[{"author":[{"orcid":"0009-0000-7590-3501","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob"}],"date_updated":"2026-10-20T08:55:33Z","date_created":"2025-08-22T08:12:55Z","year":"2025","citation":{"chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>.","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>.","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","short":"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.","ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>","apa":"Vorlaufer, J. (2025). <i>Construction of a cryo-super-resolution microscope to guide in situ structure analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>"},"supervisor":[{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"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"}],"doi":"10.15479/AT-ISTA-20206","day":"25","date_published":"2025-08-25T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"oa_version":"Published Version","month":"08","publisher":"Institute of Science and Technology Austria","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. ","_id":"20206","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"status":"public","ddc":["621","535"],"degree_awarded":"PhD","type":"dissertation","project":[{"name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"}],"title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","file":[{"relation":"source_file","date_updated":"2025-08-25T13:49:55Z","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-08-25T13:49:55Z","file_size":39735535,"file_id":"20228","checksum":"191db3367c19c9b32b65f4bc3a7c19de","creator":"jvorlauf"},{"checksum":"104400e6036921569610230c1d4899dc","creator":"jvorlauf","file_id":"20229","file_size":10947446,"file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","access_level":"open_access","date_created":"2025-08-25T13:49:56Z","content_type":"application/pdf","relation":"main_file","success":1,"date_updated":"2025-08-25T13:49:56Z"}],"publication_status":"published","fulldoi":"https://doi.org/10.15479/AT-ISTA-20206","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"19795","status":"public"}]},"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2025-08-25T13:49:56Z","page":"107","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","OA_place":"publisher","corr_author":"1"},{"date_updated":"2026-10-20T08:54:27Z","author":[{"full_name":"Bollmann, Lars","id":"47AD3038-F248-11E8-B48F-1D18A9856A87","first_name":"Lars","last_name":"Bollmann"},{"last_name":"Baracskay","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Baracskay, Peter"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","last_name":"Stella","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"publication":"Neuron","year":"2025","date_created":"2025-04-06T22:01:32Z","citation":{"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.","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>.","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>.","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>","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>"},"doi":"10.1016/j.neuron.2025.02.025","date_published":"2025-05-07T00:00:00Z","day":"07","abstract":[{"lang":"eng","text":"Hippocampal reactivation of waking neuronal assemblies in sleep is a key initial step of systems consolidation. Nevertheless, it is unclear whether reactivated assemblies are static or whether they reorganize gradually over prolonged sleep. We tracked reactivated CA1 assembly patterns over ∼20 h of sleep/rest periods and related them to assemblies seen before or after in a spatial learning paradigm using rats. We found that reactivated assembly patterns were gradually transformed and started to resemble those seen in the subsequent recall session. Periods of rapid eye movement (REM) sleep and non-REM (NREM) had antagonistic roles: whereas NREM accelerated the assembly drift, REM countered it. Moreover, only a subset of rate-changing pyramidal cells contributed to the drift, whereas stable-firing-rate cells maintained unaltered reactivation patterns. Our data suggest that prolonged sleep promotes the spontaneous reorganization of spatial assemblies, which can contribute to daily cognitive map changes or encoding new learning situations."}],"scopus_import":"1","external_id":{"pmid":["40132588"],"isi":["001510440400001"]},"oa_version":"Published Version","month":"05","publisher":"Cell Press","_id":"19506","department":[{"_id":"JoCs"}],"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).","pmid":1,"issue":"9","quality_controlled":"1","volume":113,"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"article_type":"original","intvolume":"       113","status":"public","OA_type":"hybrid","type":"journal_article","ec_funded":1,"ddc":["570"],"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425","grant_number":"I 3713-B27"}],"title":"Sleep stages antagonistically modulate reactivation drift","file":[{"access_level":"open_access","file_name":"2025_Neuron_Bollmann.pdf","content_type":"application/pdf","date_created":"2025-08-05T12:43:44Z","success":1,"date_updated":"2025-08-05T12:43:44Z","relation":"main_file","checksum":"5e57852a45a78a751dd3a5e807bf015f","creator":"dernst","file_size":27047730,"file_id":"20133"}],"publication_status":"published","fulldoi":"https://doi.org/10.1016/j.neuron.2025.02.025","isi":1,"file_date_updated":"2025-08-05T12:43:44Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","oa":1,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/","description":"News on ISTA website"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1446-1459.e6","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"license":"https://creativecommons.org/licenses/by/4.0/","PlanS_conform":"1","OA_place":"publisher","corr_author":"1"},{"doi":"10.1016/j.str.2025.01.020","date_published":"2025-04-03T00:00:00Z","day":"03","scopus_import":"1","abstract":[{"text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.","lang":"eng"}],"date_updated":"2026-10-20T08:54:10Z","author":[{"last_name":"Harar","first_name":"Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","orcid":"0000-0001-5206-1794","full_name":"Harar, Pavol"},{"last_name":"Herrmann","first_name":"Lukas","full_name":"Herrmann, Lukas"},{"full_name":"Grohs, Philipp","first_name":"Philipp","last_name":"Grohs"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"}],"publication":"Structure","date_created":"2025-03-23T23:01:27Z","year":"2025","citation":{"chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Cell Press, p. 820–827.e4, 2025.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Cell Press, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","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>","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.","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>"},"pmid":1,"issue":"4","quality_controlled":"1","volume":33,"article_type":"original","publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"intvolume":"        33","external_id":{"isi":["001463196100001"],"pmid":["39947174"]},"oa_version":"Published Version","month":"04","publisher":"Cell Press","_id":"19443","department":[{"_id":"AlMi"}],"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.","file":[{"creator":"dernst","checksum":"f346bc357a66a88cca3d0eb95793fb73","file_id":"20130","file_size":4367530,"content_type":"application/pdf","date_created":"2025-08-05T12:15:13Z","access_level":"open_access","file_name":"2025_Structure_Harar.pdf","success":1,"date_updated":"2025-08-05T12:15:13Z","relation":"main_file"}],"title":"FakET: Simulating cryo-electron tomograms with neural style transfer","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.str.2025.01.020","isi":1,"status":"public","OA_type":"hybrid","type":"journal_article","ddc":["570"],"PlanS_conform":"1","OA_place":"publisher","corr_author":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2025-08-05T12:15:13Z","oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/paloha/faket/"}]},"page":"820-827.e4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"date_published":"2025-09-01T00:00:00Z","day":"01","doi":"10.1016/j.tins.2025.07.004","abstract":[{"lang":"eng","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."}],"scopus_import":"1","publication":"Trends in Neurosciences","citation":{"ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 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>","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>.","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.","short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.","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>."},"date_created":"2025-08-10T22:01:29Z","year":"2025","date_updated":"2026-10-20T08:54:50Z","author":[{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"Hetzer","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X"},{"last_name":"Toda","first_name":"Tomohisa","full_name":"Toda, Tomohisa"}],"publication_identifier":{"eissn":["1878-108X"],"issn":["0166-2236"]},"article_type":"original","volume":48,"intvolume":"        48","issue":"9","pmid":1,"quality_controlled":"1","department":[{"_id":"MaHe"}],"_id":"20154","acknowledgement":"The work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872 – T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG, 101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank Dr Laura J. Harrison for editing assistance.","external_id":{"isi":["001568965400001"],"pmid":["40744775"]},"publisher":"Cell Press","month":"09","oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.tins.2025.07.004","isi":1,"publication_status":"published","file":[{"relation":"main_file","date_updated":"2025-12-29T13:47:27Z","success":1,"access_level":"open_access","file_name":"2025_TrendsNeurosciences_Hetzer.pdf","content_type":"application/pdf","date_created":"2025-12-29T13:47:27Z","file_id":"20873","file_size":327847,"checksum":"90942491b499f70b0bf48b8aec2e7387","creator":"dernst"}],"title":"Long-lived cellular molecules in the brain","type":"journal_article","OA_type":"hybrid","ddc":["570"],"status":"public","corr_author":"1","OA_place":"publisher","PlanS_conform":"1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"645-654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2025-12-29T13:47:27Z","has_accepted_license":"1","oa":1},{"article_type":"letter_note","publication_identifier":{"eissn":["1879-0445"]},"volume":35,"intvolume":"        35","pmid":1,"issue":"18","quality_controlled":"1","department":[{"_id":"MiSi"}],"_id":"20427","external_id":{"pmid":["40987270"],"isi":["001592664700001"]},"publisher":"Cell Press","oa_version":"None","month":"09","date_published":"2025-09-22T00:00:00Z","day":"22","doi":"10.1016/j.cub.2025.08.016","abstract":[{"lang":"eng","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."}],"scopus_import":"1","publication":"Current Biology","citation":{"chicago":"LI, ZIQIANG, and Michael K Sixt. “Cell Migration: How Animal Cells Run and Tumble.” <i>Current Biology</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">https://doi.org/10.1016/j.cub.2025.08.016</a>.","ieee":"Z. LI and M. K. Sixt, “Cell migration: How animal cells run and tumble,” <i>Current Biology</i>, vol. 35, no. 18. Cell Press, pp. R890–R892, 2025.","short":"Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892.","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>.","ista":"LI Z, Sixt MK. 2025. Cell migration: How animal cells run and tumble. Current Biology. 35(18), R890–R892.","ama":"LI Z, Sixt MK. Cell migration: How animal cells run and tumble. <i>Current Biology</i>. 2025;35(18):R890-R892. doi:<a href=\"https://doi.org/10.1016/j.cub.2025.08.016\">10.1016/j.cub.2025.08.016</a>","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>"},"year":"2025","date_created":"2025-10-05T22:01:35Z","date_updated":"2026-10-20T08:55:09Z","author":[{"last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang","full_name":"Li, Ziqiang"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"corr_author":"1","language":[{"iso":"eng"}],"page":"R890-R892","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.cub.2025.08.016","isi":1,"publication_status":"published","title":"Cell migration: How animal cells run and tumble","type":"journal_article","OA_type":"closed access","status":"public"},{"status":"public","ddc":["570"],"OA_type":"hybrid","type":"journal_article","title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","project":[{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046"},{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","grant_number":"F7814","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e"}],"file":[{"success":1,"date_updated":"2025-06-04T05:43:27Z","relation":"main_file","access_level":"open_access","file_name":"2025_DevelopmentalCell_Jaeger.pdf","content_type":"application/pdf","date_created":"2025-06-04T05:43:27Z","file_id":"19790","file_size":11936258,"checksum":"a83a4cb58f5941096d3ad91ca0172594","creator":"dernst"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.025","oa":1,"related_material":{"record":[{"status":"public","id":"22667","relation":"dissertation_contains"},{"relation":"research_data","id":"22803","status":"public"}]},"file_date_updated":"2025-06-04T05:43:27Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"794-812.e6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"dataavailabilitystatement":"FAMD RStudio code and raw data used for analysis of post-metamorphic P. waltl injection outcomes are available via Dryad repository: https://doi.org/10.5061/dryad.mpg4f4r89. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","supplementarymaterial":"yes","OA_place":"publisher","corr_author":"1","author":[{"full_name":"Jaeger, Eliza C.B.","last_name":"Jaeger","first_name":"Eliza C.B."},{"first_name":"David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941"},{"last_name":"Deryckere","first_name":"Astrid","full_name":"Deryckere, Astrid"},{"last_name":"Zorin","first_name":"Nikol","full_name":"Zorin, Nikol"},{"first_name":"Akemi L.","last_name":"Nguyen","full_name":"Nguyen, Akemi L."},{"first_name":"Georgiy","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05","last_name":"Ivanian","full_name":"Ivanian, Georgiy","orcid":"0009-0002-3999-3735"},{"first_name":"Jamie","last_name":"Woych","full_name":"Woych, Jamie"},{"first_name":"Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f","last_name":"Arnold","full_name":"Arnold, Rebecca C"},{"first_name":"Alonso","last_name":"Ortega Gurrola","full_name":"Ortega Gurrola, Alonso"},{"last_name":"Shvartsman","first_name":"Arik","full_name":"Shvartsman, Arik"},{"id":"a9492887-8972-11ed-ae7b-bfae10998254","first_name":"Francesca","last_name":"Barbieri","full_name":"Barbieri, Francesca"},{"full_name":"Toma, Florina-Alexandra","last_name":"Toma","id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","first_name":"Florina-Alexandra"},{"full_name":"Gorbsky, Gary J.","last_name":"Gorbsky","first_name":"Gary J."},{"full_name":"Horb, Marko E.","last_name":"Horb","first_name":"Marko E."},{"full_name":"Cline, Hollis T.","last_name":"Cline","first_name":"Hollis T."},{"full_name":"Shay, Timothy F.","last_name":"Shay","first_name":"Timothy F."},{"last_name":"Kelley","first_name":"Darcy B.","full_name":"Kelley, Darcy B."},{"full_name":"Yamaguchi, Ayako","first_name":"Ayako","last_name":"Yamaguchi"},{"first_name":"Mark","last_name":"Shein-Idelson","full_name":"Shein-Idelson, Mark"},{"full_name":"Tosches, Maria Antonietta","first_name":"Maria Antonietta","last_name":"Tosches"},{"orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"date_updated":"2026-10-20T08:56:33Z","date_created":"2024-02-20T09:20:32Z","year":"2025","citation":{"apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. 2025;60(5):794-812.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>, vol. 60, no. 5, Cell Press, 2025, p. 794–812.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>.","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>Developmental Cell</i>, vol. 60, no. 5. Cell Press, p. 794–812.e6, 2025.","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>."},"publication":"Developmental Cell","abstract":[{"text":"Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution.","lang":"eng"}],"scopus_import":"1","doi":"10.1016/j.devcel.2024.10.025","date_published":"2025-03-10T00:00:00Z","day":"10","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"das_tickbox":"1","oa_version":"Published Version","month":"03","publisher":"Cell Press","external_id":{"pmid":["39603234"],"isi":["001444798600001"]},"acknowledgement":"We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).","_id":"15016","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"quality_controlled":"1","issue":"5","pmid":1,"intvolume":"        60","volume":60,"researchdata_availability":"yes","article_type":"original","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]}},{"ddc":["580"],"OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1016/j.xplc.2024.101181","title":"Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1","file":[{"file_id":"19575","file_size":4443183,"checksum":"7b0e4511e43cc0da06730c3edb7c1167","creator":"dernst","date_updated":"2025-04-16T09:02:05Z","success":1,"relation":"main_file","file_name":"2025_PlantComm_Wei.pdf","access_level":"open_access","date_created":"2025-04-16T09:02:05Z","content_type":"application/pdf"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"language":[{"iso":"eng"}],"dataavailabilitystatement":"The ABCB1 structures in the substrate-unbound state, BL-bound state, and ATP plus BL-bound state have been deposited in the Protein Data Bank under accession codes 8ZPX, 8ZPZ, and 8ZQ4, respectively. The corresponding cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under accession codes EMD-60366, EMD-60369, and EMD-60370, respectively.","oa":1,"article_processing_charge":"Yes","file_date_updated":"2025-04-16T09:02:05Z","has_accepted_license":"1","OA_place":"publisher","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2025","date_created":"2024-12-04T11:21:16Z","citation":{"apa":"Wei, H., Zhu, H., Ying, W., Janssens, H., Kvasnica, M., Winne, J., … Sun, L. (2025). Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. <i>Plant Communications</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">https://doi.org/10.1016/j.xplc.2024.101181</a>","ista":"Wei H, Zhu H, Ying W, Janssens H, Kvasnica M, Winne J, Gao Y, Friml J, Ma Q, Tan S, Liu X, Russinova E, Sun L. 2025. Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications. 6(1), 101181.","ama":"Wei H, Zhu H, Ying W, et al. Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1. <i>Plant Communications</i>. 2025;6(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">10.1016/j.xplc.2024.101181</a>","short":"H. Wei, H. Zhu, W. Ying, H. Janssens, M. Kvasnica, J. Winne, Y. Gao, J. Friml, Q. Ma, S. Tan, X. Liu, E. Russinova, L. Sun, Plant Communications 6 (2025).","ieee":"H. Wei <i>et al.</i>, “Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1,” <i>Plant Communications</i>, vol. 6, no. 1. Cell Press, 2025.","mla":"Wei, H., et al. “Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC Transporter ABCB1.” <i>Plant Communications</i>, vol. 6, no. 1, 101181, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">10.1016/j.xplc.2024.101181</a>.","chicago":"Wei, H, H Zhu, W Ying, H Janssens, M Kvasnica, JM Winne, Y Gao, et al. “Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC Transporter ABCB1.” <i>Plant Communications</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.xplc.2024.101181\">https://doi.org/10.1016/j.xplc.2024.101181</a>."},"publication":"Plant Communications","author":[{"full_name":"Wei, H","first_name":"H","last_name":"Wei"},{"full_name":"Zhu, H","last_name":"Zhu","first_name":"H"},{"last_name":"Ying","first_name":"W","full_name":"Ying, W"},{"full_name":"Janssens, H","first_name":"H","last_name":"Janssens"},{"first_name":"M","last_name":"Kvasnica","full_name":"Kvasnica, M"},{"full_name":"Winne, JM","last_name":"Winne","first_name":"JM"},{"full_name":"Gao, Y","first_name":"Y","last_name":"Gao"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Ma","first_name":"Q","full_name":"Ma, Q"},{"first_name":"S","last_name":"Tan","full_name":"Tan, S"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"first_name":"E","last_name":"Russinova","full_name":"Russinova, E"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"}],"date_updated":"2026-10-20T08:56:15Z","das_tickbox":"1","scopus_import":"1","abstract":[{"text":"Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signalling initiation, which requires binding of BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure, BL was bound to the hydrophobic cavity formed by the transmembrane domain, and triggered local conformational changes. Together, our data provide additional insights into the ABC transporter-mediated BR export.","lang":"eng"}],"doi":"10.1016/j.xplc.2024.101181","day":"13","DOAJ_listed":"1","date_published":"2025-01-13T00:00:00Z","acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We thank Yaowei Wang, Yongming Luo, and Nemanja Vukašinović (VIB-UGhent, Belgium) for useful discussions and technical support. L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation. No conflict of interest is declared.","_id":"18619","department":[{"_id":"JiFr"}],"month":"01","oa_version":"Published Version","publisher":"Cell Press","external_id":{"pmid":["39497419"],"isi":["001416757300001"]},"intvolume":"         6","researchdata_availability":"yes","volume":6,"publication_identifier":{"issn":["2590-3462"]},"article_type":"original","quality_controlled":"1","pmid":1,"issue":"1","article_number":"101181"},{"status":"public","ec_funded":1,"ddc":["580"],"type":"journal_article","OA_type":"hybrid","publication_status":"published","file":[{"success":1,"date_updated":"2025-07-31T07:03:43Z","relation":"main_file","content_type":"application/pdf","date_created":"2025-07-31T07:03:43Z","file_name":"2025_PlantCell_Gallei.pdf","access_level":"open_access","file_size":53904111,"file_id":"20092","creator":"dernst","checksum":"9d3f8218ff37a29f29c48a7bbe831bd3"}],"title":"Super-resolution expansion microscopy in plant roots","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","grant_number":"ALTF 679-2018","_id":"269B5B22-B435-11E9-9278-68D0E5697425"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"isi":1,"fulldoi":"https://doi.org/10.1093/plcell/koaf006","related_material":{"record":[{"relation":"research_data","status":"public","id":"18837"},{"relation":"earlier_version","status":"public","id":"18689"}]},"oa":1,"has_accepted_license":"1","file_date_updated":"2025-07-31T07:03:43Z","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","corr_author":"1","OA_place":"publisher","author":[{"last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","last_name":"Vistunou","full_name":"Vistunou, Vitali"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854"},{"full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315"},{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-20T09:19:12Z","citation":{"chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>.","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots. The Plant Cell. 37(4), koaf006.","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>"},"date_created":"2025-02-05T06:52:06Z","year":"2025","publication":"The Plant Cell","scopus_import":"1","abstract":[{"lang":"eng","text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. "}],"date_published":"2025-04-01T00:00:00Z","day":"01","doi":"10.1093/plcell/koaf006","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"M-Shop"}],"publisher":"Oxford University Press","oa_version":"Published Version","month":"04","external_id":{"isi":["001462763100001"],"pmid":["39792900"]},"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis project has received funding from the European Research Council under the Horizon 2020 Framework Programme (grant agreement No 742985, J.F.). It has also received funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018). M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship no. 26137. The project has further received funding from the Austrian Science Fund, via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship from the Human Frontier Science Program (LT000557/2018). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"_id":"19003","quality_controlled":"1","pmid":1,"issue":"4","article_number":"koaf006","intvolume":"        37","article_type":"original","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"volume":37},{"date_created":"2025-10-12T22:01:25Z","year":"2025","citation":{"mla":"King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>, vol. 16, 8763, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>.","short":"D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025).","ieee":"D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and long-range interactions from energies and forces,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","chicago":"King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>.","apa":"King, D. S., Kim, D., Zhong, P., &#38; Cheng, B. (2025). Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>","ista":"King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range interactions from energies and forces. Nature Communications. 16, 8763.","ama":"King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>"},"publication":"Nature Communications","author":[{"full_name":"King, Daniel S.","first_name":"Daniel S.","last_name":"King"},{"last_name":"Kim","first_name":"Dongjin","full_name":"Kim, Dongjin"},{"full_name":"Zhong, Peichen","first_name":"Peichen","last_name":"Zhong"},{"last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"date_updated":"2026-10-20T09:48:07Z","das_tickbox":"1","scopus_import":"1","abstract":[{"text":"Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges.","lang":"eng"}],"doi":"10.1038/s41467-025-63852-x","day":"01","DOAJ_listed":"1","date_published":"2025-10-01T00:00:00Z","acknowledgement":"We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq) dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq) dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.","_id":"20452","department":[{"_id":"BiCh"}],"month":"10","oa_version":"Published Version","publisher":"Springer Nature","external_id":{"isi":["001586620700015"],"pmid":["41034200"]},"intvolume":"        16","researchdata_availability":"no","volume":16,"article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","pmid":1,"article_number":"8763","ddc":["000"],"OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1038/s41467-025-63852-x","file":[{"file_id":"20460","file_size":4907055,"creator":"dernst","checksum":"34b6005d349bbff85839c4e51d6c8725","success":1,"date_updated":"2025-10-13T07:54:51Z","relation":"main_file","date_created":"2025-10-13T07:54:51Z","content_type":"application/pdf","access_level":"open_access","file_name":"2025_NatureComm_King.pdf"}],"title":"Machine learning of charges and long-range interactions from energies and forces","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"dataavailabilitystatement":"The training sets, training scripts, MD input files, and trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit; see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided with this paper. Source data are provided with this paper.","oa":1,"related_material":{"record":[{"status":"public","id":"22770","relation":"research_data"}]},"has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2025-10-13T07:54:51Z","OA_place":"publisher","corr_author":"1","supplementarymaterial":"no","PlanS_conform":"1"},{"issue":"5","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["1553-7358"]},"volume":21,"intvolume":"        21","external_id":{"isi":["001481670600002"],"arxiv":["2410.09476"]},"publisher":"Public Library of Science","month":"05","oa_version":"Published Version","department":[{"_id":"GradSch"}],"_id":"19702","date_published":"2025-05-01T00:00:00Z","day":"01","DOAJ_listed":"1","doi":"10.1371/journal.pcbi.1012868","scopus_import":"1","abstract":[{"text":"Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process.","lang":"eng"}],"date_updated":"2026-10-20T09:45:59Z","author":[{"first_name":"Lenka","id":"17691681-50b9-11ef-ad56-edf4cacb21b0","last_name":"Kopfová","full_name":"Kopfová, Lenka"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"}],"publication":"PLoS Computational Biology","citation":{"ama":"Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. 2025;21(5):e1012868. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>","ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS Computational Biology. 21(5), e1012868.","apa":"Kopfová, L., &#38; Tkadlec, J. (2025). Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>","chicago":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>. Public Library of Science, 2025. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>.","mla":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>, vol. 21, no. 5, Public Library of Science, 2025, p. e1012868, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>.","ieee":"L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,” <i>PLoS Computational Biology</i>, vol. 21, no. 5. Public Library of Science, p. e1012868, 2025.","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868."},"date_created":"2025-05-18T22:02:50Z","year":"2025","OA_place":"publisher","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2025-05-19T07:45:31Z","oa":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"e1012868","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"creator":"dernst","checksum":"73e35151eebd5064972c5a07ffdf2b69","file_id":"19709","file_size":6805943,"content_type":"application/pdf","date_created":"2025-05-19T07:45:31Z","file_name":"2025_PloSCompBio_Kopfova.pdf","access_level":"open_access","relation":"main_file","date_updated":"2025-05-19T07:45:31Z","success":1}],"title":"Colonization times in Moran process on graphs","arxiv":1,"fulldoi":"https://doi.org/10.1371/journal.pcbi.1012868","isi":1,"status":"public","type":"journal_article","OA_type":"gold","ddc":["000"]},{"fulldoi":"https://doi.org/10.5281/zenodo.16415060","day":"24","date_published":"2025-07-24T00:00:00Z","doi":"10.5281/zenodo.16415060","title":"BingqingCheng/cace-lr-fit: V0","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.16415061","open_access":"1"}],"OA_type":"green","citation":{"apa":"Cheng, B., King, D., Kim, D., &#38; Zhong, P. (2025). BingqingCheng/cace-lr-fit: V0. Zenodo. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>","ista":"Cheng B, King D, Kim D, Zhong P. 2025. BingqingCheng/cace-lr-fit: V0, Zenodo, <a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","ama":"Cheng B, King D, Kim D, Zhong P. BingqingCheng/cace-lr-fit: V0. 2025. doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>","mla":"Cheng, Bingqing, et al. <i>BingqingCheng/Cace-Lr-Fit: V0</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","short":"B. Cheng, D. King, D. Kim, P. Zhong, (2025).","ieee":"B. Cheng, D. King, D. Kim, and P. Zhong, “BingqingCheng/cace-lr-fit: V0.” Zenodo, 2025.","chicago":"Cheng, Bingqing, Daniel King, Dongjin Kim, and Peichen Zhong. “BingqingCheng/Cace-Lr-Fit: V0.” Zenodo, 2025. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>."},"ddc":["000"],"date_created":"2026-08-27T12:13:55Z","year":"2025","date_updated":"2026-10-20T09:48:08Z","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng"},{"first_name":"Daniel","last_name":"King","full_name":"King, Daniel"},{"full_name":"Kim, Dongjin","first_name":"Dongjin","last_name":"Kim"},{"full_name":"Zhong, Peichen","last_name":"Zhong","first_name":"Peichen"}],"status":"public","OA_place":"repository","department":[{"_id":"BiCh"}],"_id":"22770","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20452"}]},"oa_version":"None","month":"07","oa":1},{"type":"journal_article","OA_type":"hybrid","ddc":["580"],"ec_funded":1,"status":"public","fulldoi":"https://doi.org/10.1016/j.cell.2025.08.026","isi":1,"publication_status":"published","project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"name":"Cell surface receptor complexes for auxin signaling in plants","_id":"26060676-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 985-2016"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism","file":[{"checksum":"8ac396a0806ad7f2e4e7a0c1eed712ce","creator":"dernst","file_size":17825465,"file_id":"20679","file_name":"2025_Cell_Rodriguez.pdf","access_level":"open_access","date_created":"2025-11-24T10:55:18Z","content_type":"application/pdf","date_updated":"2025-11-24T10:55:18Z","relation":"main_file","success":1}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"6138-6150.e17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-11-24T10:55:18Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"19399","relation":"earlier_version"},{"status":"for_moderation","id":"23145","relation":"dissertation_contains"}]},"oa":1,"corr_author":"1","OA_place":"publisher","PlanS_conform":"1","publication":"Cell","citation":{"chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>.","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism,” <i>Cell</i>, vol. 188, no. 22. Cell Press, p. 6138–6150.e17, 2025.","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml, Cell 188 (2025) 6138–6150.e17.","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>, vol. 188, no. 22, Cell Press, 2025, p. 6138–6150.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>.","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J. 2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. 2025;188(22):6138-6150.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>"},"year":"2025","date_created":"2025-11-19T09:44:31Z","date_updated":"2026-10-20T11:48:38Z","author":[{"last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii"},{"full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch"},{"full_name":"Yu, Yongfan","first_name":"Yongfan","last_name":"Yu"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","last_name":"Gelová"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"first_name":"Meng","last_name":"Chen","full_name":"Chen, Meng"},{"last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"first_name":"Maria Mar","last_name":"Marques-Bueno","full_name":"Marques-Bueno, Maria Mar"},{"full_name":"Quddoos, Zainab","first_name":"Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","last_name":"Quddoos"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","full_name":"Kulich, Ivan"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"30","date_published":"2025-10-30T00:00:00Z","doi":"10.1016/j.cell.2025.08.026","abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1) receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably for other self-organizing developmental phenomena.","lang":"eng"}],"department":[{"_id":"JiFr"},{"_id":"XiFe"}],"_id":"20656","acknowledgement":"We gratefully acknowledge Tongda Xu for experimental, material, and conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at the Institute of Science and Technology Austria (ISTA) for their excellent service and assistance. The research leading to these results has received funding from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003 implemented within the Palacký University Young Researcher Grant.","external_id":{"pmid":["41043433"],"isi":["001616077900005"]},"publisher":"Cell Press","month":"10","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["0092-8674"]},"volume":188,"intvolume":"       188","pmid":1,"issue":"22","quality_controlled":"1"},{"external_id":{"biorxivid":["10.1101/2025.10.17.683082"]},"month":"10","oa_version":"Preprint","_id":"23174","department":[{"_id":"JiFr"}],"acknowledgement":"We gratefully acknowledge Dr. Andrea Bleckmann, creator of pBLAX000 vector and Dr. Shiqiang Gao for donation of template used in XXM-ER cloning. This research was supported by the Laboratory Support Facility, the Plant Facility, the IT Facility and the Imaging and Optical Facility of the Institute of Science and Technology Austria. The graphical elements used in Fig. 5 were adapted and modified from Servier, https://smart.servier.com, and are used under CC BY 3.0 licence. The authors acknowledge the use of AI-tools (Microsoft Copilot, Gemini) for language refinement. All content was critically reviewed by authors.\r\n\r\nFunder Information Declared\r\nEuropean Research Council, 101142681 CYNIPS\r\nAustrian Science Fund, P 37051-B","date_updated":"2026-10-20T11:48:37Z","author":[{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","full_name":"Kulich, Ivan"},{"full_name":"Vladimirtsev, Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii","last_name":"Vladimirtsev"},{"full_name":"Huang, Shouguang","first_name":"Shouguang","last_name":"Huang"},{"full_name":"Hedrich, Rainer","first_name":"Rainer","last_name":"Hedrich"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.10.17.683082"}],"publication":"bioRxiv","year":"2025","date_created":"2026-10-19T11:44:48Z","citation":{"apa":"Randuch, M., Kulich, I., Vladimirtsev, D., Huang, S., Hedrich, R., &#38; Friml, J. (n.d.). Cytosolic Ca2+ as a universal signal for rapid root growth regulation. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.17.683082\">https://doi.org/10.1101/2025.10.17.683082</a>","ista":"Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>.","ama":"Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>","mla":"Randuch, Marek, et al. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.17.683082\">10.1101/2025.10.17.683082</a>.","short":"M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, J. Friml, BioRxiv (n.d.).","ieee":"M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, and J. Friml, “Cytosolic Ca2+ as a universal signal for rapid root growth regulation,” <i>bioRxiv</i>. .","chicago":"Randuch, Marek, Ivan Kulich, Dmitrii Vladimirtsev, Shouguang Huang, Rainer Hedrich, and Jiří Friml. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.17.683082\">https://doi.org/10.1101/2025.10.17.683082</a>."},"doi":"10.1101/2025.10.17.683082","day":"17","date_published":"2025-10-17T00:00:00Z","abstract":[{"lang":"eng","text":"Roots must continuously adapt their growth and have evolved the ability to rapidly respond to diverse environmental and hormonal cues, including the phytohormone auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic calcium (Ca²⁺) elevation, and extracellular pH increase, but how these processes lead to rapid growth regulation remains unclear. Here, we show that cytosolic Ca²⁺ acts as a universal signal integrating diverse cues for rapid regulation of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis, we demonstrate that a swift rise in cytosolic Ca²⁺ is the primary target of auxin signaling affecting growth inhibition. Disruption of Ca²⁺ influx abolishes these responses, whereas light-gated Ca²⁺ influx from the apoplast or endoplasmic reticulum stores inhibits growth. Multiple unrelated stimuli—including auxin, extracellular ATP, RALF peptides, and hydrogen peroxide—converge on this Ca²⁺-dependent mechanism. Cytosolic Ca²⁺ elevation thus represents a necessary and sufficient step for rapid growth inhibition, revealing a unifying principle of root signaling."}],"biorxivid":1,"article_processing_charge":"No","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"23145","status":"for_moderation"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"OA_place":"repository","corr_author":"1","status":"public","OA_type":"green","type":"preprint","title":"Cytosolic Ca2+ as a universal signal for rapid root growth regulation","project":[{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants"},{"grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"publication_status":"draft","fulldoi":"https://doi.org/10.1101/2025.10.17.683082"},{"doi":"10.1167/iovs.66.3.49","date_published":"2025-03-01T00:00:00Z","DOAJ_listed":"1","day":"01","scopus_import":"1","abstract":[{"text":"Purpose: Optic nerve crush (ONC) is a model for studying optic nerve trauma. Unilateral ONC induces massive retinal ganglion cell (RGC) degeneration in the affected eye, leading to vision loss within a month. A common assumption has been that the non-injured contralateral eye is unaffected due to the minimal retino-retinal projections of the RGCs at the chiasm. Yet, recently, microglia, the brain-resident macrophages, have shown a responsive phenotype in the contralateral eye after ONC. Whether RGC loss accompanies this phenotype is still controversial.\r\n\r\nMethods: Using the available RGCode algorithm and developing our own RGC-Quant deep-learning-based tool, we quantify RGC's total number and density across the entire retina after ONC.\r\n\r\nResults: We confirm a short-term microglia response in the contralateral eye after ONC, but this did not affect the microglia number. Furthermore, we cannot confirm the previously reported RGC loss between naïve and contralateral retinas 5 weeks after ONC induction across the commonly used Cx3cr1creERT2 and C57BL6/J mouse models. Neither sex nor the direct comparison of the RGC markers Brn3a and RBPMS, with Brn3a co-labeling, on average, 89% of the RBPMS+-cells, explained this discrepancy, suggesting that the early microglia-responsive phenotype does not have immediate consequences on the RGC number.\r\n\r\nConclusions: Our results corroborate that unilateral optic nerve injury elicits a microglial response in the uninjured contralateral eye but without RGC loss. Therefore, the contralateral eye should be treated separately and not as an ONC control.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_updated":"2026-10-20T22:30:07Z","author":[{"last_name":"Schoot Uiterkamp","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E"},{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E"},{"last_name":"Alamalhoda","first_name":"Mohammad","full_name":"Alamalhoda, Mohammad"},{"full_name":"Firoozi, Arsalan","last_name":"Firoozi","first_name":"Arsalan"},{"last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"}],"publication":"Investigative Ophthalmology & Visual Science","year":"2025","date_created":"2025-04-15T13:40:35Z","citation":{"chicago":"Miteva, Florianne E, Margaret E Maes, Mohammad Alamalhoda, Arsalan Firoozi, Gloria Colombo, and Sandra Siegert. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” <i>Investigative Ophthalmology &#38; Visual Science</i>. Association for Research in Vision and Ophthalmology, 2025. <a href=\"https://doi.org/10.1167/iovs.66.3.49\">https://doi.org/10.1167/iovs.66.3.49</a>.","ieee":"F. E. Miteva, M. E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, and S. Siegert, “Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye,” <i>Investigative Ophthalmology &#38; Visual Science</i>, vol. 66, no. 3. Association for Research in Vision and Ophthalmology, 2025.","short":"F.E. Miteva, M.E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, S. Siegert, Investigative Ophthalmology &#38; Visual Science 66 (2025).","mla":"Miteva, Florianne E., et al. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” <i>Investigative Ophthalmology &#38; Visual Science</i>, vol. 66, no. 3, 49, Association for Research in Vision and Ophthalmology, 2025, doi:<a href=\"https://doi.org/10.1167/iovs.66.3.49\">10.1167/iovs.66.3.49</a>.","ama":"Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. <i>Investigative Ophthalmology &#38; Visual Science</i>. 2025;66(3). doi:<a href=\"https://doi.org/10.1167/iovs.66.3.49\">10.1167/iovs.66.3.49</a>","ista":"Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. 2025. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative Ophthalmology &#38; Visual Science. 66(3), 49.","apa":"Miteva, F. E., Maes, M. E., Alamalhoda, M., Firoozi, A., Colombo, G., &#38; Siegert, S. (2025). Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. <i>Investigative Ophthalmology &#38; Visual Science</i>. Association for Research in Vision and Ophthalmology. <a href=\"https://doi.org/10.1167/iovs.66.3.49\">https://doi.org/10.1167/iovs.66.3.49</a>"},"pmid":1,"article_number":"49","issue":"3","quality_controlled":"1","volume":66,"article_type":"original","publication_identifier":{"issn":["1552-5783"]},"intvolume":"        66","external_id":{"pmid":["40126507"]},"month":"03","oa_version":"Published Version","publisher":"Association for Research in Vision and Ophthalmology","_id":"19566","department":[{"_id":"SaSi"}],"acknowledgement":"The authors thank the Scientific Service Units (SSU) of ISTA for the provided resources, specifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael Schunn, for mouse colony management and support. We thank all members of the Siegert group for constant feedback on the project and the manuscript. \r\nSupported in whole or in part by the Austrian Science Fund (FWF) [10.55776/P37131]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. ","project":[{"_id":"7be82147-9f16-11ee-852c-f44682d73140","grant_number":"P37131","name":"Dissecting the morpho-functional relationship of microglia"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"file":[{"content_type":"application/pdf","date_created":"2025-04-15T13:49:10Z","file_name":"2025_IOVS_SchootUiterkamp.pdf","access_level":"open_access","date_updated":"2025-04-15T13:49:10Z","success":1,"relation":"main_file","creator":"dernst","checksum":"e8722ce5792f6c08fe1e191f7de6f147","file_id":"19567","file_size":2721477}],"title":"Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye","publication_status":"published","fulldoi":"https://doi.org/10.1167/iovs.66.3.49","status":"public","APC_amount":"2236,02 EUR","OA_type":"gold","type":"journal_article","ddc":["570"],"OA_place":"publisher","corr_author":"1","article_processing_charge":"Yes","file_date_updated":"2025-04-15T13:49:10Z","has_accepted_license":"1","oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/siegert-lab/RGC-Quant"}],"record":[{"id":"20467","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}]},{"citation":{"ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria.","ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025.","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>."},"year":"2025","date_created":"2025-04-14T06:59:06Z","supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"author":[{"last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","full_name":"Schwarz, Lena A"}],"date_updated":"2026-10-15T22:30:03Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"date_published":"2025-04-14T00:00:00Z","day":"14","doi":"10.15479/AT-ISTA-19557","acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"_id":"19557","publisher":"Institute of Science and Technology Austria","month":"04","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","ddc":["570"],"type":"dissertation","status":"public","fulldoi":"https://doi.org/10.15479/AT-ISTA-19557","publication_status":"published","title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell 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(4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"99","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2026-10-14T22:30:02Z","related_material":{"record":[{"id":"19566","status":"public","relation":"part_of_dissertation"}]},"oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20467","publication_status":"published","title":"The role of cyclooxygenase 1 on microglial response to inflammatory stressors","file":[{"creator":"fschootu","checksum":"03537697be8c688d3a05cf948288e48f","file_id":"20484","file_size":13668588,"content_type":"application/pdf","date_created":"2025-10-17T11:09:11Z","embargo":"2026-10-14","access_level":"open_access","file_name":"2025_Miteva_Florianne_thesis.pdf","relation":"main_file","date_updated":"2026-10-14T22:30:02Z"},{"checksum":"df4930d7211cf9cfe1254b77204dc1d3","creator":"fschootu","file_id":"20525","file_size":28991918,"file_name":"2025_Miteva_florianne_thesis.docx","access_level":"closed","date_created":"2025-10-23T11:33:06Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-10-14T22:30:02Z","embargo_to":"open_access","relation":"source_file"}],"project":[{"_id":"7be82147-9f16-11ee-852c-f44682d73140","grant_number":"P37131","name":"Dissecting the morpho-functional relationship of microglia"}],"type":"dissertation","degree_awarded":"PhD","ddc":["570"],"status":"public","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"alternative_title":["ISTA Thesis"],"_id":"20467","acknowledgement":"The work presented in this Thesis was carried out at the Institute of Science and Technology\r\nAustria (ISTA), and was supported by the Austrian Science Fund (FWF) [10.55776/P37131].\r\nI would like to thank the Scientific Service Units (SSU) of ISTA for the provided resources,\r\nspecifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the\r\nPre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael\r\nSchunn, for mouse colony management and support. ","publisher":"Institute of Science and Technology Austria","month":"10","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"},{"_id":"PreCl"},{"_id":"LifeSc"}],"day":"14","date_published":"2025-10-14T00:00:00Z","doi":"10.15479/AT-ISTA-20467","supervisor":[{"last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"citation":{"ista":"Miteva FE. 2025. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria.","ama":"Miteva FE. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20467\">10.15479/AT-ISTA-20467</a>","apa":"Miteva, F. E. (2025). <i>The role of cyclooxygenase 1 on microglial response to inflammatory stressors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20467\">https://doi.org/10.15479/AT-ISTA-20467</a>","chicago":"Miteva, Florianne E. “The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20467\">https://doi.org/10.15479/AT-ISTA-20467</a>.","mla":"Miteva, Florianne E. <i>The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20467\">10.15479/AT-ISTA-20467</a>.","short":"F.E. Miteva, The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors, Institute of Science and Technology Austria, 2025.","ieee":"F. E. Miteva, “The role of cyclooxygenase 1 on microglial response to inflammatory stressors,” Institute of Science and Technology Austria, 2025."},"year":"2025","date_created":"2025-10-14T10:24:41Z","date_updated":"2026-10-14T22:30:03Z","author":[{"full_name":"Miteva, Florianne E","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Miteva"}]},{"fulldoi":"https://doi.org/10.1038/s41586-025-08669-w","isi":1,"publication_status":"published","project":[{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"title":"TIR1-produced cAMP as a second messenger in transcriptional auxin signalling","file":[{"file_size":13549245,"file_id":"20132","creator":"dernst","checksum":"f5f18081003e7a1b8e372ecb7da82e7d","relation":"main_file","success":1,"date_updated":"2025-08-05T12:29:35Z","date_created":"2025-08-05T12:29:35Z","content_type":"application/pdf","file_name":"2025_Nature_Chen.pdf","access_level":"open_access"}],"type":"journal_article","OA_type":"hybrid","ddc":["580"],"status":"public","corr_author":"1","OA_place":"publisher","PlanS_conform":"1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1011-1016","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-08-05T12:29:35Z","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/updating-the-textbook/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"19478","status":"public"}]},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"day":"24","date_published":"2025-04-24T00:00:00Z","doi":"10.1038/s41586-025-08669-w","abstract":[{"text":"The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming.","lang":"eng"}],"publication":"Nature","citation":{"chicago":"Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08669-w\">https://doi.org/10.1038/s41586-025-08669-w</a>.","mla":"Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” <i>Nature</i>, vol. 640, Springer Nature, 2025, pp. 1011–16, doi:<a href=\"https://doi.org/10.1038/s41586-025-08669-w\">10.1038/s41586-025-08669-w</a>.","short":"H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml, Nature 640 (2025) 1011–1016.","ieee":"H. Chen <i>et al.</i>, “TIR1-produced cAMP as a second messenger in transcriptional auxin signalling,” <i>Nature</i>, vol. 640. Springer Nature, pp. 1011–1016, 2025.","ista":"Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 640, 1011–1016.","ama":"Chen H, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. <i>Nature</i>. 2025;640:1011-1016. doi:<a href=\"https://doi.org/10.1038/s41586-025-08669-w\">10.1038/s41586-025-08669-w</a>","apa":"Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025). TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08669-w\">https://doi.org/10.1038/s41586-025-08669-w</a>"},"year":"2025","date_created":"2025-03-19T09:44:39Z","date_updated":"2026-10-20T22:30:07Z","author":[{"first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","full_name":"Chen, Huihuang"},{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"last_name":"Lu","id":"a8198a14-1ffe-11ee-8b67-d2bdff9d9178","first_name":"Mengting","full_name":"Lu, Mengting"},{"first_name":"M","last_name":"Kwiatkowski","full_name":"Kwiatkowski, M"},{"first_name":"Yuanrong","id":"98605edc-6ce7-11ee-95f3-cc16b866efcd","last_name":"Pei","full_name":"Pei, Yuanrong"},{"first_name":"K","last_name":"Jaworski","full_name":"Jaworski, K"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"article_type":"original","volume":640,"intvolume":"       640","pmid":1,"quality_controlled":"1","department":[{"_id":"JiFr"}],"_id":"19421","acknowledgement":"We are grateful to J. Callis and H.-Q. Yang for sharing materials and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics Facility of the Institute of Science and Technology Austria. This project has received funding from the European Research Council (101142681 CYNIPS) and Austrian Science Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project Committee of the Institute of Science and Technology Austria, and Y.P. was supported by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided by Institute of Science and Technology (IST Austria).","external_id":{"pmid":["40044868"],"isi":["001437493900001"]},"publisher":"Springer Nature","oa_version":"Published Version","month":"04"},{"publication_identifier":{"issn":["2663-337X"]},"month":"04","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","_id":"19478","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"acknowledgement":"This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B).","doi":"10.15479/AT-ISTA-19478","day":"04","date_published":"2025-04-04T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2026-10-09T22:30:04Z","author":[{"last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang"}],"supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2025-04-04T07:48:24Z","year":"2025","citation":{"ieee":"H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025.","short":"H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025.","mla":"Chen, Huihuang. <i>The CAMP Second Messenger in Auxin Signalling</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>.","chicago":"Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>.","apa":"Chen, H. (2025). <i>The cAMP second messenger in auxin signalling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>","ista":"Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria.","ama":"Chen H. The cAMP second messenger in auxin signalling. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>"},"OA_place":"publisher","corr_author":"1","file_date_updated":"2026-10-09T22:30:03Z","has_accepted_license":"1","article_processing_charge":"No","oa":1,"related_material":{"record":[{"status":"public","id":"19421","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13212","status":"public"}]},"page":"118","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"title":"The cAMP second messenger in auxin signalling","file":[{"checksum":"b154973663a1bba505683faab7ae5ead","creator":"hchen","file_id":"19526","file_size":16344814,"file_name":"Thesis_0403_Huihuang.docx","access_level":"closed","date_created":"2025-04-08T08:00:07Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","embargo_to":"open_access","date_updated":"2026-10-08T22:30:02Z"},{"access_level":"open_access","file_name":"Thesis_0406_PDFA_Huihuang_1.pdf","embargo":"2026-10-08","date_created":"2025-04-08T08:00:06Z","content_type":"application/pdf","date_updated":"2026-10-09T22:30:03Z","relation":"main_file","checksum":"0099565f024388830c125ec17375c1a0","creator":"hchen","file_id":"19527","file_size":8482147}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"},{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"publication_status":"published","fulldoi":"https://doi.org/10.15479/AT-ISTA-19478","status":"public","type":"dissertation","ec_funded":1,"ddc":["580"],"degree_awarded":"PhD"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-075-6"]},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"_id":"20798","publisher":"Institute of Science and Technology Austria","month":"12","oa_version":"Published Version","das_tickbox":"1","abstract":[{"text":"Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry.","lang":"eng"}],"day":"11","date_published":"2025-12-11T00:00:00Z","doi":"10.15479/AT-ISTA-20798","citation":{"ama":"Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>","ista":"Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria.","apa":"Wald, S. (2025). <i>Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>","chicago":"Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20798\">https://doi.org/10.15479/AT-ISTA-20798</a>.","ieee":"S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025.","short":"S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025.","mla":"Wald, Sebastian. <i>Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20798\">10.15479/AT-ISTA-20798</a>."},"date_created":"2025-12-11T11:48:11Z","year":"2025","supervisor":[{"orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"}],"author":[{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald","full_name":"Wald, Sebastian","orcid":"0000-0002-5869-1604"}],"date_updated":"2026-07-24T08:07:28Z","keyword":["entanglement-enhanced atom interferometry","cavity QED","spin-squeezing","dipole trap","quantum optics"],"corr_author":"1","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"152","related_material":{"record":[{"relation":"part_of_dissertation","id":"14759","status":"public"}]},"oa":1,"OA_embargo":"6","has_accepted_license":"1","file_date_updated":"2026-06-15T22:30:03Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20798","publication_status":"published","title":"Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry","file":[{"content_type":"application/pdf","date_created":"2025-12-12T11:53:42Z","embargo":"2026-06-15","file_name":"2025_Wald_Sebastian_Thesis.pdf","access_level":"open_access","relation":"main_file","date_updated":"2026-06-15T22:30:03Z","creator":"swald","checksum":"1be72faf529a5e8a2d03cb3d5f808b77","file_id":"20809","file_size":47536855},{"file_id":"20810","file_size":40127601,"creator":"swald","checksum":"8c3a1904dceb4bcd04bc9f14b2594bab","embargo_to":"open_access","relation":"source_file","date_updated":"2026-06-15T22:30:03Z","content_type":"application/x-zip-compressed","date_created":"2025-12-12T11:54:55Z","file_name":"2025_Wald_Sebastian_Thesis.zip","access_level":"closed"}],"doi_confirm":"1","degree_awarded":"PhD","ddc":["530"],"type":"dissertation","status":"public"},{"_id":"19498","department":[{"_id":"MaDe"}],"acknowledgement":"P.L. is a research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron Microscopy Core of the University of Illinois Chicago Research Resources Center as well as the BioCryo facility of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).","external_id":{"isi":["001460952700001"],"pmid":["39919830"]},"month":"03","oa_version":"Published Version","publisher":"Society for Neuroscience","volume":45,"article_type":"original","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"intvolume":"        45","issue":"13","article_number":"e1767232024","pmid":1,"quality_controlled":"1","publication":"Journal of Neuroscience","year":"2025","date_created":"2025-04-06T22:01:32Z","citation":{"chicago":"Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2025. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>.","mla":"Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” <i>Journal of Neuroscience</i>, vol. 45, no. 13, e1767232024, Society for Neuroscience, 2025, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>.","short":"A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond, P. Laurent, Journal of Neuroscience 45 (2025).","ieee":"A. Stratigi <i>et al.</i>, “Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans,” <i>Journal of Neuroscience</i>, vol. 45, no. 13. Society for Neuroscience, 2025.","ista":"Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 45(13), e1767232024.","ama":"Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. 2025;45(13). doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">10.1523/JNEUROSCI.1767-23.2024</a>","apa":"Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond, J. E., &#38; Laurent, P. (2025). Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1767-23.2024\">https://doi.org/10.1523/JNEUROSCI.1767-23.2024</a>"},"date_updated":"2026-07-28T11:30:41Z","author":[{"first_name":"Aikaterini","last_name":"Stratigi","full_name":"Stratigi, Aikaterini"},{"first_name":"Miguel","last_name":"Soler-García","full_name":"Soler-García, Miguel"},{"full_name":"Krout, Mia","last_name":"Krout","first_name":"Mia"},{"full_name":"Shukla, Shikha","last_name":"Shukla","first_name":"Shikha"},{"last_name":"De Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"},{"full_name":"Richmond, Janet E.","first_name":"Janet E.","last_name":"Richmond"},{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"}],"doi":"10.1523/JNEUROSCI.1767-23.2024","date_published":"2025-03-26T00:00:00Z","day":"26","abstract":[{"lang":"eng","text":"A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70."}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2025-09-27T22:30:02Z","OA_embargo":"6 months","oa":1,"OA_place":"publisher","OA_type":"hybrid","type":"journal_article","ddc":["570"],"status":"public","fulldoi":"https://doi.org/10.1523/JNEUROSCI.1767-23.2024","isi":1,"file":[{"date_updated":"2025-09-27T22:30:02Z","relation":"main_file","file_name":"2025_JourNeuroscience_Stratigi.pdf","access_level":"open_access","embargo":"2025-09-27","date_created":"2025-04-07T11:57:19Z","content_type":"application/pdf","file_size":3111735,"file_id":"19525","checksum":"7befc0168f4cd5bd2b0fcff9e2a94784","creator":"dernst"}],"title":"Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans","publication_status":"published"}]