-10-20T08:24:38Z","language":[{"iso":"eng"}],"author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"citation":{"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>","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>","ieee":"E. Benková, “Unlocking plant regeneration: The role for glutathione,” <i>Developmental Cell</i>, vol. 60, no. 8. Cell Press, pp. 1137–1139, 2025.","ista":"Benková E. 2025. Unlocking plant regeneration: The role for glutathione. Developmental Cell. 60(8), 1137–1139.","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>.","short":"E. Benková, Developmental Cell 60 (2025) 1137–1139."},"fulldoi":"https://doi.org/10.1016/j.devcel.2025.03.012","external_id":{"pmid":["40262524"],"isi":["001477400800001"]},"corr_author":"1","page":"1137-1139","intvolume":"        60","article_type":"letter_note","isi":1,"publisher":"Cell Press","date_created":"2025-04-20T22:01:28Z","date_published":"2025-04-21T00:00:00Z","type":"journal_article","status":"public","_id":"19594","year":"2025","scopus_import":"1","title":"Unlocking plant regeneration: The role for glutathione","OA_type":"closed access","oa_version":"None","abstract":[{"lang":"eng","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."}],"issue":"8","volume":60,"publication":"Developmental Cell","day":"21","doi":"10.1016/j.devcel.2025.03.012","article_processing_charge":"No","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"month":"04","quality_controlled":"1","publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_updated":"2026-10-20T08:55:34Z","oa":1,"ec_funded":1,"ddc":["570"],"author":[{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer"},{"last_name":"Semenov","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","full_name":"Semenov, Nikolai","first_name":"Nikolai"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath","first_name":"Manjunath","orcid":"0000-0003-2311-2112","last_name":"Javoor"},{"last_name":"Zens","full_name":"Zens, Bettina","first_name":"Bettina","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Agudelo Duenas","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"id":"EE8452B8-C26A-11E9-B157-E80CE6697425","full_name":"Suplata, Marek","first_name":"Marek","last_name":"Suplata"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","first_name":"Julia","last_name":"Lyudchik"},{"first_name":"Andreas","full_name":"Wartak, Andreas","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","last_name":"Wartak"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","full_name":"Schur, Florian Km","last_name":"Schur"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"intvolume":"         5","article_type":"original","fulldoi":"https://doi.org/10.1016/j.bpr.2025.100211","citation":{"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>","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>","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.","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.","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>.","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>."},"corr_author":"1","publisher":"Cell Press","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_created":"2025-06-08T22:01:22Z","DOAJ_listed":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2025","file":[{"file_size":7238179,"file_name":"2025_BiophysicalReports_Vorlaufer.pdf","checksum":"4018c833f25a3ad3b57e3577fed70334","date_updated":"2025-06-10T07:24:46Z","file_id":"19802","access_level":"open_access","creator":"dernst","date_created":"2025-06-10T07:24:46Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"_id":"19795","article_number":"100211","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.).","date_published":"2025-06-11T00:00:00Z","status":"public","related_material":{"record":[{"relation":"dissertation_contains","id":"20206","status":"public"},{"id":"22744","status":"public","relation":"dissertation_contains"}]},"type":"journal_article","OA_type":"gold","scopus_import":"1","OA_place":"publisher","title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","publication":"Biophysical Reports","volume":5,"file_date_updated":"2025-06-10T07:24:46Z","issue":"2","day":"11","doi":"10.1016/j.bpr.2025.100211","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2667-0747"]},"article_processing_charge":"Yes","has_accepted_license":"1","quality_controlled":"1","month":"06"},{"oa":1,"author":[{"last_name":"Smith","first_name":"Hannah M.","full_name":"Smith, Hannah M."},{"last_name":"Ng","full_name":"Ng, Hong Kiat","first_name":"Hong Kiat"},{"full_name":"Moodie, Joanna E.","first_name":"Joanna E.","last_name":"Moodie"},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"last_name":"Mccartney","first_name":"Daniel L.","full_name":"Mccartney, Daniel L."},{"full_name":"Bernabeu, Elena","first_name":"Elena","last_name":"Bernabeu"},{"first_name":"Archie","full_name":"Campbell, Archie","last_name":"Campbell"},{"full_name":"Redmond, Paul","first_name":"Paul","last_name":"Redmond"},{"first_name":"Adele","full_name":"Taylor, Adele","last_name":"Taylor"},{"last_name":"Page","full_name":"Page, Danielle","first_name":"Danielle"},{"last_name":"Corley","full_name":"Corley, Janie","first_name":"Janie"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"last_name":"Tay","first_name":"Darwin","full_name":"Tay, Darwin"},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"},{"last_name":"Chambers","full_name":"Chambers, John C.","first_name":"John C."},{"last_name":"Loh","full_name":"Loh, Marie","first_name":"Marie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"last_name":"Marioni","full_name":"Marioni, Riccardo E.","first_name":"Riccardo E."},{"last_name":"Hillary","full_name":"Hillary, Robert F.","first_name":"Robert F."}],"ddc":["570"],"department":[{"_id":"MaRo"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:53:52Z","date_created":"2025-01-05T23:01:56Z","publisher":"Cell Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","isi":1,"intvolume":"       112","page":"106-115","external_id":{"pmid":["39706196"],"isi":["001412498600001"]},"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.","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.","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>","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>","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>.","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.","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>."},"fulldoi":"https://doi.org/10.1016/j.ajhg.2024.11.012","OA_type":"hybrid","title":"DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts","OA_place":"publisher","scopus_import":"1","_id":"18754","year":"2025","file":[{"file_name":"2025_AJHG_Smith.pdf","file_id":"18776","date_updated":"2025-01-08T09:26:42Z","checksum":"891d120554f07da2c35d38388c29a690","file_size":2266488,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2025-01-08T09:26:42Z","success":1,"relation":"main_file"}],"type":"journal_article","related_material":{"link":[{"url":"https://github.com/marioni-group/Metabolic_trait","relation":"software"}]},"status":"public","date_published":"2025-01-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","month":"01","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"day":"02","doi":"10.1016/j.ajhg.2024.11.012","issue":"1","file_date_updated":"2025-01-08T09:26:42Z","publication":"American Journal of Human Genetics","volume":112,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"scopus_import":"1","OA_place":"publisher","title":"Cell-specific wiring routes information flow through hippocampal CA3","OA_type":"gold","date_published":"2025-08-01T00:00:00Z","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.).","status":"public","type":"journal_article","year":"2025","file":[{"success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2025-08-04T06:53:07Z","creator":"dernst","checksum":"556ff9760661ecd23949d75031043b1f","file_name":"2025_CellReports_Watson.pdf","file_id":"20106","date_updated":"2025-08-04T06:53:07Z","file_size":27695214,"access_level":"open_access"}],"article_number":"116080","_id":"20099","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"article_processing_charge":"Yes","has_accepted_license":"1","quality_controlled":"1","month":"08","project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"COE16","_id":"0a6c8641-b036-11f1-bacf-e4eec62b5bb4","name":"Neuronal circuits in health and disease (Jonas)"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","PlanS_conform":"1","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."}],"publication":"Cell Reports","file_date_updated":"2025-08-04T06:53:07Z","volume":44,"issue":"8","doi":"10.1016/j.celrep.2025.116080","day":"01","ddc":["570"],"author":[{"full_name":"Watson, Jake","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","first_name":"Victor M","last_name":"Vargas Barroso"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:55:57Z","department":[{"_id":"PeJo"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Cell Press","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_created":"2025-08-03T22:01:30Z","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1016/j.celrep.2025.116080","citation":{"short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).","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>.","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>.","ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","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.","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>","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>"},"corr_author":"1","external_id":{"isi":["001544472300002"]},"intvolume":"        44","isi":1,"article_type":"original"},{"author":[{"last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","first_name":"Jakob","full_name":"Vorlaufer, Jakob"}],"ddc":["621","535"],"oa":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_updated":"2026-10-20T08:55:33Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"alternative_title":["ISTA Thesis"],"date_created":"2025-08-22T08:12:55Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"page":"107","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-20206","citation":{"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>.","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.","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>.","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>","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>","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria."},"OA_place":"publisher","title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"19795"}]},"type":"dissertation","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. ","date_published":"2025-08-25T00:00:00Z","degree_awarded":"PhD","year":"2025","file":[{"creator":"jvorlauf","file_size":39735535,"checksum":"191db3367c19c9b32b65f4bc3a7c19de","date_updated":"2025-08-25T13:49:55Z","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","file_id":"20228","access_level":"closed","relation":"source_file","date_created":"2025-08-25T13:49:55Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-08-25T13:49:56Z","creator":"jvorlauf","access_level":"open_access","checksum":"104400e6036921569610230c1d4899dc","file_id":"20229","date_updated":"2025-08-25T13:49:56Z","file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","file_size":10947446}],"_id":"20206","month":"08","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","project":[{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"}],"supervisor":[{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G"}],"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"}],"oa_version":"Published Version","day":"25","doi":"10.15479/AT-ISTA-20206","file_date_updated":"2025-08-25T13:49:56Z"},{"year":"2025","file":[{"success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2025-08-05T12:43:44Z","creator":"dernst","checksum":"5e57852a45a78a751dd3a5e807bf015f","date_updated":"2025-08-05T12:43:44Z","file_name":"2025_Neuron_Bollmann.pdf","file_id":"20133","file_size":27047730,"access_level":"open_access"}],"_id":"19506","status":"public","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/","relation":"press_release"}]},"type":"journal_article","date_published":"2025-05-07T00:00:00Z","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).","OA_type":"hybrid","OA_place":"publisher","title":"Sleep stages antagonistically modulate reactivation drift","scopus_import":"1","day":"07","doi":"10.1016/j.neuron.2025.02.025","file_date_updated":"2025-08-05T12:43:44Z","volume":113,"publication":"Neuron","issue":"9","abstract":[{"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.","lang":"eng"}],"PlanS_conform":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","grant_number":"281511"},{"grant_number":"I 3713-B27","call_identifier":"FWF","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"pmid":1,"publication_status":"published","quality_controlled":"1","month":"05","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"JoCs"}],"date_updated":"2026-10-20T08:54:27Z","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"author":[{"id":"47AD3038-F248-11E8-B48F-1D18A9856A87","full_name":"Bollmann, Lars","first_name":"Lars","last_name":"Bollmann"},{"full_name":"Baracskay, Peter","first_name":"Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","full_name":"Stella, Federico","last_name":"Stella"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"isi":1,"article_type":"original","intvolume":"       113","page":"1446-1459.e6","external_id":{"pmid":["40132588"],"isi":["001510440400001"]},"corr_author":"1","fulldoi":"https://doi.org/10.1016/j.neuron.2025.02.025","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.","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>.","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.","ista":"Bollmann L, Baracskay P, Stella F, Csicsvari JL. 2025. Sleep stages antagonistically modulate reactivation drift. Neuron. 113(9), 1446–1459.e6.","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>","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>"},"date_created":"2025-04-06T22:01:32Z","publisher":"Cell Press","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"date_updated":"2026-10-20T08:54:10Z","language":[{"iso":"eng"}],"department":[{"_id":"AlMi"}],"ddc":["570"],"author":[{"last_name":"Harar","orcid":"0000-0001-5206-1794","first_name":"Pavol","full_name":"Harar, Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5"},{"first_name":"Lukas","full_name":"Herrmann, Lukas","last_name":"Herrmann"},{"last_name":"Grohs","first_name":"Philipp","full_name":"Grohs, Philipp"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"}],"oa":1,"fulldoi":"https://doi.org/10.1016/j.str.2025.01.020","citation":{"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>","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.","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.","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>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","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>."},"page":"820-827.e4","external_id":{"isi":["001463196100001"],"pmid":["39947174"]},"corr_author":"1","intvolume":"        33","isi":1,"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Cell Press","date_created":"2025-03-23T23:01:27Z","date_published":"2025-04-03T00:00:00Z","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.","status":"public","type":"journal_article","related_material":{"link":[{"url":"https://github.com/paloha/faket/","relation":"software"}]},"file":[{"success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2025-08-05T12:15:13Z","creator":"dernst","file_id":"20130","file_name":"2025_Structure_Harar.pdf","date_updated":"2025-08-05T12:15:13Z","checksum":"f346bc357a66a88cca3d0eb95793fb73","file_size":4367530,"access_level":"open_access"}],"year":"2025","_id":"19443","scopus_import":"1","OA_place":"publisher","title":"FakET: Simulating cryo-electron tomograms with neural style transfer","OA_type":"hybrid","oa_version":"Published Version","PlanS_conform":"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"}],"file_date_updated":"2025-08-05T12:15:13Z","publication":"Structure","volume":33,"issue":"4","day":"03","doi":"10.1016/j.str.2025.01.020","publication_identifier":{"issn":["0969-2126"],"eissn":["1878-4186"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","month":"04","publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:54:50Z","department":[{"_id":"MaHe"}],"ddc":["570"],"author":[{"last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X"},{"last_name":"Toda","first_name":"Tomohisa","full_name":"Toda, Tomohisa"}],"oa":1,"fulldoi":"https://doi.org/10.1016/j.tins.2025.07.004","citation":{"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>.","short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.","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>","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>","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.","ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 645–654."},"external_id":{"pmid":["40744775"],"isi":["001568965400001"]},"corr_author":"1","page":"645-654","intvolume":"        48","isi":1,"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Cell Press","date_created":"2025-08-10T22:01:29Z","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.","date_published":"2025-09-01T00:00:00Z","status":"public","type":"journal_article","file":[{"success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2025-12-29T13:47:27Z","creator":"dernst","file_name":"2025_TrendsNeurosciences_Hetzer.pdf","date_updated":"2025-12-29T13:47:27Z","file_id":"20873","checksum":"90942491b499f70b0bf48b8aec2e7387","file_size":327847,"access_level":"open_access"}],"year":"2025","_id":"20154","scopus_import":"1","OA_place":"publisher","title":"Long-lived cellular molecules in the brain","OA_type":"hybrid","oa_version":"Published Version","PlanS_conform":"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"}],"publication":"Trends in Neurosciences","file_date_updated":"2025-12-29T13:47:27Z","volume":48,"issue":"9","day":"01","doi":"10.1016/j.tins.2025.07.004","publication_identifier":{"eissn":["1878-108X"],"issn":["0166-2236"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","month":"09","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"date_updated":"2026-10-20T08:55:09Z","author":[{"first_name":"Ziqiang","full_name":"Li, Ziqiang","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","last_name":"Li"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"}],"intvolume":"        35","article_type":"letter_note","isi":1,"citation":{"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>","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.","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.","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>.","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>.","short":"Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892."},"fulldoi":"https://doi.org/10.1016/j.cub.2025.08.016","page":"R890-R892","corr_author":"1","external_id":{"isi":["001592664700001"],"pmid":["40987270"]},"publisher":"Cell Press","date_created":"2025-10-05T22:01:35Z","_id":"20427","year":"2025","date_published":"2025-09-22T00:00:00Z","type":"journal_article","status":"public","OA_type":"closed access","scopus_import":"1","title":"Cell migration: How animal cells run and tumble","issue":"18","publication":"Current Biology","volume":35,"day":"22","doi":"10.1016/j.cub.2025.08.016","oa_version":"None","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"}],"pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"eissn":["1879-0445"]},"month":"09","quality_controlled":"1"}]