[{"ddc":["570"],"status":"public","related_material":{"record":[{"status":"public","id":"10290","relation":"used_for_analysis_in"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"14503","creator":"fschur","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2023-11-08T20:23:07Z","content_type":"application/zip","file_name":"Computational_Toolbox_v1.2.zip","date_created":"2023-11-08T20:23:07Z","file_size":347641117,"checksum":"a8b9adeb53a4109dea4d5e39fa1acccf"},{"creator":"dernst","file_id":"14586","success":1,"relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"Readme.txt","date_updated":"2023-11-21T08:20:23Z","checksum":"14db2addbfca61a085ba301ed6f2900b","file_size":1522,"date_created":"2023-11-21T08:20:23Z"}],"abstract":[{"lang":"eng","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."}],"oa":1,"doi":"10.15479/AT:ISTA:14502","day":"21","date_published":"2023-11-21T00:00:00Z","type":"software","date_updated":"2023-11-21T08:36:02Z","tmp":{"short":"GNU AGPLv3  ","name":"GNU Affero General Public License v3.0","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html"},"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>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","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>.","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>","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>","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>.","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."},"year":"2023","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-11-21T08:20:23Z","keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"month":"11","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","date_created":"2023-11-08T19:40:54Z","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"department":[{"_id":"FlSc"}],"author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"_id":"14502","has_accepted_license":"1","license":"https://choosealicense.com/licenses/agpl-3.0/"},{"author":[{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","last_name":"Bolger-Munro","first_name":"Madison","full_name":"Bolger-Munro, Madison","orcid":"0000-0002-8176-4824"},{"full_name":"Choi, Kate","last_name":"Choi","first_name":"Kate"},{"full_name":"Cheung, Faith","first_name":"Faith","last_name":"Cheung"},{"full_name":"Liu, Yi Tian","first_name":"Yi Tian","last_name":"Liu"},{"full_name":"Dang-Lawson, May","first_name":"May","last_name":"Dang-Lawson"},{"last_name":"Deretic","first_name":"Nikola","full_name":"Deretic, Nikola"},{"full_name":"Keane, Connor","first_name":"Connor","last_name":"Keane"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"scopus_import":"1","_id":"9379","pmid":1,"intvolume":"         9","title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","date_created":"2021-05-09T22:01:37Z","department":[{"_id":"CaHe"}],"article_processing_charge":"No","publication_status":"published","file_date_updated":"2021-05-11T15:09:23Z","quality_controlled":"1","article_type":"original","publisher":"Frontiers Media","external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"isi":1,"year":"2021","citation":{"ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9, 649433, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>.","ieee":"M. Bolger-Munro <i>et al.</i>, “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9. Frontiers Media, 2021.","ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>"},"date_updated":"2023-10-18T08:19:49Z","abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"day":"13","doi":"10.3389/fcell.2021.649433","ddc":["570"],"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","volume":9,"has_accepted_license":"1","publication":"Frontiers in Cell and Developmental Biology","article_number":"649433","month":"04","oa_version":"Published Version","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-04-13T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2296-634X"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":4076024,"checksum":"8c8a03575d2f7583f88dc3b658b0976b","date_created":"2021-05-11T15:09:23Z","content_type":"application/pdf","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","date_updated":"2021-05-11T15:09:23Z","access_level":"open_access","relation":"main_file","success":1,"creator":"kschuh","file_id":"9386"}]}]