[{"month":"08","date_published":"2022-08-15T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"SaSi"}],"file":[{"file_size":7317396,"file_name":"2022_NatComm_Schulz.pdf","checksum":"191d9db0266e14a28d3a56dc7f65da84","date_created":"2022-08-29T06:44:30Z","access_level":"open_access","date_updated":"2022-08-29T06:44:30Z","success":1,"relation":"main_file","content_type":"application/pdf","creator":"cchlebak","file_id":"12002"}],"date_created":"2022-08-28T22:01:59Z","day":"15","type":"journal_article","intvolume":"        13","status":"public","publication":"Nature Communications","file_date_updated":"2022-08-29T06:44:30Z","doi":"10.1038/s41467-022-32390-1","year":"2022","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses","external_id":{"isi":["000840984400032"],"pmid":["35970889"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"4728","isi":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/dreaddful-mimicry/"}],"record":[{"id":"11945","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"research_data","id":"11542"}]},"ddc":["570"],"citation":{"chicago":"Schulz, Rouven, Medina Korkut, Alessandro Venturino, Gloria Colombo, and Sandra Siegert. “Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32390-1\">https://doi.org/10.1038/s41467-022-32390-1</a>.","apa":"Schulz, R., Korkut, M., Venturino, A., Colombo, G., &#38; Siegert, S. (2022). Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32390-1\">https://doi.org/10.1038/s41467-022-32390-1</a>","ieee":"R. Schulz, M. Korkut, A. Venturino, G. Colombo, and S. Siegert, “Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. 2022. Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. Nature Communications. 13, 4728.","short":"R. Schulz, M. Korkut, A. Venturino, G. Colombo, S. Siegert, Nature Communications 13 (2022).","ama":"Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32390-1\">10.1038/s41467-022-32390-1</a>","mla":"Schulz, Rouven, et al. “Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses.” <i>Nature Communications</i>, vol. 13, 4728, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32390-1\">10.1038/s41467-022-32390-1</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest. We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we included two additional DREADD-based chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands."}],"author":[{"id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X"},{"id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina","last_name":"Korkut","full_name":"Korkut, Medina","orcid":"0000-0003-4309-2251"},{"first_name":"Alessandro","last_name":"Venturino","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gloria","last_name":"Colombo","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"article_processing_charge":"No","volume":13,"date_updated":"2024-02-21T12:34:51Z","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"_id":"11995","oa_version":"Published Version","project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"quality_controlled":"1","acknowledgement":"The authors thank the Scientific Service Units at ISTA, in particular the Molecular Biology Service of the Lab Support Facility, Imaging & Optics Facility, and the Preclinical Facility, and the Novarino group, Harald Janoviak, and Marco Benevento for sharing reagents and expertise. This research was supported by a DOC Fellowship (24979) awarded to R.S. by the Austrian Academy of Sciences.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"102343","isi":1,"ddc":["570"],"year":"2022","doi":"10.1016/j.jbc.2022.102343","acknowledged_ssus":[{"_id":"Bio"}],"ec_funded":1,"title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","external_id":{"isi":["000884241800011"],"pmid":["35933017"]},"article_processing_charge":"No","volume":298,"oa":1,"date_updated":"2023-08-03T13:56:46Z","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"pmid":1,"_id":"12082","project":[{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"oa_version":"Published Version","quality_controlled":"1","acknowledgement":"We thank de Bono laboratory members for helpful comments on the article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable discussions and comments on how to optimize mass spec analyses of worm samples. We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z ) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement no.: 754411).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (2022).","ista":"Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.","ama":"Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. 2022;298(9). doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>","mla":"Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9, 102343, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>.","chicago":"Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>.","apa":"Artan, M., Hartl, M., Chen, W., &#38; de Bono, M. (2022). Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>","ieee":"M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans,” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9. Elsevier, 2022."},"publication_status":"published","abstract":[{"text":"Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.","lang":"eng"}],"author":[{"last_name":"Artan","full_name":"Artan, Murat","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"last_name":"Hartl","full_name":"Hartl, Markus","first_name":"Markus"},{"first_name":"Weiqiang","last_name":"Chen","full_name":"Chen, Weiqiang"},{"orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","department":[{"_id":"MaDe"}],"date_created":"2022-09-11T22:01:55Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"12092","creator":"dernst","success":1,"date_updated":"2022-09-12T08:14:50Z","access_level":"open_access","file_name":"2022_JBC_Artan.pdf","file_size":2101656,"date_created":"2022-09-12T08:14:50Z","checksum":"e726c7b9315230e6710e0b1f1d1677e9"}],"month":"09","date_published":"2022-09-01T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"publication":"Journal of Biological Chemistry","issue":"9","file_date_updated":"2022-09-12T08:14:50Z","day":"01","type":"journal_article","intvolume":"       298","status":"public"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"101866","related_material":{"record":[{"status":"public","relation":"other","id":"11478"}]},"ddc":["570"],"year":"2022","doi":"10.1016/j.xpro.2022.101866","acknowledged_ssus":[{"_id":"Bio"}],"ec_funded":1,"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","article_processing_charge":"No","volume":3,"oa":1,"date_updated":"2023-11-02T12:21:32Z","publication_identifier":{"issn":["2666-1667"]},"_id":"12117","project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017"}],"oa_version":"Published Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","citation":{"mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022.","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1"}],"author":[{"id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","full_name":"Hübschmann, Verena","last_name":"Hübschmann"},{"orcid":"0000-0003-4309-2251","last_name":"Korkut","full_name":"Korkut, Medina","first_name":"Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"has_accepted_license":"1","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"date_created":"2023-01-12T11:56:38Z","file":[{"file_size":6251945,"file_name":"2022_STARProtocols_Huebschmann.pdf","checksum":"3c71b8a60633d42c2f77c49025d5559b","date_created":"2023-01-23T09:50:51Z","access_level":"open_access","date_updated":"2023-01-23T09:50:51Z","success":1,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"12340"}],"month":"12","article_type":"letter_note","date_published":"2022-12-16T00:00:00Z","scopus_import":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"publication":"STAR Protocols","issue":"4","file_date_updated":"2023-01-23T09:50:51Z","day":"16","type":"journal_article","intvolume":"         3","status":"public"},{"publication":"Nature","issue":"7934","page":"133-138","day":"03","type":"journal_article","intvolume":"       611","status":"public","department":[{"_id":"JiFr"}],"date_created":"2023-01-12T12:06:05Z","month":"11","date_published":"2022-11-03T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"volume":611,"date_updated":"2023-10-03T11:04:53Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"pmid":1,"_id":"12144","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","citation":{"chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>.","ieee":"L. Qi <i>et al.</i>, “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” <i>Nature</i>, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>","ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>.","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. 2022;611(7934):133-138. doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>"},"publication_status":"published","abstract":[{"text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.","lang":"eng"}],"author":[{"full_name":"Qi, Linlin","last_name":"Qi","orcid":"0000-0001-5187-8401","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"last_name":"Kwiatkowski","full_name":"Kwiatkowski, Mateusz","first_name":"Mateusz"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang","last_name":"Chen"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593","last_name":"Sinclair","full_name":"Sinclair, Scott A","first_name":"Scott A"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia"},{"first_name":"Charo I.","full_name":"del Genio, Charo I.","last_name":"del Genio"},{"last_name":"Kubeš","full_name":"Kubeš, Martin F.","first_name":"Martin F."},{"first_name":"Richard","last_name":"Napier","full_name":"Napier, Richard"},{"first_name":"Krzysztof","full_name":"Jaworski, Krzysztof","last_name":"Jaworski"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"isi":1,"main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf"}],"doi":"10.1038/s41586-022-05369-7","year":"2022","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ec_funded":1,"title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","external_id":{"pmid":["36289340"],"isi":["000875061600013"]}},{"status":"public","intvolume":"        18","type":"journal_article","day":"01","file_date_updated":"2023-01-27T07:32:01Z","page":"1482-1493","issue":"12","publication":"Nature Physics","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","date_published":"2022-12-01T00:00:00Z","article_type":"original","month":"12","date_created":"2023-01-16T09:45:19Z","file":[{"checksum":"c86a8e8d80d1bfc46d56a01e88a2526a","date_created":"2023-01-27T07:32:01Z","file_size":36703569,"file_name":"2022_NaturePhysics_Pinheiro.pdf","access_level":"open_access","date_updated":"2023-01-27T07:32:01Z","success":1,"creator":"dernst","file_id":"12412","relation":"main_file","content_type":"application/pdf"}],"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"has_accepted_license":"1","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","full_name":"Kardos, Roland","first_name":"Roland"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"keyword":["General Physics and Astronomy"],"abstract":[{"text":"Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Nunes Pinheiro, Diana C, Roland Kardos, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” <i>Nature Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41567-022-01787-6\">https://doi.org/10.1038/s41567-022-01787-6</a>.","ieee":"D. C. Nunes Pinheiro, R. Kardos, E. B. Hannezo, and C.-P. J. Heisenberg, “Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming,” <i>Nature Physics</i>, vol. 18, no. 12. Springer Nature, pp. 1482–1493, 2022.","apa":"Nunes Pinheiro, D. C., Kardos, R., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2022). Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-022-01787-6\">https://doi.org/10.1038/s41567-022-01787-6</a>","short":"D.C. Nunes Pinheiro, R. Kardos, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 18 (2022) 1482–1493.","ista":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. 2022. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 18(12), 1482–1493.","mla":"Nunes Pinheiro, Diana C., et al. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” <i>Nature Physics</i>, vol. 18, no. 12, Springer Nature, 2022, pp. 1482–93, doi:<a href=\"https://doi.org/10.1038/s41567-022-01787-6\">10.1038/s41567-022-01787-6</a>.","ama":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. <i>Nature Physics</i>. 2022;18(12):1482-1493. doi:<a href=\"https://doi.org/10.1038/s41567-022-01787-6\">10.1038/s41567-022-01787-6</a>"},"acknowledgement":"We thank K. Sampath, A. Pauli and Y. Bellaїche for feedback on the manuscript. We also thank the members of the Heisenberg group, in particular A. Schauer and F. Nur Arslan, for help, technical advice and discussions, and the Bioimaging and Life Science facilities at IST\r\nAustria for continuous support. We thank C. Flandoli for the artwork in the figures. This work was supported by postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P. and the European Union (European Research Council starting grant 851288 to É.H. and European Research Council advanced grant 742573 to C.-P.H.).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","project":[{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","_id":"12209","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"volume":18,"oa":1,"date_updated":"2023-08-04T09:15:58Z","article_processing_charge":"No","title":"Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming","external_id":{"isi":["000871319900002"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1038/s41567-022-01787-6","year":"2022","ddc":["570"],"isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"publication":"Molecular Plant","issue":"10","page":"1533-1542","file_date_updated":"2023-01-30T07:46:51Z","day":"03","type":"journal_article","intvolume":"        15","status":"public","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_created":"2023-01-16T09:51:49Z","file":[{"date_updated":"2023-01-30T07:46:51Z","access_level":"open_access","file_name":"2022_MolecularPlant_Johnson.pdf","file_size":2307251,"date_created":"2023-01-30T07:46:51Z","checksum":"04d5c12490052d03e4dc4412338a43dd","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"12435","success":1}],"month":"10","article_type":"original","date_published":"2022-10-03T00:00:00Z","scopus_import":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2023-08-04T09:39:24Z","volume":15,"oa":1,"publication_identifier":{"issn":["1674-2052"]},"pmid":1,"_id":"12239","oa_version":"Published Version","project":[{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","citation":{"short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>"},"publication_status":"published","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"keyword":["Plant Science","Molecular Biology"],"author":[{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"ddc":["580"],"year":"2022","doi":"10.1016/j.molp.2022.09.003","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","external_id":{"isi":["000882769800009"],"pmid":["36081349"]}},{"title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"doi":"10.1038/s41593-022-01167-6","year":"2022","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","description":"News on ISTA website","relation":"press_release"}],"record":[{"status":"public","id":"12378","relation":"dissertation_contains"}]},"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.","lang":"eng"}],"keyword":["General Neuroscience"],"author":[{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","last_name":"Cubero","first_name":"Ryan J"},{"first_name":"Lida","full_name":"Kanari, Lida","last_name":"Kanari"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro"},{"full_name":"Schulz, Rouven","last_name":"Schulz","orcid":"0000-0001-5297-733X","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martina","full_name":"Scolamiero, Martina","last_name":"Scolamiero"},{"full_name":"Agerberg, Jens","last_name":"Agerberg","first_name":"Jens"},{"first_name":"Hansruedi","last_name":"Mathys","full_name":"Mathys, Hansruedi"},{"first_name":"Li-Huei","last_name":"Tsai","full_name":"Tsai, Li-Huei"},{"last_name":"Chachólski","full_name":"Chachólski, Wojciech","first_name":"Wojciech"},{"first_name":"Kathryn","full_name":"Hess, Kathryn","last_name":"Hess"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra"}],"citation":{"short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>.","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022."},"publication_status":"published","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"_id":"12244","pmid":1,"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","grant_number":"715571"}],"oa_version":"Published Version","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","article_processing_charge":"No","date_updated":"2024-03-25T23:30:10Z","volume":25,"oa":1,"scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"10","date_published":"2022-10-01T00:00:00Z","article_type":"original","date_created":"2023-01-16T09:53:07Z","file":[{"success":1,"creator":"dernst","file_id":"12437","relation":"main_file","content_type":"application/pdf","checksum":"28431146873096f52e0107b534f178c9","date_created":"2023-01-30T08:06:56Z","file_size":23789835,"file_name":"2022_NatureNeuroscience_Colombo.pdf","access_level":"open_access","date_updated":"2023-01-30T08:06:56Z"}],"has_accepted_license":"1","department":[{"_id":"SaSi"}],"intvolume":"        25","status":"public","day":"01","type":"journal_article","publication":"Nature Neuroscience","issue":"10","file_date_updated":"2023-01-30T08:06:56Z","page":"1379-1393"},{"scopus_import":"1","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"month":"09","date_published":"2022-09-15T00:00:00Z","article_type":"original","date_created":"2023-01-16T10:04:15Z","file":[{"access_level":"open_access","date_updated":"2023-01-30T11:50:53Z","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","date_created":"2023-01-30T11:50:53Z","file_size":8506811,"file_name":"2022_eLife_Sumser.pdf","file_id":"12463","creator":"dernst","relation":"main_file","content_type":"application/pdf","success":1}],"has_accepted_license":"1","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"intvolume":"        11","status":"public","day":"15","type":"journal_article","publication":"eLife","file_date_updated":"2023-01-30T11:50:53Z","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","external_id":{"isi":["000892204300001"],"pmid":["36040301"]},"year":"2022","doi":"10.7554/elife.79848","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"ec_funded":1,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"79848","isi":1,"abstract":[{"text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo.","lang":"eng"}],"author":[{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","last_name":"Sumser","first_name":"Anton L"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"last_name":"Ben Simon","full_name":"Ben Simon, Yoav","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"citation":{"chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>"},"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"_id":"12288","pmid":1,"quality_controlled":"1","oa_version":"Published Version","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020"},{"grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","article_processing_charge":"No","date_updated":"2023-08-04T10:29:48Z","oa":1,"volume":11},{"ddc":["580"],"isi":1,"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","year":"2022","doi":"10.1038/s41586-022-05187-x","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"ec_funded":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"pmid":1,"_id":"12291","oa_version":"Submitted Version","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","volume":609,"oa":1,"date_updated":"2023-11-07T08:16:09Z","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"}],"author":[{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Branka D.","full_name":"Živanović, Branka D.","last_name":"Živanović"},{"first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Mónika","full_name":"Hrtyan, Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek","first_name":"Marek"},{"last_name":"Rýdza","full_name":"Rýdza, Nikola","first_name":"Nikola"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"full_name":"Teplova, Anastasiia","last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"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"}],"citation":{"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>.","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.","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.","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>.","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>"},"publication_status":"published","date_created":"2023-01-16T10:04:48Z","file":[{"file_size":79774945,"file_name":"Friml Nature 2022_merged.pdf","checksum":"a6055c606aefb900bf62ae3e7d15f921","date_created":"2023-11-02T17:12:37Z","access_level":"open_access","date_updated":"2023-11-02T17:12:37Z","success":1,"relation":"main_file","content_type":"application/pdf","file_id":"14483","creator":"amally"}],"has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"09","article_type":"original","date_published":"2022-09-15T00:00:00Z","publication":"Nature","issue":"7927","file_date_updated":"2023-11-02T17:12:37Z","page":"575-581","intvolume":"       609","status":"public","day":"15","type":"journal_article"},{"type":"dissertation","day":"29","status":"public","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"page":"113","file_date_updated":"2023-01-25T10:52:46Z","date_published":"2022-09-29T00:00:00Z","month":"09","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"degree_awarded":"PhD","has_accepted_license":"1","date_created":"2023-01-25T10:43:24Z","file":[{"success":1,"file_id":"12369","creator":"cchlebak","content_type":"application/pdf","relation":"main_file","date_created":"2023-01-25T10:52:46Z","checksum":"e54a3e69b83ebf166544164afd25608e","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","file_size":14581024,"date_updated":"2023-01-25T10:52:46Z","access_level":"open_access"}],"citation":{"chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>.","apa":"Arslan, F. N. (2022). <i>Remodeling of E-cadherin-mediated contacts via cortical  flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022.","mla":"Arslan, Feyza N. <i>Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>"},"publication_status":"published","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan","full_name":"Arslan, Feyza N"}],"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"article_processing_charge":"No","oa":1,"date_updated":"2023-08-08T13:14:10Z","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-025-1 "]},"_id":"12368","ec_funded":1,"year":"2022","doi":"10.15479/at:ista:12153","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"title":"Remodeling of E-cadherin-mediated contacts via cortical  flows","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"alternative_title":["ISTA Thesis"],"ddc":["570"],"related_material":{"record":[{"id":"9350","relation":"part_of_dissertation","status":"public"}]}},{"citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>."},"publication_status":"published","author":[{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","last_name":"Colombo","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902"}],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:40:37Z","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2663-337X"]},"_id":"12378","ec_funded":1,"year":"2022","doi":"10.15479/at:ista:12378","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"alternative_title":["ISTA Thesis"],"ddc":["570"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12244","status":"public"}]},"type":"dissertation","day":"11","supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert"}],"status":"public","page":"142","file_date_updated":"2023-04-12T22:30:03Z","date_published":"2022-11-11T00:00:00Z","month":"11","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"has_accepted_license":"1","degree_awarded":"PhD","file":[{"embargo_to":"open_access","date_updated":"2023-04-12T22:30:03Z","access_level":"closed","file_name":"Gloria_Colombo_Thesis.docx","file_size":23890382,"date_created":"2023-01-25T14:31:32Z","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"cchlebak","file_id":"12379"},{"date_updated":"2023-04-12T22:30:03Z","access_level":"open_access","date_created":"2023-01-25T14:31:36Z","checksum":"8af4319c18b516e8758e9a6cb02b103b","file_name":"Gloria_Colombo_Thesis.pdf","file_size":13802421,"embargo":"2023-04-11","creator":"cchlebak","file_id":"12380","content_type":"application/pdf","relation":"main_file"}],"date_created":"2023-01-25T14:27:43Z"},{"month":"07","date_published":"2022-07-11T00:00:00Z","article_type":"original","publisher":"Springer Nature","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"date_created":"2021-08-06T09:09:11Z","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"11642","creator":"dernst","success":1,"access_level":"open_access","date_updated":"2022-07-25T07:11:32Z","file_size":11475325,"file_name":"2022_NatureImmunology_Assen.pdf","checksum":"628e7b49809f22c75b428842efe70c68","date_created":"2022-07-25T07:11:32Z"}],"day":"11","type":"journal_article","intvolume":"        23","status":"public","publication":"Nature Immunology","file_date_updated":"2022-07-25T07:11:32Z","page":"1246-1255","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"year":"2022","doi":"10.1038/s41590-022-01257-4","ec_funded":1,"external_id":{"isi":["000822975900002"]},"title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"ddc":["570"],"publication_status":"published","citation":{"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>.","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.","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.","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.","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>.","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>"},"abstract":[{"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.","lang":"eng"}],"author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","full_name":"Assen, Frank P","last_name":"Assen","orcid":"0000-0003-3470-6119"},{"first_name":"Jun","full_name":"Abe, Jun","last_name":"Abe"},{"last_name":"Hons","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"first_name":"Gabriel","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brown","full_name":"Brown, Markus","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ludewig, Burkhard","last_name":"Ludewig","first_name":"Burkhard"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","last_name":"Weninger","full_name":"Weninger, Wolfgang"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjiv A.","last_name":"Luther","full_name":"Luther, Sanjiv A."},{"last_name":"Stein","full_name":"Stein, Jens V.","first_name":"Jens V."},{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-4561-241X","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_updated":"2023-08-02T06:53:07Z","volume":23,"article_processing_charge":"No","_id":"9794","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","quality_controlled":"1"},{"date_updated":"2023-08-04T11:01:21Z","oa":1,"volume":229,"article_processing_charge":"Yes (via OA deal)","_id":"8582","publication_identifier":{"issn":["0028646X"],"eissn":["14698137"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","citation":{"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>.","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.","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.","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.","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>.","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>"},"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."}],"author":[{"orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"von Wangenheim","full_name":"von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","first_name":"Daniel"},{"last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser","last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser","orcid":"0000-0002-8821-8236"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"de Rycke","full_name":"de Rycke, Riet","first_name":"Riet"},{"first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Ke, Meiyu","last_name":"Ke","first_name":"Meiyu"},{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen","full_name":"Chen, Xu"},{"last_name":"Dettmer","full_name":"Dettmer, Jan","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"}],"year":"2021","doi":"10.1111/nph.16887","ec_funded":1,"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","external_id":{"isi":["000570187900001"]},"issue":"1","publication":"New Phytologist","page":"351-369","file_date_updated":"2021-02-04T09:44:17Z","day":"01","type":"journal_article","intvolume":"       229","status":"public","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"file":[{"creator":"dernst","file_id":"9084","content_type":"application/pdf","relation":"main_file","success":1,"date_updated":"2021-02-04T09:44:17Z","access_level":"open_access","date_created":"2021-02-04T09:44:17Z","checksum":"b45621607b4cab97eeb1605ab58e896e","file_name":"2021_NewPhytologist_Li.pdf","file_size":4061962}],"date_created":"2020-09-28T08:59:28Z","month":"01","article_type":"original","date_published":"2021-01-01T00:00:00Z","publisher":"Wiley","scopus_import":"1","language":[{"iso":"eng"}]},{"status":"public","intvolume":"       303","type":"journal_article","day":"01","file_date_updated":"2021-02-04T07:49:25Z","publication":"Plant Science","language":[{"iso":"eng"}],"publisher":"Elsevier","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","article_type":"original","month":"02","date_created":"2020-12-09T14:48:28Z","file":[{"file_id":"9083","creator":"dernst","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2021-02-04T07:49:25Z","checksum":"a7f2562bdca62d67dfa88e271b62a629","date_created":"2021-02-04T07:49:25Z","file_size":12563728,"file_name":"2021_PlantScience_Gelova.pdf"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"has_accepted_license":"1","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"author":[{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"first_name":"Markéta","full_name":"Pernisová, Markéta","last_name":"Pernisová"},{"first_name":"Géraldine","full_name":"Brunoud, Géraldine","last_name":"Brunoud"},{"first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav","first_name":"Jaroslav"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"first_name":"Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","first_name":"Jakub"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"last_name":"Čovanová","full_name":"Čovanová, Milada","first_name":"Milada"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>."},"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"_id":"8931","pmid":1,"publication_identifier":{"issn":["0168-9452"]},"volume":303,"date_updated":"2024-10-29T10:22:43Z","oa":1,"article_processing_charge":"Yes (via OA deal)","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.plantsci.2020.110750","year":"2021","ddc":["580"],"related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"article_number":"110750","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"year":"2021","doi":"10.1073/pnas.2010054118","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"isi":1,"article_number":"e2010054118","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"citation":{"ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118.","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021).","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"author":[{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F","last_name":"Düllberg","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748"},{"first_name":"Albert","full_name":"Auer, Albert","last_name":"Auer","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola"},{"first_name":"Katrin","orcid":"0000-0002-2429-7668","full_name":"Loibl, Katrin","last_name":"Loibl","id":"3760F32C-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin"}],"article_processing_charge":"No","oa":1,"volume":118,"date_updated":"2023-08-04T11:20:46Z","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"pmid":1,"_id":"8988","oa_version":"Published Version","project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"quality_controlled":"1","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"01","date_published":"2021-01-05T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"date_created":"2021-01-03T23:01:23Z","day":"05","type":"journal_article","intvolume":"       118","status":"public","publication":"PNAS","issue":"1"},{"type":"journal_article","day":"01","status":"public","intvolume":"        40","file_date_updated":"2021-02-11T12:28:29Z","issue":"3","publication":"EMBO Journal","date_published":"2021-02-01T00:00:00Z","article_type":"original","month":"02","language":[{"iso":"eng"}],"publisher":"Embo Press","scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"has_accepted_license":"1","file":[{"date_updated":"2021-02-11T12:28:29Z","access_level":"open_access","file_name":"2021_Embo_Otvos.pdf","file_size":2358617,"date_created":"2021-02-11T12:28:29Z","checksum":"dc55c900f3b061d6c2790b8813d759a3","content_type":"application/pdf","relation":"main_file","file_id":"9110","creator":"dernst","success":1}],"date_created":"2021-01-17T23:01:12Z","publication_status":"published","citation":{"chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>.","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>"},"author":[{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","last_name":"Ötvös","first_name":"Krisztina"},{"last_name":"Marconi","full_name":"Marconi, Marco","first_name":"Marco"},{"first_name":"Andrea","full_name":"Vega, Andrea","last_name":"Vega"},{"last_name":"O’Brien","full_name":"O’Brien, Jose","first_name":"Jose"},{"first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abualia, Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Antonielli","full_name":"Antonielli, Livio","first_name":"Livio"},{"first_name":"Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","last_name":"Zhang","full_name":"Zhang, Yuzhou","first_name":"Yuzhou"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","last_name":"Cuesta","orcid":"0000-0003-1923-2410","first_name":"Candela"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"}],"abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"oa":1,"volume":40,"date_updated":"2024-03-25T23:30:22Z","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9010","pmid":1,"publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.15252/embj.2020106862","year":"2021","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"isi":1,"article_number":"e106862","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"related_material":{"record":[{"id":"10303","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage","relation":"press_release"}]}},{"acknowledgement":"We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic zebrafish lines, the Heisenberg lab for technical assistance and feedback on the manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"oa_version":"None","quality_controlled":"1","pmid":1,"_id":"9245","publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-0716-0969-9"],"eisbn":["978-1-0716-0970-5"],"eissn":["1940-6029"]},"volume":2218,"date_updated":"2022-06-03T10:57:55Z","article_processing_charge":"No","editor":[{"first_name":"Roland","full_name":"Dosch, Roland","last_name":"Dosch"}],"author":[{"first_name":"Peng","last_name":"Xia","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data."}],"publication_status":"published","citation":{"chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, 2218:117–28. Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>.","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in <i>Germline Development in the Zebrafish</i>, vol. 2218, R. Dosch, Ed. Humana, 2021, pp. 117–128.","apa":"Xia, P., &#38; Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), <i>Germline Development in the Zebrafish</i> (Vol. 2218, pp. 117–128). Humana. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>","ista":"Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa layer after laser surgery. In: Germline Development in the Zebrafish. Methods in Molecular Biology, vol. 2218, 117–128.","short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana, 2021, pp. 117–128.","mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, vol. 2218, Humana, 2021, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>.","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. <i>Germline Development in the Zebrafish</i>. Vol 2218. Humana; 2021:117-128. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>"},"alternative_title":["Methods in Molecular Biology"],"title":"Quantifying tissue tension in the granulosa layer after laser surgery","external_id":{"pmid":["33606227"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1007/978-1-0716-0970-5_10","year":"2021","page":"117-128","publication":"Germline Development in the Zebrafish","status":"public","intvolume":"      2218","type":"book_chapter","day":"20","date_created":"2021-03-14T23:01:34Z","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"publisher":"Humana","scopus_import":"1","date_published":"2021-02-20T00:00:00Z","month":"02"},{"publication":"Plant Physiology","issue":"2","file_date_updated":"2021-11-11T15:07:51Z","page":"1122–1142","intvolume":"       186","status":"public","day":"01","type":"journal_article","file":[{"creator":"cziletti","file_id":"10273","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2021-11-11T15:07:51Z","checksum":"532bb9469d3b665907f06df8c383eade","date_created":"2021-11-11T15:07:51Z","file_size":2289127,"file_name":"2021_PlantPhysio_Narasimhan.pdf"}],"date_created":"2021-03-26T12:08:38Z","has_accepted_license":"1","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","language":[{"iso":"eng"}],"month":"06","article_type":"original","date_published":"2021-06-01T00:00:00Z","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"pmid":1,"_id":"9287","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"quality_controlled":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","article_processing_charge":"Yes (in subscription journal)","volume":186,"oa":1,"date_updated":"2024-10-29T10:22:43Z","abstract":[{"text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. ","lang":"eng"}],"author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"full_name":"Tan, Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"E","last_name":"Himschoot","full_name":"Himschoot, E"},{"first_name":"R","full_name":"Wang, R","last_name":"Wang"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"J","last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J"},{"last_name":"Aniento","full_name":"Aniento, F","first_name":"F"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021."},"publication_status":"published","related_material":{"link":[{"relation":"erratum","url":"10.1093/plphys/kiab380"}],"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"doi":"10.1093/plphys/kiab134","year":"2021","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1},{"article_processing_charge":"No","date_updated":"2023-09-05T13:03:34Z","volume":31,"oa":1,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","quality_controlled":"1","acknowledgement":"We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.).","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"pmid":1,"_id":"9290","citation":{"chicago":"Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">https://doi.org/10.1016/j.cub.2021.02.028</a>.","ieee":"M. Glanc <i>et al.</i>, “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” <i>Current Biology</i>, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021.","apa":"Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">https://doi.org/10.1016/j.cub.2021.02.028</a>","short":"M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930.","ista":"Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930.","ama":"Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. <i>Current Biology</i>. 2021;31(9):1918-1930. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">10.1016/j.cub.2021.02.028</a>","mla":"Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” <i>Current Biology</i>, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.028\">10.1016/j.cub.2021.02.028</a>."},"publication_status":"published","author":[{"first_name":"Matous","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"K","last_name":"Van Gelderen","full_name":"Van Gelderen, K"},{"first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"full_name":"Naramoto, S","last_name":"Naramoto","first_name":"S"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang"},{"id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","orcid":"0000-0003-2267-106X","last_name":"Domjan","full_name":"Domjan, David","first_name":"David"},{"first_name":"L","last_name":"Vcelarova","full_name":"Vcelarova, L"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"full_name":"de Koning, E","last_name":"de Koning","first_name":"E"},{"first_name":"M","last_name":"van Dop","full_name":"van Dop, M"},{"first_name":"E","full_name":"Rademacher, E","last_name":"Rademacher"},{"first_name":"S","last_name":"Janson","full_name":"Janson, S"},{"first_name":"X","full_name":"Wei, X","last_name":"Wei"},{"last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Rybel","full_name":"De Rybel, B","first_name":"B"},{"last_name":"Offringa","full_name":"Offringa, R","first_name":"R"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"abstract":[{"lang":"eng","text":"Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development."}],"isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"ec_funded":1,"doi":"10.1016/j.cub.2021.02.028","year":"2021","acknowledged_ssus":[{"_id":"Bio"}],"title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","external_id":{"pmid":["33705718"],"isi":["000653077800004"]},"file_date_updated":"2021-04-01T10:53:42Z","page":"1918-1930","publication":"Current Biology","issue":"9","type":"journal_article","day":"10","status":"public","intvolume":"        31","department":[{"_id":"JiFr"}],"has_accepted_license":"1","date_created":"2021-03-26T12:09:33Z","file":[{"checksum":"b1723040ecfd8c81194185472eb62546","date_created":"2021-04-01T10:53:42Z","file_size":4324371,"file_name":"2021_CurrentBiology_Glanc.pdf","access_level":"open_access","date_updated":"2021-04-01T10:53:42Z","success":1,"file_id":"9303","creator":"dernst","relation":"main_file","content_type":"application/pdf"}],"article_type":"original","date_published":"2021-03-10T00:00:00Z","month":"03","language":[{"iso":"eng"}],"publisher":"Elsevier"},{"ddc":["570"],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","description":"News on IST Homepage","relation":"press_release"}]},"isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","external_id":{"pmid":["33730596"],"isi":["000636734000022"]},"ec_funded":1,"year":"2021","doi":"10.1016/j.cell.2021.02.017","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"project":[{"grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"V00736","call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","name":"Tissue material properties in embryonic development"}],"quality_controlled":"1","oa_version":"Published Version","acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"pmid":1,"_id":"9316","article_processing_charge":"No","oa":1,"volume":184,"date_updated":"2023-08-07T14:33:59Z","author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou","full_name":"Petridou, Nicoletta"},{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"}],"abstract":[{"text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.","lang":"eng"}],"citation":{"chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>.","apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., &#38; Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” <i>Cell</i>, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19.","mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>.","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. 2021;184(7):1914-1928.e19. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>"},"publication_status":"published","file":[{"success":1,"creator":"cziletti","file_id":"9534","relation":"main_file","content_type":"application/pdf","checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","date_created":"2021-06-08T10:04:10Z","file_size":11405875,"file_name":"2021_Cell_Petridou.pdf","access_level":"open_access","date_updated":"2021-06-08T10:04:10Z"}],"date_created":"2021-04-11T22:01:14Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Elsevier","date_published":"2021-04-01T00:00:00Z","article_type":"original","month":"04","page":"1914-1928.e19","file_date_updated":"2021-06-08T10:04:10Z","publication":"Cell","issue":"7","status":"public","intvolume":"       184","type":"journal_article","day":"01"}]