[{"publication_status":"published","article_type":"original","oa":1,"title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","file":[{"file_id":"11692","creator":"dernst","date_updated":"2022-07-29T07:53:20Z","access_level":"open_access","file_size":2351220,"relation":"main_file","success":1,"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","content_type":"application/pdf","file_name":"2022_ACSPhysChemAU_Dubini.pdf","date_created":"2022-07-29T07:53:20Z"}],"page":"237-246","abstract":[{"lang":"eng","text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark."}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"file_date_updated":"2022-07-29T07:53:20Z","license":"https://creativecommons.org/licenses/by/4.0/","publication":"ACS Physical Chemistry Au","acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","type":"journal_article","_id":"10758","intvolume":"         2","doi":"10.1021/acsphyschemau.1c00050","ddc":["540"],"date_created":"2022-02-16T11:18:21Z","language":[{"iso":"eng"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","month":"02","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","issue":"3","department":[{"_id":"NMR"}],"corr_author":"1","date_updated":"2025-04-15T06:53:09Z","citation":{"apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., &#38; Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. 2022;2(3):237-246. doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>.","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>."},"publisher":"American Chemical Society","status":"public","publication_identifier":{"eissn":["2694-2445"]},"external_id":{"pmid":["35637781"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","pmid":1,"author":[{"full_name":"Dubini, Romeo C. A.","last_name":"Dubini","first_name":"Romeo C. A."},{"full_name":"Korytiaková, Eva","last_name":"Korytiaková","first_name":"Eva"},{"last_name":"Schinkel","full_name":"Schinkel, Thea","first_name":"Thea"},{"last_name":"Heinrichs","full_name":"Heinrichs, Pia","first_name":"Pia"},{"full_name":"Carell, Thomas","last_name":"Carell","first_name":"Thomas"},{"orcid":"0000-0001-8729-7326","last_name":"Rovo","full_name":"Rovo, Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra"}],"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563"}]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-02-11T00:00:00Z","volume":2},{"intvolume":"        34","doi":"10.1093/plcell/koac071","_id":"10841","date_created":"2022-03-08T13:47:51Z","language":[{"iso":"eng"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"EM-Fac"}],"acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","type":"journal_article","publication":"Plant Cell","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"project":[{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"publication_status":"published","article_type":"original","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"oa":1,"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","page":"2150-2173","pmid":1,"author":[{"last_name":"Dahhan","full_name":"Dahhan, DA","first_name":"DA"},{"full_name":"Reynolds, GD","last_name":"Reynolds","first_name":"GD"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"first_name":"D","last_name":"Eeckhout","full_name":"Eeckhout, D"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"K","last_name":"Yperman","full_name":"Yperman, K"},{"first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"last_name":"Vang","full_name":"Vang, N","first_name":"N"},{"first_name":"X","full_name":"Yan, X","last_name":"Yan"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"last_name":"Heese","full_name":"Heese, A","first_name":"A"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"J","full_name":"Pan, J","last_name":"Pan"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"article_processing_charge":"No","date_published":"2022-06-01T00:00:00Z","volume":34,"date_updated":"2025-05-14T11:06:15Z","publisher":"Oxford University Press","citation":{"ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022."},"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"isi":1,"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"status":"public","quality_controlled":"1","scopus_import":"1","oa_version":"Preprint","issue":"6","day":"01","month":"06"},{"_id":"11182","ddc":["570"],"intvolume":"         2","doi":"10.1002/cpz1.407","date_created":"2022-04-17T22:01:46Z","language":[{"iso":"eng"}],"year":"2022","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","file_date_updated":"2022-05-02T08:16:10Z","publication":"Current Protocols","type":"journal_article","acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","abstract":[{"text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.","lang":"eng"}],"article_type":"original","publication_status":"published","oa":1,"article_number":"e407","file":[{"success":1,"relation":"main_file","file_size":2142703,"access_level":"open_access","date_updated":"2022-05-02T08:16:10Z","creator":"dernst","file_id":"11347","date_created":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf","checksum":"72152d005c367777f6cf2f6a477f0d52","content_type":"application/pdf"}],"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","has_accepted_license":"1","article_processing_charge":"No","external_id":{"pmid":["35384410"]},"pmid":1,"author":[{"first_name":"Janina","full_name":"Kroll, Janina","last_name":"Kroll"},{"first_name":"Mauricio J.A.","full_name":"Ruiz-Fernandez, Mauricio J.A.","last_name":"Ruiz-Fernandez"},{"last_name":"Braun","full_name":"Braun, Malte B.","first_name":"Malte B."},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369"}],"OA_place":"publisher","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":2,"date_published":"2022-04-05T00:00:00Z","department":[{"_id":"NanoFab"}],"date_updated":"2024-10-14T13:16:54Z","citation":{"ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. 2022;2(4). doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” <i>Current Protocols</i>, vol. 2, no. 4. Wiley, 2022.","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>, vol. 2, no. 4, e407, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>.","chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>.","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., &#38; Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. Wiley. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022)."},"publisher":"Wiley","status":"public","publication_identifier":{"eissn":["2691-1299"]},"oa_version":"Published Version","OA_type":"hybrid","scopus_import":"1","quality_controlled":"1","issue":"4","day":"05","month":"04"},{"acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","type":"journal_article","publication":"Nature Immunology","file_date_updated":"2022-07-25T07:11:32Z","language":[{"iso":"eng"}],"date_created":"2021-08-06T09:09:11Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"intvolume":"        23","doi":"10.1038/s41590-022-01257-4","_id":"9794","title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","file":[{"content_type":"application/pdf","checksum":"628e7b49809f22c75b428842efe70c68","file_name":"2022_NatureImmunology_Assen.pdf","date_created":"2022-07-25T07:11:32Z","file_id":"11642","date_updated":"2022-07-25T07:11:32Z","creator":"dernst","file_size":11475325,"access_level":"open_access","success":1,"relation":"main_file"}],"page":"1246-1255","article_type":"original","publication_status":"published","oa":1,"ec_funded":1,"project":[{"name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"abstract":[{"lang":"eng","text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion."}],"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"isi":1,"status":"public","date_updated":"2025-06-11T13:52:43Z","publisher":"Springer Nature","citation":{"ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. <i>Nature Immunology</i>. 2022;23:1246-1255. doi:<a href=\"https://doi.org/10.1038/s41590-022-01257-4\">10.1038/s41590-022-01257-4</a>","chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” <i>Nature Immunology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41590-022-01257-4\">https://doi.org/10.1038/s41590-022-01257-4</a>.","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” <i>Nature Immunology</i>, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:<a href=\"https://doi.org/10.1038/s41590-022-01257-4\">10.1038/s41590-022-01257-4</a>.","ieee":"F. P. Assen <i>et al.</i>, “Multitier mechanics control stromal adaptations in swelling lymph nodes,” <i>Nature Immunology</i>, vol. 23. Springer Nature, pp. 1246–1255, 2022.","ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-022-01257-4\">https://doi.org/10.1038/s41590-022-01257-4</a>","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255."},"department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-07-11T00:00:00Z","volume":23,"pmid":1,"author":[{"first_name":"Frank P","full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen","orcid":"0000-0003-3470-6119"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"first_name":"Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","full_name":"Hons, Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Tommaso","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","orcid":"0000-0001-9732-3815"},{"first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"first_name":"Burkhard","last_name":"Ludewig","full_name":"Ludewig, Burkhard"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Weninger","full_name":"Weninger, Wolfgang","first_name":"Wolfgang"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Sanjiv A.","last_name":"Luther","full_name":"Luther, Sanjiv A."},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X","first_name":"Michael K"}],"has_accepted_license":"1","article_processing_charge":"No","external_id":{"pmid":["35817845"],"isi":["000822975900002"]},"month":"07","day":"11","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version"},{"doi":"10.1073/pnas.2122030119","ddc":["570"],"intvolume":"       119","_id":"10766","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"year":"2022","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-02-20T23:01:31Z","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2022-02-21T08:45:11Z","acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013"}],"article_number":"e2122030119","oa":1,"article_type":"original","publication_status":"published","file":[{"file_id":"10780","date_updated":"2022-02-21T08:45:11Z","creator":"dernst","file_size":1609678,"access_level":"open_access","relation":"main_file","success":1,"checksum":"d49f83c3580613966f71768ddb9a55a5","content_type":"application/pdf","file_name":"2022_PNAS_Slovakova.pdf","date_created":"2022-02-21T08:45:11Z"}],"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","pmid":1,"author":[{"full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova","first_name":"Jana"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","full_name":"Arslan, Feyza N","last_name":"Arslan","orcid":"0000-0001-5809-9566"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346"},{"first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["35165179"],"isi":["000766926900009"]},"has_accepted_license":"1","date_published":"2022-02-14T00:00:00Z","volume":119,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"related_material":{"record":[{"id":"9750","relation":"earlier_version","status":"public"}]},"citation":{"mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. National Academy of Sciences, 2022.","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>"},"publisher":"National Academy of Sciences","date_updated":"2026-04-02T12:54:56Z","corr_author":"1","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1091-6490"]},"isi":1,"status":"public","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","issue":"8","day":"14","month":"02"},{"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"corr_author":"1","date_updated":"2026-04-07T11:50:54Z","publisher":"American Physical Society","citation":{"short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>"},"status":"public","publication_identifier":{"eissn":["2475-9953"]},"isi":1,"external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"article_processing_charge":"No","author":[{"first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix","last_name":"Pertl","orcid":"0000-0003-0463-5794"},{"last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A"},{"first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B","last_name":"Shafeek","orcid":"0000-0001-7180-6050"},{"full_name":"Cramer, Tobias","last_name":"Cramer","first_name":"Tobias"},{"first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis"}],"related_material":{"record":[{"id":"20203","relation":"dissertation_contains","status":"public"}]},"volume":6,"date_published":"2022-12-29T00:00:00Z","day":"29","month":"12","scopus_import":"1","oa_version":"Preprint","arxiv":1,"quality_controlled":"1","issue":"12","publication":"Physical Review Materials","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","type":"journal_article","_id":"12109","doi":"10.1103/PhysRevMaterials.6.125605","intvolume":"         6","language":[{"iso":"eng"}],"date_created":"2023-01-08T23:00:53Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"year":"2022","article_type":"original","publication_status":"published","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"oa":1,"article_number":"125605","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","abstract":[{"lang":"eng","text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale."}],"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"ec_funded":1},{"file":[{"date_updated":"2023-11-02T17:12:37Z","creator":"amally","file_id":"14483","success":1,"relation":"main_file","file_size":79774945,"access_level":"open_access","file_name":"Friml Nature 2022_merged.pdf","content_type":"application/pdf","checksum":"a6055c606aefb900bf62ae3e7d15f921","date_created":"2023-11-02T17:12:37Z"}],"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","page":"575-581","article_type":"original","publication_status":"published","oa":1,"ec_funded":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988"}],"abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"type":"journal_article","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","publication":"Nature","file_date_updated":"2023-11-02T17:12:37Z","date_created":"2023-01-16T10:04:48Z","language":[{"iso":"eng"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"ddc":["580"],"intvolume":"       609","doi":"10.1038/s41586-022-05187-x","_id":"12291","month":"09","day":"15","issue":"7927","quality_controlled":"1","oa_version":"Submitted Version","scopus_import":"1","isi":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"status":"public","date_updated":"2026-04-07T11:52:15Z","publisher":"Springer Nature","citation":{"apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>."},"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"corr_author":"1","volume":609,"date_published":"2022-09-15T00:00:00Z","related_material":{"record":[{"id":"19395","relation":"dissertation_contains","status":"public"},{"status":"public","id":"20364","relation":"dissertation_contains"}]},"author":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C"},{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge"},{"first_name":"Branka D.","full_name":"Živanović, Branka D.","last_name":"Živanović"},{"first_name":"Minxia","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou"},{"first_name":"Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter"},{"first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","last_name":"Hrtyan"},{"first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha"},{"last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"first_name":"Koji","full_name":"Takahashi, Koji","last_name":"Takahashi"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anastasiia","full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova"},{"last_name":"Kinoshita","full_name":"Kinoshita, Toshinori","first_name":"Toshinori"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"}],"pmid":1,"article_processing_charge":"No","has_accepted_license":"1","external_id":{"pmid":["36071161"],"isi":["000851357500002"]}},{"ddc":["540"],"doi":"10.1021/acsenergylett.2c01711","intvolume":"         7","_id":"12065","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-09-08T09:51:09Z","language":[{"iso":"eng"}],"file_date_updated":"2023-01-20T08:43:51Z","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","type":"journal_article","publication":"ACS Energy Letters","abstract":[{"text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth.","lang":"eng"}],"oa":1,"publication_status":"published","article_type":"original","page":"3112-3119","title":"Exclusive solution discharge in Li-O₂ batteries?","file":[{"file_id":"12319","creator":"dernst","date_updated":"2023-01-20T08:43:51Z","access_level":"open_access","file_size":3827583,"relation":"main_file","success":1,"content_type":"application/pdf","checksum":"cf0bed3a2535c11d27244cd029dbc1d0","file_name":"2022_ACSEnergyLetters_Prehal.pdf","date_created":"2023-01-20T08:43:51Z"}],"author":[{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"last_name":"Mondal","full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip"},{"last_name":"Lovicar","orcid":"0000-0001-6206-4200","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","full_name":"Lovicar, Ludek","first_name":"Ludek"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"}],"pmid":1,"external_id":{"isi":["000860787000001"],"pmid":["36120663"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","volume":7,"date_published":"2022-08-29T00:00:00Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"dissertation_contains","id":"20607","status":"public"}]},"citation":{"apa":"Prehal, C., Mondal, S., Lovicar, L., &#38; Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>","ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. 2022;7(9):3112-3119. doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” <i>ACS Energy Letters</i>, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022.","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>.","chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>."},"publisher":"American Chemical Society","date_updated":"2026-04-07T12:27:23Z","corr_author":"1","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"isi":1,"publication_identifier":{"eissn":["2380-8195"]},"status":"public","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","issue":"9","day":"29","month":"08"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-07-07T00:00:00Z","volume":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"status":"public","id":"14530","relation":"dissertation_contains"}]},"pmid":1,"author":[{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H"},{"first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","orcid":"0000-0002-7903-3010","first_name":"Susanne"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"first_name":"Armel","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn"},{"full_name":"Tsai, Li Huei","last_name":"Tsai","first_name":"Li Huei"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"article_processing_charge":"No","has_accepted_license":"1","external_id":{"pmid":["38596707"]},"publication_identifier":{"eissn":["2753-149X"]},"status":"public","date_updated":"2026-04-07T13:29:13Z","citation":{"ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford University Press, 2022.","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>.","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022)."},"publisher":"Oxford University Press","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"corr_author":"1","issue":"1","quality_controlled":"1","oa_version":"Published Version","month":"07","day":"07","date_created":"2022-02-25T07:52:11Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         1","ddc":["570"],"doi":"10.1093/oons/kvac009","_id":"10791","type":"journal_article","acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","publication":"Oxford Open Neuroscience","file_date_updated":"2023-08-16T08:00:30Z","ec_funded":1,"project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","call_identifier":"FP7"},{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","file":[{"file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","checksum":"822e76e056c07099d1fb27d1ece5941b","content_type":"application/pdf","date_created":"2023-08-16T08:00:30Z","creator":"dernst","date_updated":"2023-08-16T08:00:30Z","file_id":"14061","relation":"main_file","success":1,"access_level":"open_access","file_size":4846551}],"article_number":"kvac009","article_type":"original","publication_status":"published","oa":1},{"title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","page":"47-62.e9","article_type":"original","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497"}],"ec_funded":1,"project":[{"grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients"}],"abstract":[{"lang":"eng","text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes."}],"acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","type":"journal_article","publication":"Developmental Cell","date_created":"2022-01-30T23:01:33Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2022","intvolume":"        57","ddc":["570"],"doi":"10.1016/j.devcel.2021.11.024","_id":"10703","month":"01","day":"10","issue":"1","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"status":"public","date_updated":"2026-06-13T22:31:02Z","citation":{"chicago":"Gaertner, Florian, Patricia Dos Reis Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>.","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>, vol. 57, no. 1, Cell Press, 2022, p. 47–62.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>.","ieee":"F. Gaertner <i>et al.</i>, “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” <i>Developmental Cell</i>, vol. 57, no. 1. Cell Press, p. 47–62.e9, 2022.","ama":"Gaertner F, Dos Reis Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. 2022;57(1):47-62.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>","short":"F. Gaertner, P. Dos Reis Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","ista":"Gaertner F, Dos Reis Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","apa":"Gaertner, F., Dos Reis Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>"},"publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"volume":57,"date_published":"2022-01-10T00:00:00Z","related_material":{"record":[{"status":"public","id":"20149","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"12726","status":"public"},{"relation":"dissertation_contains","id":"14530","status":"public"},{"status":"public","relation":"dissertation_contains","id":"12401"}]},"author":[{"first_name":"Florian","full_name":"Gaertner, Florian","last_name":"Gaertner"},{"orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues","full_name":"Dos Reis Rodrigues, Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","first_name":"Patricia"},{"last_name":"De Vries","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","first_name":"Miroslav"},{"full_name":"Aguilera, Juan","last_name":"Aguilera","first_name":"Juan"},{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"first_name":"Alexander F","last_name":"Leithner","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F"},{"first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan","orcid":"0000-0003-1671-393X"},{"last_name":"Kopf","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","first_name":"Aglaja"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K"}],"pmid":1,"article_processing_charge":"No","external_id":{"pmid":["34919802"],"isi":["000768933800005"]}},{"doi":"10.1021/acs.chemmater.1c02910","intvolume":"        33","_id":"15260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","date_created":"2024-04-03T07:23:30Z","language":[{"iso":"eng"}],"type":"journal_article","publication":"Chemistry of Materials","abstract":[{"lang":"eng","text":"Significant advances in the synthesis and processing of colloidal nanocrystals have given scientists and engineers access to a vast library of building blocks with precisely defined size, shape, and composition. These materials have inspired exciting prospects to enable bottom-up fabrication of programmable materials with properties by design. Successfully assembling and connecting the building blocks into superstructures in which constituent nanocrystals can purposefully interact requires robust understanding of and control over a complex interplay of dynamic physicochemical processes. Fluid interfaces provide an advantageous experimental workbench to both probe and control these processes. Despite the ostensible simplicity of fabricating nanocrystal assemblies at a fluid interface, sensitivity to processing conditions and limited reproducibility have underscored the complexity of this process. In situ studies have provided mechanistic insights into the competing dynamics of key subprocesses including solvent spreading and evaporation, superlattice formation, ligand detachment kinetics, and nanocrystal attachment. Understanding how these subprocesses influence the complex choreography of self-assembly, structure transformation, and oriented attachment processes presents a rich research challenge. In this context, we present a detailed methodology for self-assembly and attachment of lead chalcogenide nanocrystals at a liquid–gas interface as a model system for the fabrication of mono- and multilayer cubic connected superlattices. We discuss key experimental parameters such as the characteristics of the building blocks and processing conditions and detailed steps from colloidal nanocrystal injection to superlattice transfer. We hope that this Methods/Protocols paper will provide guidance for future advances in the exciting path toward bringing the prospect of nanocrystal-based programmable materials to fruition."}],"oa":1,"main_file_link":[{"url":"https://www.osti.gov/servlets/purl/1836502","open_access":"1"}],"article_type":"original","publication_status":"published","page":"9457-9472","title":"Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface","author":[{"first_name":"Jessica","last_name":"Cimada daSilva","full_name":"Cimada daSilva, Jessica"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X","first_name":"Daniel"},{"first_name":"Tyler A.","full_name":"Dunbar, Tyler A.","last_name":"Dunbar"},{"first_name":"Tobias","last_name":"Hanrath","full_name":"Hanrath, Tobias"}],"article_processing_charge":"No","date_published":"2021-12-16T00:00:00Z","volume":33,"citation":{"short":"J. Cimada daSilva, D. Balazs, T.A. Dunbar, T. Hanrath, Chemistry of Materials 33 (2021) 9457–9472.","ista":"Cimada daSilva J, Balazs D, Dunbar TA, Hanrath T. 2021. Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface. Chemistry of Materials. 33(24), 9457–9472.","apa":"Cimada daSilva, J., Balazs, D., Dunbar, T. A., &#38; Hanrath, T. (2021). Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface. <i>Chemistry of Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemmater.1c02910\">https://doi.org/10.1021/acs.chemmater.1c02910</a>","mla":"Cimada daSilva, Jessica, et al. “Fundamental Processes and Practical Considerations of Lead Chalcogenide Mesocrystals Formed via Self-Assembly and Directed Attachment of Nanocrystals at a Fluid Interface.” <i>Chemistry of Materials</i>, vol. 33, no. 24, American Chemical Society, 2021, pp. 9457–72, doi:<a href=\"https://doi.org/10.1021/acs.chemmater.1c02910\">10.1021/acs.chemmater.1c02910</a>.","chicago":"Cimada daSilva, Jessica, Daniel Balazs, Tyler A. Dunbar, and Tobias Hanrath. “Fundamental Processes and Practical Considerations of Lead Chalcogenide Mesocrystals Formed via Self-Assembly and Directed Attachment of Nanocrystals at a Fluid Interface.” <i>Chemistry of Materials</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acs.chemmater.1c02910\">https://doi.org/10.1021/acs.chemmater.1c02910</a>.","ieee":"J. Cimada daSilva, D. Balazs, T. A. Dunbar, and T. Hanrath, “Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface,” <i>Chemistry of Materials</i>, vol. 33, no. 24. American Chemical Society, pp. 9457–9472, 2021.","ama":"Cimada daSilva J, Balazs D, Dunbar TA, Hanrath T. Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface. <i>Chemistry of Materials</i>. 2021;33(24):9457-9472. doi:<a href=\"https://doi.org/10.1021/acs.chemmater.1c02910\">10.1021/acs.chemmater.1c02910</a>"},"publisher":"American Chemical Society","date_updated":"2024-04-03T13:50:53Z","department":[{"_id":"LifeSc"}],"publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"status":"public","quality_controlled":"1","scopus_import":"1","oa_version":"Submitted Version","issue":"24","day":"16","month":"12","keyword":["Materials Chemistry","General Chemical Engineering","General Chemistry"]},{"type":"conference_abstract","status":"public","publication":"Proceedings of the Internet NanoGe Conference on Nanocrystals","date_updated":"2024-10-09T21:08:49Z","citation":{"ama":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In: <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació Scito; 2021. doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>","ieee":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, and T. Hanrath, “Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics,” in <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, Virtual, 2021.","chicago":"Balazs, Daniel, Jessica Cimada da Silva, Tyler Dunbar, Maria Ibáñez, and Tobias Hanrath. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació Scito, 2021. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>.","mla":"Balazs, Daniel, et al. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, 050, Fundació Scito, 2021, doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>.","apa":"Balazs, D., Cimada da Silva, J., Dunbar, T., Ibáñez, M., &#38; Hanrath, T. (2021). Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Virtual: Fundació Scito. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>","ista":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. 2021. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. Proceedings of the Internet NanoGe Conference on Nanocrystals. iNCNC: Internet nanoGe Conference on Nanocrystals, 050.","short":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, T. Hanrath, in:, Proceedings of the Internet NanoGe Conference on Nanocrystals, Fundació Scito, 2021."},"publisher":"Fundació Scito","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"corr_author":"1","date_created":"2024-04-03T08:28:26Z","language":[{"iso":"eng"}],"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-08T00:00:00Z","doi":"10.29363/nanoge.incnc.2021.050","author":[{"last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel"},{"first_name":"Jessica","last_name":"Cimada da Silva","full_name":"Cimada da Silva, Jessica"},{"full_name":"Dunbar, Tyler","last_name":"Dunbar","first_name":"Tyler"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"last_name":"Hanrath","full_name":"Hanrath, Tobias","first_name":"Tobias"}],"article_processing_charge":"No","_id":"15280","title":"Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics","month":"06","day":"08","article_number":"050","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.29363/nanoge.incnc.2021.050"}],"oa":1,"quality_controlled":"1","conference":{"location":"Virtual","end_date":"2021-07-02","start_date":"2021-06-28","name":"iNCNC: Internet nanoGe Conference on Nanocrystals"},"oa_version":"Published Version"},{"day":"24","month":"08","keyword":["General Medicine"],"quality_controlled":"1","oa_version":"Published Version","issue":"3","date_updated":"2024-04-09T06:51:50Z","citation":{"ama":"Rubel P, Fayn J, Macfarlane PW, Pani D, Schlögl A, Värri A. The history and challenges of SCP-ECG: The standard communication protocol for computer-assisted electrocardiography. <i>Hearts</i>. 2021;2(3):384-409. doi:<a href=\"https://doi.org/10.3390/hearts2030031\">10.3390/hearts2030031</a>","ieee":"P. Rubel, J. Fayn, P. W. Macfarlane, D. Pani, A. Schlögl, and A. Värri, “The history and challenges of SCP-ECG: The standard communication protocol for computer-assisted electrocardiography,” <i>Hearts</i>, vol. 2, no. 3. MDPI, pp. 384–409, 2021.","mla":"Rubel, Paul, et al. “The History and Challenges of SCP-ECG: The Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>Hearts</i>, vol. 2, no. 3, MDPI, 2021, pp. 384–409, doi:<a href=\"https://doi.org/10.3390/hearts2030031\">10.3390/hearts2030031</a>.","chicago":"Rubel, Paul, Jocelyne Fayn, Peter W. Macfarlane, Danilo Pani, Alois Schlögl, and Alpo Värri. “The History and Challenges of SCP-ECG: The Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>Hearts</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/hearts2030031\">https://doi.org/10.3390/hearts2030031</a>.","apa":"Rubel, P., Fayn, J., Macfarlane, P. W., Pani, D., Schlögl, A., &#38; Värri, A. (2021). The history and challenges of SCP-ECG: The standard communication protocol for computer-assisted electrocardiography. <i>Hearts</i>. MDPI. <a href=\"https://doi.org/10.3390/hearts2030031\">https://doi.org/10.3390/hearts2030031</a>","ista":"Rubel P, Fayn J, Macfarlane PW, Pani D, Schlögl A, Värri A. 2021. The history and challenges of SCP-ECG: The standard communication protocol for computer-assisted electrocardiography. Hearts. 2(3), 384–409.","short":"P. Rubel, J. Fayn, P.W. Macfarlane, D. Pani, A. Schlögl, A. Värri, Hearts 2 (2021) 384–409."},"publisher":"MDPI","department":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2673-3846"]},"status":"public","author":[{"first_name":"Paul","full_name":"Rubel, Paul","last_name":"Rubel"},{"first_name":"Jocelyne","last_name":"Fayn","full_name":"Fayn, Jocelyne"},{"first_name":"Peter W.","full_name":"Macfarlane, Peter W.","last_name":"Macfarlane"},{"first_name":"Danilo","last_name":"Pani","full_name":"Pani, Danilo"},{"orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois"},{"full_name":"Värri, Alpo","last_name":"Värri","first_name":"Alpo"}],"has_accepted_license":"1","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":2,"date_published":"2021-08-24T00:00:00Z","publication_status":"published","article_type":"review","oa":1,"title":"The history and challenges of SCP-ECG: The standard communication protocol for computer-assisted electrocardiography","file":[{"access_level":"open_access","file_size":3539897,"relation":"main_file","success":1,"file_id":"15302","creator":"dernst","date_updated":"2024-04-09T06:49:47Z","date_created":"2024-04-09T06:49:47Z","checksum":"f67142b1e1e8ca5cd7a6a6798f46375e","content_type":"application/pdf","file_name":"2021_Hearts_Rubel.pdf"}],"page":"384-409","abstract":[{"text":"Ever since the first publication of the standard communication protocol for computer-assisted electrocardiography (SCP-ECG), prENV 1064, in 1993, by the European Committee for Standardization (CEN), SCP-ECG has become a leading example in health informatics, enabling open, secure, and well-documented digital data exchange at a low cost, for quick and efficient cardiovascular disease detection and management. Based on the experiences gained, since the 1970s, in computerized electrocardiology, and on the results achieved by the pioneering, international cooperative research on common standards for quantitative electrocardiography (CSE), SCP-ECG was designed, from the beginning, to empower personalized medicine, thanks to serial ECG analysis. The fundamental concept behind SCP-ECG is to convey the necessary information for ECG re-analysis, serial comparison, and interpretation, and to structure the ECG data and metadata in sections that are mostly optional in order to fit all use cases. SCP-ECG is open to the storage of the ECG signal and ECG measurement data, whatever the ECG recording modality or computation method, and can store the over-reading trails and ECG annotations, as well as any computerized or medical interpretation reports. Only the encoding syntax and the semantics of the ECG descriptors and of the diagnosis codes are standardized. We present all of the landmarks in the development and publication of SCP-ECG, from the early 1990s to the 2009 International Organization for Standardization (ISO) SCP-ECG standards, including the latest version published by CEN in 2020, which now encompasses rest and stress ECGs, Holter recordings, and protocol-based trials.","lang":"eng"}],"file_date_updated":"2024-04-09T06:49:47Z","type":"journal_article","acknowledgement":"This research received no external funding. The authors thank the large number of researchers, engineers, cardiologists, and clinicians from academia, industry, and normalization organizations who contributed to the development and testing of the SCP-ECG standards.","publication":"Hearts","doi":"10.3390/hearts2030031","intvolume":"         2","ddc":["610"],"_id":"15285","date_created":"2024-04-03T09:03:31Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021"},{"abstract":[{"text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders.","lang":"eng"}],"oa":1,"article_type":"original","publication_status":"published","page":"59-65","file":[{"relation":"main_file","success":1,"file_size":6848513,"access_level":"open_access","date_updated":"2022-01-10T13:41:40Z","creator":"alisjak","file_id":"10612","date_created":"2022-01-10T13:41:40Z","file_name":"2021_Parkinsonism_Venezia.pdf","checksum":"360681585acb51e80d17c6b213c56b55","content_type":"application/pdf"}],"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","_id":"10607","doi":"10.1016/j.parkreldis.2021.09.007","intvolume":"        91","ddc":["610"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","date_created":"2022-01-09T23:01:26Z","language":[{"iso":"eng"}],"file_date_updated":"2022-01-10T13:41:40Z","publication":"Parkinsonism & Related Disorders","acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","type":"journal_article","scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","day":"01","month":"10","article_processing_charge":"No","has_accepted_license":"1","external_id":{"isi":["000701142900012"],"pmid":["34530328"]},"author":[{"last_name":"Venezia","full_name":"Venezia, Serena","first_name":"Serena"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"first_name":"Gregor K.","last_name":"Wenning","full_name":"Wenning, Gregor K."},{"first_name":"Nadia","full_name":"Stefanova, Nadia","last_name":"Stefanova"}],"pmid":1,"date_published":"2021-10-01T00:00:00Z","volume":91,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"EM-Fac"}],"publisher":"Elsevier","citation":{"chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>.","mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91, Elsevier, 2021, pp. 59–65, doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>.","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91. Elsevier, pp. 59–65, 2021.","ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. 2021;91:59-65. doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism &#38; Related Disorders 91 (2021) 59–65.","ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism &#38; Related Disorders. 91, 59–65.","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., &#38; Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>"},"date_updated":"2023-08-17T06:36:01Z","status":"public","isi":1,"publication_identifier":{"eissn":["1873-5126"],"issn":["1353-8020"]}},{"keyword":["Immunology","Immunology and Allergy"],"month":"05","day":"01","issue":"5","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","status":"public","isi":1,"publication_identifier":{"issn":["0105-4538"],"eissn":["1398-9995"]},"department":[{"_id":"Bio"}],"date_updated":"2023-09-05T15:58:53Z","citation":{"ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556.","apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556.","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. 2021;76(5):1553-1556. doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>","mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>.","chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>.","ieee":"C. L. Pranger <i>et al.</i>, “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” <i>Allergy</i>, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021."},"publisher":"Wiley","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-05-01T00:00:00Z","volume":76,"has_accepted_license":"1","external_id":{"isi":["000577708800001"],"pmid":["32990982"]},"article_processing_charge":"No","pmid":1,"author":[{"first_name":"Christina L.","full_name":"Pranger, Christina L.","last_name":"Pranger"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","first_name":"Judit"},{"last_name":"Köhler","full_name":"Köhler, Verena K.","first_name":"Verena K."},{"first_name":"Isabella","full_name":"Pali‐Schöll, Isabella","last_name":"Pali‐Schöll"},{"last_name":"Fiocchi","full_name":"Fiocchi, Alessandro","first_name":"Alessandro"},{"first_name":"Sophia N.","last_name":"Karagiannis","full_name":"Karagiannis, Sophia N."},{"first_name":"Olatz","last_name":"Zenarruzabeitia","full_name":"Zenarruzabeitia, Olatz"},{"last_name":"Borrego","full_name":"Borrego, Francisco","first_name":"Francisco"},{"first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim"}],"file":[{"date_created":"2022-03-08T11:23:16Z","file_name":"2021_Allergy_Pranger.pdf","checksum":"9526f9554112fc027c9f7fa540c488cd","content_type":"application/pdf","relation":"main_file","success":1,"file_size":626081,"access_level":"open_access","date_updated":"2022-03-08T11:23:16Z","creator":"dernst","file_id":"10837"}],"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","page":"1553-1556","publication_status":"published","article_type":"letter_note","oa":1,"publication":"Allergy","acknowledgement":"This  work  was  supported  by  the  Austrian  Science  Fund  (FWF)  grants  MCCA  W1248-B30  and  SFB  F4606-B28  to  EJJ.  CP  received  a  short-term research fellowship of the European Federation of Immunological Societies  (EFIS-IL)  for  a  research  visit  at  Biocruces  Bizkaia  Health  Research  Institute,  Barakaldo,  Spain.  VKK  received  an  EFIS-IL  short-term  research  fellowship  for  a  research  visit  at  King’s  College  London.  The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK).  The  authors  acknowledge  support  by  the  Medical  Research  Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer  Research  UK  King's  Health  Partners  Centre  at  King's  College  London   (C604/A25135)   (SNK);   CRUK/NIHR   in   England/DoH   for   Scotland,  Wales  and  Northern  Ireland  Experimental  Cancer  Medicine  Centre  (C10355/A15587)  (SNK).  The  views  expressed  are  those  of  the  author(s)  and  not  necessarily  those  of  the  NHS,  the  NIHR  or  the  Department  of  Health.  Additionally,  this  work  was  funded  by  Instituto  de  Salud  Carlos  III  through  the  project  \"PI16/01223\"  (Co-funded  by  European Regional Development Fund; “A way to make Europe”) to FB and  by  the  Department  of  Health,  Basque  Government  through  the  project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","type":"journal_article","file_date_updated":"2022-03-08T11:23:16Z","language":[{"iso":"eng"}],"date_created":"2022-03-08T11:19:05Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2021","_id":"10836","intvolume":"        76","ddc":["570"],"doi":"10.1111/all.14604"},{"department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"date_updated":"2025-04-14T07:43:46Z","citation":{"ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>.","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>.","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021."},"publisher":"Elsevier","status":"public","isi":1,"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"article_processing_charge":"Yes","has_accepted_license":"1","external_id":{"isi":["000706409200006"]},"author":[{"first_name":"Murat","orcid":"0000-0001-8945-6992","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat"},{"first_name":"Stephen","full_name":"Barratt, Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","last_name":"Barratt"},{"full_name":"Flynn, Sean M.","last_name":"Flynn","first_name":"Sean M."},{"full_name":"Begum, Farida","last_name":"Begum","first_name":"Farida"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"orcid":"0000-0001-8347-0443","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","first_name":"Mario"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":297,"date_published":"2021-09-01T00:00:00Z","day":"01","month":"09","scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","issue":"3","file_date_updated":"2021-10-11T12:20:58Z","publication":"Journal of Biological Chemistry","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","type":"journal_article","_id":"10117","ddc":["612"],"doi":"10.1016/J.JBC.2021.101094","intvolume":"       297","date_created":"2021-10-10T22:01:23Z","language":[{"iso":"eng"}],"year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","article_type":"original","oa":1,"article_number":"101094","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","file":[{"content_type":"application/pdf","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_name":"2021_JBC_Artan.pdf","date_created":"2021-10-11T12:20:58Z","file_id":"10121","creator":"cchlebak","date_updated":"2021-10-11T12:20:58Z","access_level":"open_access","file_size":1680010,"relation":"main_file","success":1}],"abstract":[{"lang":"eng","text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism."}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1},{"acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","type":"journal_article","publication":"EMBO Journal","file_date_updated":"2021-12-13T14:54:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","language":[{"iso":"eng"}],"date_created":"2021-10-24T22:01:34Z","ddc":["610"],"intvolume":"        40","doi":"10.15252/embj.2021108714","_id":"10179","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","file":[{"file_name":"2021_EMBO_Bajaj.pdf","checksum":"78d2d02e775322297e774f72810a41a4","content_type":"application/pdf","date_created":"2021-12-13T14:54:14Z","date_updated":"2021-12-13T14:54:14Z","creator":"alisjak","file_id":"10541","success":1,"relation":"main_file","file_size":7819881,"access_level":"open_access"}],"article_number":"e108714","oa":1,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"isi":1,"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"status":"public","citation":{"ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714."},"publisher":"Embo Press","date_updated":"2023-08-14T08:05:23Z","department":[{"_id":"Bio"}],"volume":40,"date_published":"2021-10-18T00:00:00Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"author":[{"full_name":"Bajaj, Sunanjay","last_name":"Bajaj","first_name":"Sunanjay"},{"first_name":"Joshua A.","full_name":"Bagley, Joshua A.","last_name":"Bagley"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Abel","last_name":"Vertesy","full_name":"Vertesy, Abel"},{"first_name":"Sakurako","full_name":"Nagumo Wong, Sakurako","last_name":"Nagumo Wong"},{"full_name":"Krenn, Veronica","last_name":"Krenn","first_name":"Veronica"},{"first_name":"Julie","full_name":"Lévi-Strauss, Julie","last_name":"Lévi-Strauss"},{"last_name":"Knoblich","full_name":"Knoblich, Juergen A.","first_name":"Juergen A."}],"external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","month":"10","day":"18","issue":"23","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version"},{"volume":599,"date_published":"2021-11-11T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","id":"10095","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","relation":"press_release","description":"News on IST Webpage"}]},"author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"first_name":"Inge","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"first_name":"Lana","full_name":"Shabala, Lana","last_name":"Shabala"},{"first_name":"Wouter","full_name":"Smet, Wouter","last_name":"Smet"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"pmid":1,"article_processing_charge":"No","external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"isi":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"status":"public","date_updated":"2025-07-10T11:49:46Z","publisher":"Springer Nature","citation":{"ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277."},"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"corr_author":"1","issue":"7884","quality_controlled":"1","scopus_import":"1","oa_version":"Preprint","month":"11","keyword":["Multidisciplinary"],"day":"11","date_created":"2021-11-07T23:01:25Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","intvolume":"       599","doi":"10.1038/s41586-021-04037-6","_id":"10223","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","type":"journal_article","publication":"Nature","ec_funded":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"abstract":[{"text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.","lang":"eng"}],"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","page":"273-277","article_type":"original","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"oa":1},{"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","month":"11","day":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"volume":22,"date_published":"2021-11-04T00:00:00Z","author":[{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"first_name":"Michael","full_name":"Tsoory, Michael","last_name":"Tsoory"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"first_name":"Sylvia","last_name":"Badurek","full_name":"Badurek, Sylvia"},{"full_name":"Pitzer, Claudia","last_name":"Pitzer","first_name":"Claudia"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"full_name":"Ward, Jonathan","last_name":"Ward","first_name":"Jonathan"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300","last_name":"Schunn","first_name":"Michael"},{"last_name":"Noldus","full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J."},{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"external_id":{"isi":["000714350000001"]},"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"isi":1,"status":"public","date_updated":"2023-08-14T11:47:35Z","citation":{"apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. 2021;22. doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>","ieee":"L. Restivo <i>et al.</i>, “Towards best practices in research: Role of academic core facilities,” <i>EMBO Reports</i>, vol. 22. EMBO Press, 2021.","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>, vol. 22, e53824, EMBO Press, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>.","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>. EMBO Press, 2021. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>."},"publisher":"EMBO Press","department":[{"_id":"PreCl"}],"abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"title":"Towards best practices in research: Role of academic core facilities","file":[{"date_created":"2022-05-16T07:07:41Z","checksum":"74743baa6ef431ef60c3de3bc4da045a","content_type":"application/pdf","file_name":"2021_EmboReports_Restivo.pdf","file_size":488583,"access_level":"open_access","relation":"main_file","success":1,"file_id":"11381","date_updated":"2022-05-16T07:07:41Z","creator":"dernst"}],"article_number":"e53824","article_type":"original","publication_status":"published","oa":1,"date_created":"2021-11-14T23:01:24Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","doi":"10.15252/embr.202153824","ddc":["570"],"intvolume":"        22","_id":"10283","type":"journal_article","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","publication":"EMBO Reports","file_date_updated":"2022-05-16T07:07:41Z"},{"day":"01","month":"01","scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","issue":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"date_updated":"2025-06-12T06:32:24Z","publisher":"Wiley","citation":{"ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(1):351-369. doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>","chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>.","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>.","ieee":"H. Li <i>et al.</i>, “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369."},"status":"public","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"isi":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000570187900001"],"pmid":["32810889"]},"pmid":1,"author":[{"last_name":"Li","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Hongjiang","first_name":"Hongjiang"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","last_name":"von Wangenheim","first_name":"Daniel"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda","orcid":"0000-0002-8821-8236"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"orcid":"0000-0001-7263-0560","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T"},{"first_name":"Riet","last_name":"de Rycke","full_name":"de Rycke, Riet"},{"first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"last_name":"Gütl","id":"381929CE-F248-11E8-B48F-1D18A9856A87","full_name":"Gütl, Daniel J","first_name":"Daniel J"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","first_name":"Peter"},{"first_name":"Meiyu","full_name":"Ke, Meiyu","last_name":"Ke"},{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu"},{"first_name":"Jan","full_name":"Dettmer, Jan","last_name":"Dettmer"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":229,"date_published":"2021-01-01T00:00:00Z","publication_status":"published","article_type":"original","oa":1,"file":[{"file_name":"2021_NewPhytologist_Li.pdf","checksum":"b45621607b4cab97eeb1605ab58e896e","content_type":"application/pdf","date_created":"2021-02-04T09:44:17Z","date_updated":"2021-02-04T09:44:17Z","creator":"dernst","file_id":"9084","success":1,"relation":"main_file","file_size":4061962,"access_level":"open_access"}],"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","page":"351-369","abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"file_date_updated":"2021-02-04T09:44:17Z","publication":"New Phytologist","type":"journal_article","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","_id":"8582","ddc":["580"],"intvolume":"       229","doi":"10.1111/nph.16887","date_created":"2020-09-28T08:59:28Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]