[{"issue":"6795","publication":"Science","intvolume":"       392","corr_author":"1","publication_status":"published","ec_funded":1,"OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":392,"year":"2026","article_processing_charge":"No","scopus_import":"1","date_created":"2026-04-26T22:01:46Z","publisher":"AAAS","language":[{"iso":"eng"}],"_id":"21762","department":[{"_id":"MaLo"},{"_id":"FlSc"},{"_id":"GradSch"},{"_id":"EM-Fac"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","grant_number":"101076260","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery"}],"article_number":"eaea6343","author":[{"first_name":"Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","last_name":"Springstein"},{"first_name":"Manjunath","orcid":"0000-0003-2311-2112","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath","last_name":"Javoor"},{"first_name":"Daniela","full_name":"Megrian, Daniela","last_name":"Megrian"},{"full_name":"Hajdu, Roman","last_name":"Hajdu","first_name":"Roman","id":"ffab949d-133f-11ed-8f02-94de21ace503"},{"last_name":"Hanke","full_name":"Hanke, Dustin M.","first_name":"Dustin M."},{"orcid":"0000-0002-9561-1239","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina"},{"first_name":"Gregor L.","full_name":"Weiss, Gregor L.","last_name":"Weiss"},{"full_name":"Schur, Florian Km","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"quality_controlled":"1","status":"public","external_id":{"pmid":["41990175"]},"title":"Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape","article_type":"original","acknowledgement":"We thank all members of the Loose lab at ISTA for helpful discussions; M. Kojic for critical reading of the manuscript; A. Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids, as well as cyanobacterial strains; T. Dagan and F. Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions; N. Sapay and A. Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins; V.-V. Hodirnau for support in cryo-ET data collection; and J. Hansen for advice about cryo-EM data processing.\r\nThis work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp), the Electron Microscopy Facility (EMF), and the Lab Support Facility (LSF). This work was funded by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant 101034413 to B.L.S.); the European Research Council (ERC) of the European Union (grant ActinID 101076260 to F.K.M.S.); the Swiss National Science Foundation (starting grant TMSGI3_226208 to G.L.W.); and the Jean-Jacques et Letitia Lopez-Loreta Foundation (G.L.W.).","date_updated":"2026-04-28T13:29:05Z","pmid":1,"date_published":"2026-04-16T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low–copy number plasmids. In multicellular cyanobacteria such as Anabaena sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal system named CorMR with a function in cell shape control rather than DNA segregation. Live-cell imaging, in vitro reconstitution, and cryo–electron microscopy revealed that CorM formed dynamically unstable, antiparallel double-stranded filaments that were recruited to the membrane by CorR through an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which excluded them from the poles and division plane. Comparative genomics indicated that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria."}],"oa_version":"None","day":"16","type":"journal_article","doi":"10.1126/science.aea6343","month":"04","citation":{"mla":"Springstein, Benjamin L., et al. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>, vol. 392, no. 6795, eaea6343, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>.","ieee":"B. L. Springstein <i>et al.</i>, “Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape,” <i>Science</i>, vol. 392, no. 6795. AAAS, 2026.","chicago":"Springstein, Benjamin L, Manjunath Javoor, Daniela Megrian, Roman Hajdu, Dustin M. Hanke, Bettina Zens, Gregor L. Weiss, Florian KM Schur, and Martin Loose. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>.","apa":"Springstein, B. L., Javoor, M., Megrian, D., Hajdu, R., Hanke, D. M., Zens, B., … Loose, M. (2026). Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>","short":"B.L. Springstein, M. Javoor, D. Megrian, R. Hajdu, D.M. Hanke, B. Zens, G.L. Weiss, F.K. Schur, M. Loose, Science 392 (2026).","ama":"Springstein BL, Javoor M, Megrian D, et al. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. 2026;392(6795). doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>","ista":"Springstein BL, Javoor M, Megrian D, Hajdu R, Hanke DM, Zens B, Weiss GL, Schur FK, Loose M. 2026. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. 392(6795), eaea6343."},"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]}},{"date_created":"2026-07-19T22:01:48Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","_id":"22372","language":[{"iso":"eng"}],"das_tickbox":"1","publisher":"Springer Nature","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"department":[{"_id":"FlSc"}],"author":[{"last_name":"Lin","full_name":"Lin, Tien Chen","first_name":"Tien Chen"},{"last_name":"Coles","full_name":"Coles, Charlotte H.","first_name":"Charlotte H."},{"first_name":"Eissa","full_name":"Alfadil, Eissa","last_name":"Alfadil"},{"full_name":"Fäßler, Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Andreas","full_name":"Husch, Andreas","last_name":"Husch"},{"last_name":"Dupraz","full_name":"Dupraz, Sebastian","first_name":"Sebastian"},{"last_name":"Pietralla","full_name":"Pietralla, Thorben","first_name":"Thorben"},{"first_name":"Akihiro","last_name":"Narita","full_name":"Narita, Akihiro"},{"first_name":"Max","full_name":"Schelski, Max","last_name":"Schelski"},{"full_name":"Flynn, Kevin C.","last_name":"Flynn","first_name":"Kevin C."},{"full_name":"Stern, Sina","last_name":"Stern","first_name":"Sina"},{"last_name":"Möhl","full_name":"Möhl, Christoph","first_name":"Christoph"},{"last_name":"Hilton","full_name":"Hilton, Brett J.","first_name":"Brett J."},{"last_name":"Vauti","full_name":"Vauti, Franz","first_name":"Franz"},{"last_name":"Arnold","full_name":"Arnold, Hans Henning","first_name":"Hans Henning"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","last_name":"Schur","full_name":"Schur, Florian Km"},{"last_name":"Bradke","full_name":"Bradke, Frank","first_name":"Frank"}],"supplementarymaterial":"yes","publication":"Nature","OA_type":"hybrid","has_accepted_license":"1","oa":1,"PlanS_conform":"1","publication_status":"epub_ahead","year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/","researchdata_availability":"yes","date_published":"2026-07-08T00:00:00Z","pmid":1,"dataavailabilitystatement":"The raw data of the representative images have been deposited into Zenodo (https://doi.org/10.5281/zenodo.20118606)99. Owing to the large file size of the raw image data and the processed data used in the analyses that generated the graphs, we archived the image files in the read-only file archive at the DZNE institute. We provide raw data files upon request. The request can be directed to and will be fulfilled by the lead contact F.B. Source data are provided with this paper. The custom ImageJ macro used for generating kymographs, extracting neurite tip positions and protein intensities is available at GitHub (https://github.com/darkbreaker0/IJ_NeuriteGrowthScript) and Zenodo (https://doi.org/10.5281/zenodo.20118606)99. The custom R and Python scripts used in the study are available at GitHub (https://github.com/darkbreaker0/Arp3_neuronal_polarization_2026) and Zenodo (https://doi.org/10.5281/zenodo.20118606)99. The code used for polarity determination of the actin filament in tomograms is available at Zenodo (https://doi.org/10.5281/zenodo.20081075)93.","main_file_link":[{"url":"https://doi.org/10.1038/s41586-026-10755-6","open_access":"1"}],"day":"08","oa_version":"Published Version","abstract":[{"text":"Neurons acquire polarity by specifying one neurite as the axon, whereas the others become dendrites. But how this fundamental asymmetry is established remains unclear1. Neuronal polarization has been thought to rely primarily on growth cones that sense external cues2. Here we show that growth cones alone do not direct this process and that the soma acts as a central organizer of neuronal polarization. Using live imaging and genetic loss-of-function approaches in vivo, combined with optogenetic control and local cytoskeletal perturbations in cultured neurons, we uncover a soma-initiated oscillatory program that primes axon selection. Periodic actin branching that depends on the actin-related protein 2/3 (ARP2/3) complex at the soma remodels a global actomyosin network, thereby generating an actin wave that retracts neurites before propagating into a single neurite tip. Exposure to this wave relaxes local actomyosin contractility, which drives a transient microtubule-based protrusion and biases this neurite towards axon fate. As the cell exits this oscillatory stage, this neurite can overcome global inhibition and extend independently of ARP2/3, whereas actomyosin activity suppresses axon formation in the remaining neurites so that they subsequently become dendrites. This soma-driven mechanism ensures the emergence of a single axon independent of environmental cues and underpins the unidirectional information flow in neuronal circuits.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41586-026-10755-6","citation":{"ieee":"T. C. Lin <i>et al.</i>, “An intrinsic cytoskeletal oscillator establishes neuronal polarity,” <i>Nature</i>. Springer Nature, 2026.","mla":"Lin, Tien Chen, et al. “An Intrinsic Cytoskeletal Oscillator Establishes Neuronal Polarity.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-026-10755-6\">10.1038/s41586-026-10755-6</a>.","ama":"Lin TC, Coles CH, Alfadil E, et al. An intrinsic cytoskeletal oscillator establishes neuronal polarity. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-026-10755-6\">10.1038/s41586-026-10755-6</a>","short":"T.C. Lin, C.H. Coles, E. Alfadil, F. Fäßler, A. Husch, S. Dupraz, T. Pietralla, A. Narita, M. Schelski, K.C. Flynn, S. Stern, C. Möhl, B.J. Hilton, F. Vauti, H.H. Arnold, F.K. Schur, F. Bradke, Nature (2026).","ista":"Lin TC, Coles CH, Alfadil E, Fäßler F, Husch A, Dupraz S, Pietralla T, Narita A, Schelski M, Flynn KC, Stern S, Möhl C, Hilton BJ, Vauti F, Arnold HH, Schur FK, Bradke F. 2026. An intrinsic cytoskeletal oscillator establishes neuronal polarity. Nature.","apa":"Lin, T. C., Coles, C. H., Alfadil, E., Fäßler, F., Husch, A., Dupraz, S., … Bradke, F. (2026). An intrinsic cytoskeletal oscillator establishes neuronal polarity. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-026-10755-6\">https://doi.org/10.1038/s41586-026-10755-6</a>","chicago":"Lin, Tien Chen, Charlotte H. Coles, Eissa Alfadil, Florian Fäßler, Andreas Husch, Sebastian Dupraz, Thorben Pietralla, et al. “An Intrinsic Cytoskeletal Oscillator Establishes Neuronal Polarity.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-026-10755-6\">https://doi.org/10.1038/s41586-026-10755-6</a>."},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"07","status":"public","quality_controlled":"1","OA_place":"publisher","title":"An intrinsic cytoskeletal oscillator establishes neuronal polarity","external_id":{"pmid":["42420447"]},"article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"date_updated":"2026-07-20T14:18:10Z","acknowledgement":"We thank O. Gruss, E. Handley, H. Herzel, A. Kania, A. Koseska, E. Kiermaier, D. Manstein, C. Niessen, K. Rottner, J. Schiweck, G. Tavosanis, D. Wachten, R. Wedlich-Söldner and W. Witke for critically reading and discussing the manuscript; C. Günter and V. Štimac for feedback on data presentation; B. Randel, J. Benner, L. Meyn and A.-T. Pham for technical assistance; L. M. Neußer, K. Herz, K. Van-De-Kamp and M. Diwo for their support on mice maintenance; H. Fried, I. Koenig, S. Filser and Y. Fu for their technical support on experimental setup; and M. Aghabeig for writing the Fiji macro scripts. C.H.C. was a Human Frontier Science Program Long-term Postdoctoral Fellow (LT000100/2013). F.B. is supported by the Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), the International Foundation for Research in Paraplegia, Wings for Life, ERANET AXON REPAIR, ERANET RATER SCI and the Chan–Zuckerberg Initiative (CZI). F.B. is also funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)–Project-ID 227953431–SFB 1089, SFB 1690 as well as SFB 1158 and SPP 2395. F.B. is a member of the excellence cluster ImmunoSensation2 (EXC2151–390873048) and the iBehave NRW network. F.B. is a recipient of the Roger de Spoelberch Prize. F.K.M.S. acknowledges support from Austrian Science Fund (FWF): P33367. A.N. is supported by JSPS KAKENHI (grant numbers 18H02410 and 21H02440). Open access funding provided by Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) in der Helmholtz-Gemeinschaft."},{"publication":"Advanced Science","supplementarymaterial":"yes","oa":1,"OA_type":"gold","has_accepted_license":"1","publication_status":"epub_ahead","PlanS_conform":"1","year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-07-26T19:01:34Z","article_processing_charge":"Yes","scopus_import":"1","language":[{"iso":"eng"}],"_id":"22403","publisher":"Wiley","das_tickbox":"1","article_number":"e76620","department":[{"_id":"FlSc"},{"_id":"GradSch"}],"author":[{"first_name":"Shengbo","full_name":"You, Shengbo","last_name":"You"},{"full_name":"Varnavides, Georgios","last_name":"Varnavides","first_name":"Georgios"},{"last_name":"Khavnekar","full_name":"Khavnekar, Sagar","first_name":"Sagar"},{"full_name":"Palatkin, Nikita","last_name":"Palatkin","first_name":"Nikita"},{"last_name":"Shao","full_name":"Shao, Sihan","first_name":"Sihan"},{"last_name":"Wu","full_name":"Wu, Mingjian","first_name":"Mingjian"},{"first_name":"Daniel","full_name":"Stroppa, Daniel","last_name":"Stroppa"},{"first_name":"Darya","id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0","last_name":"Chernikova","full_name":"Chernikova, Darya"},{"first_name":"Baixu","full_name":"Zhu, Baixu","last_name":"Zhu"},{"first_name":"Ricardo","last_name":"Egoavil","full_name":"Egoavil, Ricardo"},{"first_name":"Stefano","full_name":"Vespucci, Stefano","last_name":"Vespucci"},{"full_name":"Krishnan, Dileep","last_name":"Krishnan","first_name":"Dileep"},{"first_name":"Xingchen","full_name":"Ye, Xingchen","last_name":"Ye"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM"},{"full_name":"Spiecker, Erdmann","last_name":"Spiecker","first_name":"Erdmann"},{"first_name":"Philipp","full_name":"Pelz, Philipp","last_name":"Pelz"}],"status":"public","OA_place":"publisher","quality_controlled":"1","title":"Gap‐free information transfer in 4D‐STEM via fusion of complementary scattering channels","external_id":{"arxiv":["2512.19460"]},"article_type":"original","ddc":["570","600"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-07-27T06:04:57Z","acknowledgement":"We thank Tadahiro Yokosawa for support and discussions during the experiments. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Project HyperScaleEM, Grant agreement No. 101164581) and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Research Training Group GRK 3103 CorMic: Korrelative Materialmikroskopie – Von nanostrukturierten funktionalen Filmen zu hierarchischen Funktionsmaterialien (project number 537140136). B.Z. and X.Y. were supported by the U.S. National Science Foundation under award CHE-2404338. X.Y. also thanks the Principal Investigator Development in Sustainability Grant from the American Chemical Society.","main_file_link":[{"url":"https://doi.org/10.1002/advs.76620","open_access":"1"}],"date_published":"2026-07-23T00:00:00Z","dataavailabilitystatement":"The data that support the findings of this study are openly available in Zenodo at https://doi.org/10.5281/zenodo.18008901. The reconstruction code is available as an open-source repository at the scatterem github repo.","researchdata_availability":"yes","day":"23","arxiv":1,"abstract":[{"lang":"eng","text":"Linear phase‐contrast scanning transmission electron microscopy (STEM) techniques compatible with high‐throughput 4D‐STEM acquisition are widely used to enhance phase contrast in weakly scattering and beam‐sensitive materials. In these modalities, contrast transfer is often suppressed at low spatial frequencies, resulting in a characteristic contrast gap that limits contrast. Approaches that retain low‐frequency phase contrast exist but typically require substantially increased experimental complexity, restricting routine use. Dark‐field STEM imaging captures this missing low‐frequency information through electrons scattered outside the bright‐field disk, but discards a large fraction of the scattered signal and is therefore dose‐inefficient. Fused Full‐field STEM (FF‐STEM) is introduced as a 4D‐STEM imaging modality that overcomes these limitations by combining ptychographic phase reconstruction with tilt‐corrected dark‐field imaging within a single acquisition. Bright‐field data are used to estimate probe aberrations and reconstruct a high‐resolution phase image, while dark‐field data provide complementary low‐frequency contrast. The two channels are fused in Fourier space using Wiener‐band weighting based on the spectral signal‐to‐noise ratio, yielding transfer‐gap‐free images with high contrast. FF‐STEM preserves the upsampling and depth‐sectioning capabilities of ptychography, adds robust low‐frequency contrast characteristic of dark‐field imaging, and enables dose‐efficient, near–real‐time reconstruction."}],"oa_version":"Published Version","DOAJ_listed":"1","type":"journal_article","doi":"10.1002/advs.76620","month":"07","publication_identifier":{"eissn":["2198-3844"]},"citation":{"ieee":"S. You <i>et al.</i>, “Gap‐free information transfer in 4D‐STEM via fusion of complementary scattering channels,” <i>Advanced Science</i>. Wiley, 2026.","mla":"You, Shengbo, et al. “Gap‐free Information Transfer in 4D‐STEM via Fusion of Complementary Scattering Channels.” <i>Advanced Science</i>, e76620, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/advs.76620\">10.1002/advs.76620</a>.","ama":"You S, Varnavides G, Khavnekar S, et al. Gap‐free information transfer in 4D‐STEM via fusion of complementary scattering channels. <i>Advanced Science</i>. 2026. doi:<a href=\"https://doi.org/10.1002/advs.76620\">10.1002/advs.76620</a>","short":"S. You, G. Varnavides, S. Khavnekar, N. Palatkin, S. Shao, M. Wu, D. Stroppa, D. Chernikova, B. Zhu, R. Egoavil, S. Vespucci, D. Krishnan, X. Ye, F.K. Schur, E. Spiecker, P. Pelz, Advanced Science (2026).","ista":"You S, Varnavides G, Khavnekar S, Palatkin N, Shao S, Wu M, Stroppa D, Chernikova D, Zhu B, Egoavil R, Vespucci S, Krishnan D, Ye X, Schur FK, Spiecker E, Pelz P. 2026. Gap‐free information transfer in 4D‐STEM via fusion of complementary scattering channels. Advanced Science., e76620.","apa":"You, S., Varnavides, G., Khavnekar, S., Palatkin, N., Shao, S., Wu, M., … Pelz, P. (2026). Gap‐free information transfer in 4D‐STEM via fusion of complementary scattering channels. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.76620\">https://doi.org/10.1002/advs.76620</a>","chicago":"You, Shengbo, Georgios Varnavides, Sagar Khavnekar, Nikita Palatkin, Sihan Shao, Mingjian Wu, Daniel Stroppa, et al. “Gap‐free Information Transfer in 4D‐STEM via Fusion of Complementary Scattering Channels.” <i>Advanced Science</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/advs.76620\">https://doi.org/10.1002/advs.76620</a>."}},{"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","quality_controlled":"1","OA_place":"publisher","status":"public","acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","date_updated":"2026-04-07T11:48:07Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"article_type":"original","DOAJ_listed":"1","abstract":[{"lang":"eng","text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases."}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"day":"11","date_published":"2025-06-11T00:00:00Z","file":[{"file_id":"19802","content_type":"application/pdf","file_size":7238179,"date_created":"2025-06-10T07:24:46Z","date_updated":"2025-06-10T07:24:46Z","success":1,"file_name":"2025_BiophysicalReports_Vorlaufer.pdf","checksum":"4018c833f25a3ad3b57e3577fed70334","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_identifier":{"eissn":["2667-0747"]},"citation":{"ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Elsevier, 2025.","mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>"},"month":"06","doi":"10.1016/j.bpr.2025.100211","type":"journal_article","intvolume":"         5","corr_author":"1","issue":"2","publication":"Biophysical Reports","volume":5,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","file_date_updated":"2025-06-10T07:24:46Z","ec_funded":1,"publication_status":"published","has_accepted_license":"1","OA_type":"gold","oa":1,"publisher":"Elsevier","language":[{"iso":"eng"}],"_id":"19795","scopus_import":"1","article_processing_charge":"Yes","date_created":"2025-06-08T22:01:22Z","related_material":{"record":[{"id":"20206","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501"},{"first_name":"Nikolai","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","full_name":"Semenov, Nikolai","last_name":"Semenov"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","orcid":"0000-0003-2311-2112","full_name":"Javoor, Manjunath","last_name":"Javoor"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","last_name":"Zens"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas"},{"last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba"},{"id":"EE8452B8-C26A-11E9-B157-E80CE6697425","first_name":"Marek","full_name":"Suplata, Marek","last_name":"Suplata"},{"first_name":"Wiebke","orcid":"0000-0003-0201-2315","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Andreas","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","full_name":"Wartak, Andreas","last_name":"Wartak"},{"orcid":"0000-0003-4790-8078","first_name":"Florian Km","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian Km"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G"}],"project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_number":"100211"},{"date_updated":"2026-05-20T08:20:27Z","acknowledgement":"We thank C. Cuveillier, J. Delaroche, T. Ferraro, and A. Zanchi for help with TIRF experiments, electron microscopy preparation, data analysis, and cell cultures, respectively; A. Antkowiak, C. Bosc, C. Fassier, A. Fourest-Lieuvin, and V. Brandt for helpful discussions. We acknowledge the contribution of the Photonic Imaging Center of Grenoble Institute Neuroscience which is part of the ISdV core facility and certified by the IBiSA label and ICM.Quant (RRID:SCR_026393) core facility of the Paris Brain Institute (ICM); the AniRA lentivector production facility from the CELPHEDIA Infrastructure and SFR Biosciences (UAR3444/CNRS, US8/Inserm, ENS de Lyon, UCBL); the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp, A. Schloegl and S. Elefante); and the Electron Microscopy Facility (EMF, V.V. Hodirnau). The software programs used for the processing were supported by SBGrid (www.sbgrid.org). This work was supported by the Agence Nationale pour la Recherche (AXYON: ANR-18-CE16-0009-01, S.H.), Austrian Science Fund (FWF) grants (P33367, F.K.M.S.; E435, J.M.H.), ChanZuckerberg Initiative (CZI) grant (DAF2021-234754, F.K.M.S.), Hereditary Disease Foundation Research Grant (HDF 990846, M.C.), European Union (ERC: ActinID 101076260, F.K.M.S.), Fondation pour la Recherche Médicale (FRM: équipe labellisée DEQ202203014675, S.H.; PhD fellowship, FDT202001010865, R.C.), Korea Health Industry Development Institute (KHIDI) (Korea-Switzerland global research support grant: RS-2023-00266300, J.-J.S.), National Research Foundation (NRF) of Korea (Korea-Austria collaborative grant NRF-2019K1A3A1A181160, J.-J.S. and F.K.M.S.; NRF-2020R1A2B5B03001517 and RS-2024-00333346 and RS-2024-00436173, J.-J.S.; 2021R1C1C1006700, D.K.).","article_type":"original","ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization","external_id":{"pmid":["40971423"],"isi":["001575751700013"]},"APC_amount":"1395,61 EUR","status":"public","OA_place":"publisher","quality_controlled":"1","month":"09","publication_identifier":{"issn":["2375-2548"]},"citation":{"ieee":"R. Carpentier <i>et al.</i>, “Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization,” <i>Science Advances</i>, vol. 11, no. 38. AAAS, 2025.","mla":"Carpentier, Rémi, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” <i>Science Advances</i>, vol. 11, no. 38, eadw4124, AAAS, 2025, doi:<a href=\"https://doi.org/10.1126/sciadv.adw4124\">10.1126/sciadv.adw4124</a>.","short":"R. Carpentier, J. Kim, M. Capizzi, H. Kim, F. Fäßler, J. Hansen, M.J. Kim, E. Denarier, B. Blot, M. Degennaro, S. Labou, I. Arnal, M.J. Marcaida, M.D. Peraro, D. Kim, F.K. Schur, J.-J. Song, S. Humbert, Science Advances 11 (2025).","ama":"Carpentier R, Kim J, Capizzi M, et al. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. <i>Science Advances</i>. 2025;11(38). doi:<a href=\"https://doi.org/10.1126/sciadv.adw4124\">10.1126/sciadv.adw4124</a>","ista":"Carpentier R, Kim J, Capizzi M, Kim H, Fäßler F, Hansen J, Kim MJ, Denarier E, Blot B, Degennaro M, Labou S, Arnal I, Marcaida MJ, Peraro MD, Kim D, Schur FK, Song J-J, Humbert S. 2025. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. Science Advances. 11(38), eadw4124.","chicago":"Carpentier, Rémi, Jaesung Kim, Mariacristina Capizzi, Hyeongju Kim, Florian Fäßler, Jesse Hansen, Min Jeong Kim, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” <i>Science Advances</i>. AAAS, 2025. <a href=\"https://doi.org/10.1126/sciadv.adw4124\">https://doi.org/10.1126/sciadv.adw4124</a>.","apa":"Carpentier, R., Kim, J., Capizzi, M., Kim, H., Fäßler, F., Hansen, J., … Humbert, S. (2025). Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adw4124\">https://doi.org/10.1126/sciadv.adw4124</a>"},"type":"journal_article","doi":"10.1126/sciadv.adw4124","day":"19","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Huntingtin protein (HTT), named for its role in Huntington’s disease, has been best understood as a scaffolding protein that promotes vesicle transport by molecular motors along microtubules. Here, we show that HTT also interacts with the actin cytoskeleton, and its loss of function disturbs the morphology and function of the axonal growth cone. We demonstrate that HTT organizes F-actin into bundles. Cryo–electron tomography (cryo-ET) and subtomogram averaging (STA) structural analyses reveal that HTT’s N-terminal HEAT and Bridge domains wrap around F-actin, while the C-terminal HEAT domain is displaced; furthermore, HTT dimerizes via the N-HEAT domain to bridge parallel actin filaments separated by ~20 nanometers. Our study provides the structural basis for understanding how HTT interacts with and organizes the actin cytoskeleton."}],"DOAJ_listed":"1","file":[{"creator":"dernst","checksum":"4e2407bdabf8d53f399eb8a20d86218e","relation":"main_file","access_level":"open_access","date_updated":"2025-09-23T07:57:51Z","file_name":"2025_ScienceAdvance_Carpentier.pdf","success":1,"date_created":"2025-09-23T07:57:51Z","file_size":3599137,"file_id":"20372","content_type":"application/pdf"}],"isi":1,"pmid":1,"date_published":"2025-09-19T00:00:00Z","file_date_updated":"2025-09-23T07:57:51Z","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":11,"oa":1,"OA_type":"gold","has_accepted_license":"1","publication_status":"published","PlanS_conform":"1","intvolume":"        11","corr_author":"1","publication":"Science Advances","issue":"38","author":[{"first_name":"Rémi","full_name":"Carpentier, Rémi","last_name":"Carpentier"},{"last_name":"Kim","full_name":"Kim, Jaesung","first_name":"Jaesung"},{"full_name":"Capizzi, Mariacristina","last_name":"Capizzi","first_name":"Mariacristina"},{"full_name":"Kim, Hyeongju","last_name":"Kim","first_name":"Hyeongju"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"full_name":"Hansen, Jesse","last_name":"Hansen","orcid":"0000-0001-7967-2085","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"first_name":"Min Jeong","last_name":"Kim","full_name":"Kim, Min Jeong"},{"first_name":"Eric","last_name":"Denarier","full_name":"Denarier, Eric"},{"full_name":"Blot, Béatrice","last_name":"Blot","first_name":"Béatrice"},{"first_name":"Marine","full_name":"Degennaro, Marine","last_name":"Degennaro"},{"first_name":"Sophia","last_name":"Labou","full_name":"Labou, Sophia"},{"first_name":"Isabelle","full_name":"Arnal, Isabelle","last_name":"Arnal"},{"last_name":"Marcaida","full_name":"Marcaida, Maria J.","first_name":"Maria J."},{"full_name":"Peraro, Matteo Dal","last_name":"Peraro","first_name":"Matteo Dal"},{"first_name":"Doory","full_name":"Kim, Doory","last_name":"Kim"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur"},{"first_name":"Ji-Joon","last_name":"Song","full_name":"Song, Ji-Joon"},{"full_name":"Humbert, Sandrine","last_name":"Humbert","first_name":"Sandrine"}],"article_number":"eadw4124","department":[{"_id":"FlSc"}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"grant_number":"101076260","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"language":[{"iso":"eng"}],"_id":"20370","publisher":"AAAS","date_created":"2025-09-22T08:00:52Z","article_processing_charge":"Yes","scopus_import":"1"},{"OA_place":"publisher","quality_controlled":"1","status":"public","page":"268-276","external_id":{"oaworkid":["W4402316284"],"pmid":["39242978"],"isi":["001306564000001"]},"APC_amount":"12348 EUR","title":"Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice","ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","acknowledgement":"This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice.","date_updated":"2026-03-16T12:55:18Z","isi":1,"date_published":"2025-02-01T00:00:00Z","pmid":1,"oaworkid":1,"file":[{"date_created":"2025-04-23T07:02:33Z","file_size":13724041,"file_id":"19608","content_type":"application/pdf","checksum":"c641ad94afb28917b20425db676fc3ee","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2025-04-23T07:02:33Z","file_name":"2025_NatureStrucBio_Obr.pdf","success":1}],"abstract":[{"lang":"eng","text":"Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa_version":"Published Version","day":"01","doi":"10.1038/s41594-024-01390-8","type":"journal_article","month":"02","citation":{"ieee":"M. Obr <i>et al.</i>, “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 268–276, 2025.","mla":"Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 268–76, doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>.","short":"M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural &#38; Molecular Biology 32 (2025) 268–276.","ama":"Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:268-276. doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>","ista":"Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural &#38; Molecular Biology. 32, 268–276.","apa":"Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>","chicago":"Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>."},"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"publication":"Nature Structural & Molecular Biology","corr_author":"1","intvolume":"        32","publication_status":"published","oa":1,"OA_type":"hybrid","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":32,"file_date_updated":"2025-04-23T07:02:33Z","year":"2025","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_created":"2024-09-08T10:29:06Z","publisher":"Springer Nature","_id":"17884","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"},{"_id":"LeSa"}],"project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"author":[{"last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971","first_name":"Mathias","full_name":"Percipalle, Mathias","last_name":"Percipalle"},{"full_name":"Chernikova, Darya","last_name":"Chernikova","first_name":"Darya","id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0"},{"last_name":"Yang","full_name":"Yang, Huixin","first_name":"Huixin"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","last_name":"Thader"},{"id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Pinke","full_name":"Pinke, Gergely"},{"full_name":"Porley, Dario J","last_name":"Porley","first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mansky, Louis M.","last_name":"Mansky","first_name":"Louis M."},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."},{"first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM"}]},{"keyword":["Molecular Biology","Structural Biology"],"corr_author":"1","intvolume":"        31","publication":"Nature Structural & Molecular Biology","year":"2024","file_date_updated":"2024-07-22T11:27:22Z","volume":31,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","OA_type":"hybrid","oa":1,"publication_status":"published","_id":"14979","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2024-02-12T09:59:45Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18766"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","first_name":"Julia","full_name":"Datler, Julia","last_name":"Datler"},{"first_name":"Jesse","orcid":"0000-0001-7967-2085","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","last_name":"Hansen"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Thader, Andreas","last_name":"Thader"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"last_name":"Bauer","full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur"}],"project":[{"call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","external_id":{"isi":["001158144600002"],"pmid":["38316877"]},"APC_amount":"11700 EUR","page":"1114-1123","status":"public","quality_controlled":"1","OA_place":"publisher","date_updated":"2026-04-07T12:59:44Z","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"day":"01","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"file":[{"date_created":"2024-07-22T11:27:22Z","file_size":17485494,"content_type":"application/pdf","file_id":"17307","access_level":"open_access","relation":"main_file","checksum":"bda7bf65d81455480efaed8ca293b0db","creator":"dernst","file_name":"2024_NatureStrucBio_Datler.pdf","success":1,"date_updated":"2024-07-22T11:27:22Z"}],"pmid":1,"date_published":"2024-07-01T00:00:00Z","isi":1,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"citation":{"apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024."},"month":"07","type":"journal_article","doi":"10.1038/s41594-023-01201-6"},{"author":[{"orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina"},{"first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","last_name":"Hansen"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"last_name":"Datler","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"full_name":"Alanko, Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H"},{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_number":"e202309125","publisher":"Rockefeller University Press","language":[{"iso":"eng"}],"_id":"15146","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","date_created":"2024-03-21T06:45:51Z","volume":223,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","file_date_updated":"2024-03-25T12:52:04Z","ec_funded":1,"publication_status":"published","has_accepted_license":"1","oa":1,"intvolume":"       223","corr_author":"1","issue":"6","publication":"Journal of Cell Biology","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024)."},"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"month":"03","doi":"10.1083/jcb.202309125","type":"journal_article","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"oa_version":"Published Version","day":"20","date_published":"2024-03-20T00:00:00Z","pmid":1,"isi":1,"file":[{"content_type":"application/pdf","file_id":"15188","date_created":"2024-03-25T12:52:04Z","file_size":11907016,"success":1,"file_name":"2024_JCB_Zens.pdf","date_updated":"2024-03-25T12:52:04Z","access_level":"open_access","relation":"main_file","checksum":"90d1984a93660735e506c2a304bc3f73","creator":"dernst"}],"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","date_updated":"2025-09-04T13:17:16Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"article_type":"original","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","quality_controlled":"1","status":"public"},{"related_material":{"record":[{"id":"12334","status":"public","relation":"part_of_dissertation"},{"id":"14979","status":"public","relation":"part_of_dissertation"}]},"date_created":"2025-01-07T10:23:12Z","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"18766","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"author":[{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Datler","full_name":"Datler, Julia"}],"supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"corr_author":"1","keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"oa":1,"has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-01-07T12:15:14Z","year":"2024","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","degree_awarded":"PhD","file":[{"file_id":"18769","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":38814932,"date_created":"2025-01-07T12:15:11Z","date_updated":"2025-01-07T12:15:11Z","file_name":"PhD_thesis_Julia_Datler.docx","creator":"jstanger","checksum":"3e51cab327c754045c3d29c1a50cc9a9","relation":"source_file","access_level":"closed"},{"date_updated":"2025-01-07T12:15:14Z","success":1,"file_name":"PhD_thesis_Julia_Datler.pdf","creator":"jstanger","checksum":"22fabe5b97950bf852212f6edb555173","relation":"main_file","access_level":"open_access","file_id":"18770","content_type":"application/pdf","date_created":"2025-01-07T12:15:14Z","file_size":12044865}],"date_published":"2024-12-30T00:00:00Z","day":"30","abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Published Version","type":"dissertation","doi":"10.15479/at:ista:18766","month":"12","publication_identifier":{"isbn":["978-3-99078-049-7"],"issn":["2663-337X"]},"citation":{"mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>.","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>.","apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>"},"status":"public","OA_place":"publisher","title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","page":"106","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"date_updated":"2026-04-07T12:59:44Z","alternative_title":["ISTA thesis"],"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample."},{"status":"public","OA_place":"publisher","quality_controlled":"1","title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","external_id":{"pmid":["38117593"]},"article_type":"original","ddc":["570"],"tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"date_updated":"2025-01-29T08:16:20Z","acknowledgement":"We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"date_updated":"2025-01-29T08:12:11Z","success":1,"file_name":"2024_MolecularBioCell_Sarkany.pdf","checksum":"d7deb6390f294da69321cfbe352ed611","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"18935","content_type":"application/pdf","file_size":1699180,"date_created":"2025-01-29T08:12:11Z"}],"date_published":"2024-03-01T00:00:00Z","pmid":1,"day":"01","oa_version":"Published Version","abstract":[{"text":"The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .","lang":"eng"}],"type":"journal_article","doi":"10.1091/mbc.e23-07-0289","month":"03","citation":{"apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., &#38; Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>","chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2024. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>.","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024).","ista":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1.","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. 2024;35(3). doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>","mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>.","ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3. American Society for Cell Biology, 2024."},"publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"publication":"Molecular Biology of the Cell","issue":"3","intvolume":"        35","oa":1,"OA_type":"hybrid","has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-01-29T08:12:11Z","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":35,"date_created":"2025-01-29T07:58:40Z","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","language":[{"iso":"eng"}],"_id":"18934","publisher":"American Society for Cell Biology","article_number":"mr1","department":[{"_id":"FlSc"}],"author":[{"first_name":"Zsuzsa","last_name":"Sárkány","full_name":"Sárkány, Zsuzsa"},{"full_name":"Figueiredo, Francisco","last_name":"Figueiredo","id":"8125cbe2-9661-11ed-a754-afe96018f37d","first_name":"Francisco"},{"full_name":"Macedo-Ribeiro, Sandra","last_name":"Macedo-Ribeiro","first_name":"Sandra"},{"first_name":"Pedro M.","last_name":"Martins","full_name":"Martins, Pedro M."}]},{"page":"131","title":"Structural characterization of spumavirus capsid assemblies","OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T13:21:01Z","ddc":["570"],"abstract":[{"text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies.","lang":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"day":"26","date_published":"2024-09-26T00:00:00Z","degree_awarded":"PhD","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18149","file_size":14213128,"date_created":"2024-09-26T13:40:33Z","file_name":"PhD_thesis_DPorley_final_20240919.docx","embargo_to":"open_access","date_updated":"2025-03-25T23:30:03Z","relation":"source_file","access_level":"closed","creator":"dporley","checksum":"3b8b0bacfe61112f3852744f3170e468"},{"file_id":"18150","content_type":"application/pdf","file_size":18583031,"date_created":"2024-09-26T13:41:39Z","embargo":"2025-03-25","date_updated":"2025-03-25T23:30:03Z","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","checksum":"6c3a652a8eede874118e11d66a63652f","creator":"dporley","access_level":"open_access","relation":"main_file"}],"citation":{"mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>"},"publication_identifier":{"isbn":["978-3-99078-041-1"],"issn":["2663-337X"]},"month":"09","doi":"10.15479/at:ista:18101","type":"dissertation","corr_author":"1","supervisor":[{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2024","file_date_updated":"2025-03-25T23:30:03Z","ec_funded":1,"publication_status":"published","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","_id":"18101","language":[{"iso":"eng"}],"article_processing_charge":"No","date_created":"2024-09-20T10:21:03Z","author":[{"full_name":"Porley, Dario J","last_name":"Porley","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","first_name":"Dario J"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}]},{"date_created":"2023-01-23T07:26:42Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14562"},{"id":"18766","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","article_processing_charge":"No","_id":"12334","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","article_number":"add6495","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"author":[{"first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath","orcid":"0000-0003-2311-2112","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler"},{"full_name":"Döring, Hermann","last_name":"Döring","first_name":"Hermann"},{"full_name":"Hofer, Florian","last_name":"Hofer","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publication":"Science Advances","issue":"3","keyword":["Multidisciplinary"],"corr_author":"1","intvolume":"         9","has_accepted_license":"1","oa":1,"publication_status":"published","year":"2023","file_date_updated":"2023-01-23T07:45:54Z","volume":9,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-01-23T07:45:54Z","file_name":"2023_ScienceAdvances_Faessler.pdf","success":1,"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"12335","content_type":"application/pdf","file_size":1756234,"date_created":"2023-01-23T07:45:54Z"}],"date_published":"2023-01-20T00:00:00Z","pmid":1,"isi":1,"day":"20","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.</jats:p>","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","doi":"10.1126/sciadv.add6495","citation":{"mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>.","ieee":"F. Fäßler <i>et al.</i>, “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” <i>Science Advances</i>, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add6495\">https://doi.org/10.1126/sciadv.add6495</a>","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. <i>Science Advances</i>. 2023;9(3). doi:<a href=\"https://doi.org/10.1126/sciadv.add6495\">10.1126/sciadv.add6495</a>","short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495."},"publication_identifier":{"issn":["2375-2548"]},"month":"01","status":"public","quality_controlled":"1","title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","external_id":{"isi":["000964550100015"],"pmid":["36662867"]},"article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"date_updated":"2026-04-07T12:59:44Z","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R."},{"pmid":1,"date_published":"2023-02-01T00:00:00Z","isi":1,"file":[{"file_id":"12728","content_type":"application/pdf","file_size":10045006,"date_created":"2023-03-16T07:58:16Z","date_updated":"2023-03-16T07:58:16Z","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","success":1,"checksum":"4e7069845e3dad22bb44fb71ec624c60","creator":"dernst","access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","abstract":[{"text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.","lang":"eng"}],"day":"01","doi":"10.1042/bst20220221","type":"journal_article","citation":{"mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>.","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” <i>Biochemical Society Transactions</i>, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","apa":"Fäßler, F., Javoor, M., &#38; Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. 2023;51(1):87-99. doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99."},"publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"month":"02","quality_controlled":"1","status":"public","external_id":{"pmid":["36695514"],"isi":["000926043100001"]},"page":"87-99","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"article_type":"original","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","date_updated":"2025-04-23T08:47:15Z","scopus_import":"1","article_processing_charge":"No","date_created":"2023-01-27T10:08:19Z","publisher":"Portland Press","language":[{"iso":"eng"}],"_id":"12421","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"department":[{"_id":"FlSc"}],"author":[{"full_name":"Fäßler, Florian","last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"last_name":"Javoor","full_name":"Javoor, Manjunath","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"issue":"1","publication":"Biochemical Society Transactions","keyword":["Biochemistry"],"corr_author":"1","intvolume":"        51","publication_status":"published","has_accepted_license":"1","oa":1,"volume":51,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","file_date_updated":"2023-03-16T07:58:16Z"},{"publication_status":"published","has_accepted_license":"1","oa":1,"volume":19,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","file_date_updated":"2023-09-06T06:41:52Z","issue":"8","publication":"PLoS Pathogens","intvolume":"        19","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"department":[{"_id":"FlSc"}],"article_number":"e1011562","author":[{"first_name":"Jana","last_name":"Koch","full_name":"Koch, Jana"},{"full_name":"Xin, Qilin","last_name":"Xin","first_name":"Qilin"},{"first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin"},{"first_name":"Alicia","full_name":"Schäfer, Alicia","last_name":"Schäfer"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"first_name":"Holda A.","full_name":"Anagho, Holda A.","last_name":"Anagho"},{"first_name":"Aiste","full_name":"Kudulyte, Aiste","last_name":"Kudulyte"},{"full_name":"Woltereck, Lea","last_name":"Woltereck","first_name":"Lea"},{"first_name":"Susann","last_name":"Kummer","full_name":"Kummer, Susann"},{"full_name":"Campos, Joaquin","last_name":"Campos","first_name":"Joaquin"},{"first_name":"Zina M.","last_name":"Uckeley","full_name":"Uckeley, Zina M."},{"first_name":"Lesley","last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley"},{"first_name":"Hans Georg","last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian Km","full_name":"Schur, Florian Km","last_name":"Schur"},{"first_name":"Claudio","full_name":"Acuna, Claudio","last_name":"Acuna"},{"last_name":"Lozach","full_name":"Lozach, Pierre Yves","first_name":"Pierre Yves"}],"scopus_import":"1","article_processing_charge":"Yes","date_created":"2023-09-03T22:01:14Z","publisher":"Public Library of Science","_id":"14255","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"article_type":"original","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","date_updated":"2025-04-15T08:24:50Z","quality_controlled":"1","status":"public","external_id":{"isi":["001050846300004"],"pmid":["37578957"]},"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","doi":"10.1371/journal.ppat.1011562","type":"journal_article","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"citation":{"mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562."},"month":"08","pmid":1,"date_published":"2023-08-14T00:00:00Z","isi":1,"file":[{"date_created":"2023-09-06T06:41:52Z","file_size":4458336,"file_id":"14269","content_type":"application/pdf","checksum":"47ca3bb54b27f28b05644be0ad064bc6","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2023-09-06T06:41:52Z","file_name":"2023_PloSPathogens_Koch.pdf","success":1}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","abstract":[{"text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.","lang":"eng"}],"day":"14"},{"corr_author":"1","oa":1,"has_accepted_license":"1","file_date_updated":"2023-11-20T11:49:58Z","contributor":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","contributor_type":"researcher","last_name":"Fäßler"},{"last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","contributor_type":"researcher"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","contributor_type":"researcher","last_name":"Datler"},{"last_name":"Döring","first_name":"Hermann","contributor_type":"researcher"},{"last_name":"Hofer","first_name":"Florian","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","contributor_type":"researcher"},{"last_name":"Dimchev","contributor_type":"researcher","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A"},{"last_name":"Hodirnau","contributor_type":"researcher","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"contributor_type":"researcher","first_name":"Jan","last_name":"Faix"},{"first_name":"Klemens","contributor_type":"researcher","last_name":"Rottner"},{"contributor_type":"researcher","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur"}],"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"12334","status":"public","relation":"used_in_publication"}]},"date_created":"2023-11-20T09:22:33Z","article_processing_charge":"No","_id":"14562","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"author":[{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"status":"public","title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","ddc":["570"],"tmp":{"short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"date_updated":"2025-04-23T08:46:21Z","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","license":"https://creativecommons.org/licenses/by-sa/4.0/","file":[{"access_level":"open_access","relation":"main_file","checksum":"e9bab797b44614f144a5b02d9636f8c3","creator":"fschur","success":1,"file_name":"Figure2.zip","date_updated":"2023-11-20T10:27:17Z","date_created":"2023-11-20T10:27:17Z","file_size":1581687449,"content_type":"application/zip","file_id":"14570"},{"creator":"fschur","checksum":"4efd388cccd03c549fc90f6e46d37006","relation":"main_file","access_level":"open_access","date_updated":"2023-11-20T10:29:18Z","success":1,"file_name":"SupplementaryFigure3.zip","file_size":116088565,"date_created":"2023-11-20T10:29:18Z","file_id":"14571","content_type":"application/zip"},{"date_updated":"2023-11-20T10:44:39Z","success":1,"file_name":"Figure5.zip","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89","creator":"fschur","access_level":"open_access","relation":"main_file","file_id":"14572","content_type":"application/zip","date_created":"2023-11-20T10:44:39Z","file_size":5154614201},{"access_level":"open_access","relation":"main_file","checksum":"83aee17d621a05d865f68f39c8892d27","creator":"fschur","success":1,"file_name":"SupplementaryFigure7.zip","date_updated":"2023-11-20T10:46:00Z","file_size":1277893286,"date_created":"2023-11-20T10:46:00Z","content_type":"application/zip","file_id":"14573"},{"access_level":"open_access","relation":"main_file","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","creator":"fschur","file_name":"SupplementaryFigure9.zip","success":1,"date_updated":"2023-11-20T10:46:08Z","date_created":"2023-11-20T10:46:08Z","file_size":228485124,"content_type":"application/zip","file_id":"14574"},{"file_name":"SupplementaryFigure10.zip","success":1,"date_updated":"2023-11-20T10:46:32Z","relation":"main_file","access_level":"open_access","creator":"fschur","checksum":"4f3644e5feabe4824486d56885bb79fe","content_type":"application/zip","file_id":"14575","file_size":1226788198,"date_created":"2023-11-20T10:46:32Z"},{"date_updated":"2023-11-20T10:46:17Z","file_name":"SupplementaryFigure11.zip","success":1,"creator":"fschur","checksum":"96167f722ed0ca78e30681cd1573b9d7","relation":"main_file","access_level":"open_access","file_id":"14576","content_type":"application/zip","date_created":"2023-11-20T10:46:17Z","file_size":277577131},{"relation":"main_file","access_level":"open_access","creator":"fschur","checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","file_name":"SupplementaryFigure15.zip","success":1,"date_updated":"2023-11-20T10:46:29Z","file_size":591483468,"date_created":"2023-11-20T10:46:29Z","content_type":"application/zip","file_id":"14577"},{"date_created":"2023-11-20T10:47:00Z","file_size":1709528579,"content_type":"application/zip","file_id":"14578","relation":"main_file","access_level":"open_access","creator":"fschur","checksum":"4d437c04fdb3c1e699618063c4bd21c3","file_name":"SupplementaryFigure17.zip","success":1,"date_updated":"2023-11-20T10:47:00Z"},{"checksum":"967b5378a4f16c43f490eae328afe50e","creator":"fschur","access_level":"open_access","relation":"main_file","date_updated":"2023-11-20T11:26:36Z","file_name":"SupplementaryFigure4.zip","success":1,"file_size":1920765280,"date_created":"2023-11-20T11:26:36Z","file_id":"14581","content_type":"application/zip"},{"access_level":"open_access","relation":"main_file","checksum":"11899986cf0b471d258fe168ee33a3ea","creator":"fschur","file_name":"Figure1_partA.zip","success":1,"date_updated":"2023-11-20T11:38:12Z","file_size":3013566196,"date_created":"2023-11-20T11:38:12Z","content_type":"application/zip","file_id":"14583"},{"date_updated":"2023-11-20T11:43:23Z","success":1,"file_name":"Figure1_partB.zip","checksum":"c452afe1ab506d58d32e601d5b3878bb","creator":"fschur","access_level":"open_access","relation":"main_file","file_id":"14584","content_type":"application/zip","file_size":3250260203,"date_created":"2023-11-20T11:43:23Z"},{"file_size":1460,"date_created":"2023-11-20T11:49:58Z","content_type":"text/rtf","file_id":"14585","access_level":"open_access","relation":"main_file","checksum":"223c98eceecbe65dd268f4f363a620d8","creator":"fschur","file_name":"ReadMe.rtf","success":1,"date_updated":"2023-11-20T11:49:58Z"}],"date_published":"2023-11-21T00:00:00Z","day":"21","abstract":[{"lang":"eng","text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"type":"research_data","doi":"10.15479/AT:ISTA:14562","month":"11","citation":{"ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>","short":"F.K. Schur, (2023).","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","mla":"Schur, Florian KM. <i>Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>."}},{"language":[{"iso":"eng"}],"_id":"14784","publisher":"American Association for the Advancement of Science","date_created":"2024-01-10T09:48:01Z","article_processing_charge":"Yes","author":[{"last_name":"Gallardo-Dodd","full_name":"Gallardo-Dodd, Carlos J.","first_name":"Carlos J."},{"first_name":"Christian","full_name":"Oertlin, Christian","last_name":"Oertlin"},{"full_name":"Record, Julien","last_name":"Record","first_name":"Julien"},{"last_name":"Galvani","full_name":"Galvani, Rômulo G.","first_name":"Rômulo G."},{"first_name":"Christian","last_name":"Sommerauer","full_name":"Sommerauer, Christian"},{"first_name":"Nikolai V.","full_name":"Kuznetsov, Nikolai V.","last_name":"Kuznetsov"},{"first_name":"Evangelos","last_name":"Doukoumopoulos","full_name":"Doukoumopoulos, Evangelos"},{"full_name":"Ali, Liaqat","last_name":"Ali","first_name":"Liaqat"},{"last_name":"Oliveira","full_name":"Oliveira, Mariana M. S.","first_name":"Mariana M. S."},{"last_name":"Seitz","full_name":"Seitz, Christina","first_name":"Christina"},{"full_name":"Percipalle, Mathias","last_name":"Percipalle","first_name":"Mathias","id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971"},{"full_name":"Nikić, Tijana","last_name":"Nikić","first_name":"Tijana"},{"first_name":"Anastasia A.","last_name":"Sadova","full_name":"Sadova, Anastasia A."},{"first_name":"Sofia M.","last_name":"Shulgina","full_name":"Shulgina, Sofia M."},{"first_name":"Vjacheslav A.","full_name":"Shmarov, Vjacheslav A.","last_name":"Shmarov"},{"last_name":"Kutko","full_name":"Kutko, Olga V.","first_name":"Olga V."},{"first_name":"Daria D.","full_name":"Vlasova, Daria D.","last_name":"Vlasova"},{"last_name":"Orlova","full_name":"Orlova, Kseniya D.","first_name":"Kseniya D."},{"first_name":"Marina P.","last_name":"Rykova","full_name":"Rykova, Marina P."},{"full_name":"Andersson, John","last_name":"Andersson","first_name":"John"},{"full_name":"Percipalle, Piergiorgio","last_name":"Percipalle","first_name":"Piergiorgio"},{"first_name":"Claudia","full_name":"Kutter, Claudia","last_name":"Kutter"},{"first_name":"Sergey A.","last_name":"Ponomarev","full_name":"Ponomarev, Sergey A."},{"full_name":"Westerberg, Lisa S.","last_name":"Westerberg","first_name":"Lisa S."}],"article_number":"adg1610","department":[{"_id":"FlSc"}],"intvolume":"         9","keyword":["Multidisciplinary"],"publication":"Science Advances","issue":"34","file_date_updated":"2024-01-16T09:35:28Z","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":9,"oa":1,"has_accepted_license":"1","publication_status":"published","day":"25","abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"oa_version":"Published Version","file":[{"success":1,"file_name":"2023_ScienceAdvances_GallardoDodd.pdf","date_updated":"2024-01-16T09:35:28Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"b9072e20e2d5d9d34d2c53319bafee41","content_type":"application/pdf","file_id":"14809","file_size":1596639,"date_created":"2024-01-16T09:35:28Z"}],"isi":1,"pmid":1,"date_published":"2023-08-25T00:00:00Z","month":"08","publication_identifier":{"issn":["2375-2548"]},"citation":{"apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>.","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. 2023;9(34). doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>.","ieee":"C. J. Gallardo-Dodd <i>et al.</i>, “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” <i>Science Advances</i>, vol. 9, no. 34. American Association for the Advancement of Science, 2023."},"type":"journal_article","doi":"10.1126/sciadv.adg1610","title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"status":"public","quality_controlled":"1","date_updated":"2024-09-09T08:03:13Z","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","article_type":"original","ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"ddc":["570"],"tmp":{"legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","short":"GNU AGPLv3  ","name":"GNU Affero General Public License v3.0"},"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-11-21T08:20:23Z","year":"2023","date_updated":"2026-07-06T12:57:43Z","status":"public","corr_author":"1","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"department":[{"_id":"FlSc"}],"doi":"10.15479/AT:ISTA:14502","type":"software","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"month":"11","author":[{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Fäßler, Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"citation":{"mla":"Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>."},"date_published":"2023-11-21T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"10290"}]},"license":"https://choosealicense.com/licenses/agpl-3.0/","file":[{"file_id":"14503","content_type":"application/zip","file_size":347641117,"date_created":"2023-11-08T20:23:07Z","date_updated":"2023-11-08T20:23:07Z","success":1,"file_name":"Computational_Toolbox_v1.2.zip","creator":"fschur","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","relation":"main_file","access_level":"open_access"},{"date_created":"2023-11-21T08:20:23Z","file_size":1522,"file_id":"14586","content_type":"text/plain","checksum":"14db2addbfca61a085ba301ed6f2900b","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2023-11-21T08:20:23Z","file_name":"Readme.txt","success":1}],"date_created":"2023-11-08T19:40:54Z","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"day":"21","_id":"14502"},{"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T13:49:23Z","ddc":["570"],"page":"187","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","OA_place":"publisher","status":"public","month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>"},"doi":"10.15479/at:ista:12491","type":"dissertation","abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"day":"02","date_published":"2023-02-02T00:00:00Z","file":[{"date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","checksum":"069d87f025e0799bf9e3c375664264f2","creator":"bzens","access_level":"open_access","relation":"main_file","file_id":"12527","content_type":"application/pdf","file_size":23082464,"date_created":"2023-02-07T13:07:38Z","embargo":"2024-02-07"},{"file_name":"PhDThesis_BettinaZens_2023_final.docx","embargo_to":"open_access","date_updated":"2024-02-08T23:30:04Z","relation":"source_file","access_level":"closed","creator":"bzens","checksum":"8c66ed203495d6e078ed1002a866520c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12528","date_created":"2023-02-07T13:09:05Z","file_size":106169509}],"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2024-02-08T23:30:04Z","year":"2023","publication_status":"published","oa":1,"has_accepted_license":"1","corr_author":"1","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"author":[{"first_name":"Bettina","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"publisher":"Institute of Science and Technology Austria","_id":"12491","language":[{"iso":"eng"}],"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8586"}]},"date_created":"2023-02-02T14:50:20Z"},{"keyword":["Structural Biology"],"corr_author":"1","intvolume":"       214","issue":"2","publication":"Journal of Structural Biology","volume":214,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","file_date_updated":"2022-08-02T11:07:58Z","publication_status":"published","has_accepted_license":"1","oa":1,"publisher":"Elsevier","_id":"11155","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","date_created":"2022-04-15T07:10:26Z","author":[{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","last_name":"Obr","full_name":"Obr, Martin"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"first_name":"Lingbo","full_name":"Yu, Lingbo","last_name":"Yu"},{"first_name":"Abhay","last_name":"Kotecha","full_name":"Kotecha, Abhay"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur"}],"project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"department":[{"_id":"FlSc"}],"article_number":"107852","external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","quality_controlled":"1","status":"public","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","date_updated":"2025-04-15T08:24:50Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"article_type":"original","abstract":[{"lang":"eng","text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes."}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"day":"01","pmid":1,"date_published":"2022-06-01T00:00:00Z","isi":1,"file":[{"content_type":"application/pdf","file_id":"11722","file_size":7080863,"date_created":"2022-08-02T11:07:58Z","success":1,"file_name":"2022_JourStructuralBiology_Obr.pdf","date_updated":"2022-08-02T11:07:58Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"0b1eb53447aae8e95ae4c12d193b0b00"}],"publication_identifier":{"issn":["1047-8477"]},"citation":{"ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>."},"month":"06","type":"journal_article","doi":"10.1016/j.jsb.2022.107852"},{"issue":"11","publication":"Current Biology","intvolume":"        32","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication_status":"published","oa":1,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":32,"file_date_updated":"2022-08-05T06:29:18Z","year":"2022","article_processing_charge":"No","scopus_import":"1","date_created":"2022-05-04T06:22:06Z","publisher":"Elsevier","language":[{"iso":"eng"}],"_id":"11351","department":[{"_id":"FlSc"}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"author":[{"first_name":"William J.","full_name":"Nicolas, William J.","last_name":"Nicolas"},{"orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM"},{"first_name":"Grant","last_name":"Jensen","full_name":"Jensen, Grant"},{"first_name":"Elliot","full_name":"Meyerowitz, Elliot","last_name":"Meyerowitz"}],"quality_controlled":"1","status":"public","page":"P2375-2389","external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","date_updated":"2025-04-15T08:25:40Z","isi":1,"date_published":"2022-06-06T00:00:00Z","pmid":1,"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"af3f24d97c016d844df237abef987639","success":1,"file_name":"2022_CurrentBiology_Nicolas.pdf","date_updated":"2022-08-05T06:29:18Z","file_size":12827717,"date_created":"2022-08-05T06:29:18Z","content_type":"application/pdf","file_id":"11730"}],"oa_version":"Published Version","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"day":"06","doi":"10.1016/j.cub.2022.04.024","type":"journal_article","month":"06","citation":{"ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>"},"publication_identifier":{"issn":["0960-9822"]}}]