--- _id: '11341' abstract: - lang: eng text: Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9. acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: Bio acknowledgement: We thank the IST Austria Life Science Facility, the Miba Machine Shop and M. Lukačišinová for support with the liquid handling robot; the Bioimaging Facility at IST Austria, J. Power and B. Meier at the University of Cologne, and C. Göttlinger at the FACS Analysis Facility at the Institute for Genetics, University of Cologne, for support with flow cytometry experiments; L. Horst for the development of the automated experimental methods in Cologne; J. Parenteau, S. Abou Elela, G. Stormo, M. Springer and M. Schuldiner for providing us with yeast strains; B. Fernando, T. Fink, G. Ansmann and G. Chevreau for technical support; H. Köver, G. Tkačik, N. Barton, A. Angermayr and B. Kavčič for support during laboratory relocation; D. Siekhaus, M. Springer and all the members of the Bollenbach group for support and discussions; and K. Mitosch, M. Lukačišinová, G. Liti and A. de Luna for critical reading of our manuscript. This work was supported in part by an Austrian Science Fund (FWF) standalone grant P 27201-B22 (to T.B.), HFSP program Grant RGP0042/2013 (to T.B.), EU Marie Curie Career Integration Grant No. 303507, and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). A.E.-C. was supported by a Georg Forster fellowship from the Alexander von Humboldt Foundation. article_processing_charge: No article_type: original author: - first_name: Martin full_name: Lukacisin, Martin id: 298FFE8C-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisin orcid: 0000-0001-6549-4177 - first_name: Adriana full_name: Espinosa-Cantú, Adriana last_name: Espinosa-Cantú - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Lukacisin M, Espinosa-Cantú A, Bollenbach MT. Intron-mediated induction of phenotypic heterogeneity. Nature. 2022;605:113-118. doi:10.1038/s41586-022-04633-0 apa: Lukacisin, M., Espinosa-Cantú, A., & Bollenbach, M. T. (2022). Intron-mediated induction of phenotypic heterogeneity. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-04633-0 chicago: Lukacisin, Martin, Adriana Espinosa-Cantú, and Mark Tobias Bollenbach. “Intron-Mediated Induction of Phenotypic Heterogeneity.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-04633-0. ieee: M. Lukacisin, A. Espinosa-Cantú, and M. T. Bollenbach, “Intron-mediated induction of phenotypic heterogeneity,” Nature, vol. 605. Springer Nature, pp. 113–118, 2022. ista: Lukacisin M, Espinosa-Cantú A, Bollenbach MT. 2022. Intron-mediated induction of phenotypic heterogeneity. Nature. 605, 113–118. mla: Lukacisin, Martin, et al. “Intron-Mediated Induction of Phenotypic Heterogeneity.” Nature, vol. 605, Springer Nature, 2022, pp. 113–18, doi:10.1038/s41586-022-04633-0. short: M. Lukacisin, A. Espinosa-Cantú, M.T. Bollenbach, Nature 605 (2022) 113–118. date_created: 2022-05-01T22:01:42Z date_published: 2022-05-05T00:00:00Z date_updated: 2025-04-14T09:40:45Z day: '05' ddc: - '570' doi: 10.1038/s41586-022-04633-0 ec_funded: 1 external_id: isi: - '000784934100003' pmid: - '35444278' file: - access_level: open_access checksum: d68cd1596bb9fd819b750fe47c8a138a content_type: application/pdf creator: dernst date_created: 2022-08-05T06:08:24Z date_updated: 2022-08-05T06:08:24Z file_id: '11727' file_name: 2022_Nature_Lukacisin.pdf file_size: 25360311 relation: main_file success: 1 file_date_updated: 2022-08-05T06:08:24Z has_accepted_license: '1' intvolume: ' 605' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 113-118 pmid: 1 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Intron-mediated induction of phenotypic heterogeneity 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) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 605 year: '2022' ... --- _id: '9794' abstract: - lang: eng text: 'Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion.' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: PreCl - _id: LifeSc 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. article_processing_charge: No article_type: original author: - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Burkhard full_name: Ludewig, Burkhard last_name: Ludewig - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Wolfgang full_name: Weninger, Wolfgang last_name: Weninger - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Sanjiv A. full_name: Luther, Sanjiv A. last_name: Luther - first_name: Jens V. full_name: Stein, Jens V. last_name: Stein - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X citation: ama: Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4 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. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4 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.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4. ieee: F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022. ista: Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255. mla: Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4. 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. corr_author: '1' date_created: 2021-08-06T09:09:11Z date_published: 2022-07-11T00:00:00Z date_updated: 2025-06-11T13:52:43Z day: '11' ddc: - '570' department: - _id: SiHi - _id: CaHe - _id: EdHa - _id: EM-Fac - _id: Bio - _id: MiSi doi: 10.1038/s41590-022-01257-4 ec_funded: 1 external_id: isi: - '000822975900002' pmid: - '35817845' file: - access_level: open_access checksum: 628e7b49809f22c75b428842efe70c68 content_type: application/pdf creator: dernst date_created: 2022-07-25T07:11:32Z date_updated: 2022-07-25T07:11:32Z file_id: '11642' file_name: 2022_NatureImmunology_Assen.pdf file_size: 11475325 relation: main_file success: 1 file_date_updated: 2022-07-25T07:11:32Z has_accepted_license: '1' intvolume: ' 23' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1246-1255 pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular Navigation Along Spatial Gradients publication: Nature Immunology publication_identifier: eissn: - 1529-2916 issn: - 1529-2908 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2022' ... --- _id: '10766' abstract: - lang: eng text: Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: PreCl acknowledgement: 'We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).' article_number: e2122030119 article_processing_charge: No article_type: original author: - first_name: Jana full_name: Slovakova, Jana id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87 last_name: Slovakova - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(8). doi:10.1073/pnas.2122030119 apa: Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119 chicago: Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119. ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8. National Academy of Sciences, 2022. ista: Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119. mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119. short: J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022). corr_author: '1' date_created: 2022-02-20T23:01:31Z date_published: 2022-02-14T00:00:00Z date_updated: 2026-04-02T12:54:56Z day: '14' ddc: - '570' department: - _id: CaHe - _id: EM-Fac - _id: Bio doi: 10.1073/pnas.2122030119 ec_funded: 1 external_id: isi: - '000766926900009' pmid: - '35165179' file: - access_level: open_access checksum: d49f83c3580613966f71768ddb9a55a5 content_type: application/pdf creator: dernst date_created: 2022-02-21T08:45:11Z date_updated: 2022-02-21T08:45:11Z file_id: '10780' file_name: 2022_PNAS_Slovakova.pdf file_size: 1609678 relation: main_file success: 1 file_date_updated: 2022-02-21T08:45:11Z has_accepted_license: '1' intvolume: ' 119' isi: 1 issue: '8' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 2521E28E-B435-11E9-9278-68D0E5697425 grant_number: 187-2013 name: Modulation of adhesion function in cell-cell contact formation by cortical tension publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: record: - id: '9750' relation: earlier_version status: public scopus_import: '1' status: public title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 119 year: '2022' ... --- _id: '10826' abstract: - lang: eng text: Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp acknowledgement: "We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB)." article_number: e68040 article_processing_charge: No article_type: original author: - first_name: Giulio full_name: Valperga, Giulio id: 67F289DE-0D8F-11EA-9BDD-54AE3DDC885E last_name: Valperga orcid: 0000-0001-6726-3890 - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 citation: ama: Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040 apa: Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68040 chicago: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040. ieee: G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife, vol. 11. eLife Sciences Publications, 2022. ista: Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040. mla: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife, vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040. short: G. Valperga, M. de Bono, ELife 11 (2022). corr_author: '1' date_created: 2022-03-06T23:01:52Z date_published: 2022-02-24T00:00:00Z date_updated: 2026-04-02T12:45:39Z day: '24' ddc: - '570' department: - _id: MaDe doi: 10.7554/eLife.68040 external_id: isi: - '000763432300001' pmid: - '35201977' file: - access_level: open_access checksum: cc1b9bf866d0f61f965556e0dd03d3ac content_type: application/pdf creator: dernst date_created: 2022-03-07T07:39:25Z date_updated: 2022-03-07T07:39:25Z file_id: '10830' file_name: 2022_eLife_Valperga.pdf file_size: 4095591 relation: main_file success: 1 file_date_updated: 2022-03-07T07:39:25Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E grant_number: 209504/A/17/Z name: Molecular mechanisms of neural circuit function publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans 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) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 11 year: '2022' ... --- _id: '10934' abstract: - lang: eng text: 'FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. ' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_processing_charge: No author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: ' 0000-0001-9198-2182 ' citation: ama: Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:10.15479/AT:ISTA:10934 apa: Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934 chicago: Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934. ieee: P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022. ista: Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934. mla: Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934. short: P. Radler, (2022). contributor: - contributor_type: supervisor first_name: Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - contributor_type: researcher first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer - contributor_type: researcher first_name: Paulo last_name: Caldas - contributor_type: researcher first_name: David id: B9577E20-AA38-11E9-AC9A-0930E6697425 last_name: Michalik - contributor_type: researcher first_name: Natalia last_name: Baranova corr_author: '1' date_created: 2022-03-31T11:32:32Z date_published: 2022-04-05T00:00:00Z date_updated: 2026-04-03T22:30:04Z day: '05' ddc: - '572' department: - _id: GradSch - _id: MaLo doi: 10.15479/AT:ISTA:10934 ec_funded: 1 file: - access_level: open_access checksum: 52d50202e04e9daa618a58e686d8ab58 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pradler date_created: 2022-04-22T10:15:19Z date_updated: 2022-04-22T10:15:19Z file_id: '11328' file_name: Inventory for Data repository.docx file_size: 13469 relation: main_file success: 1 - 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Written by Christoph Sommer. relation: software url: https://doi.org/10.5281/zenodo.6400639 record: - id: '11373' relation: used_in_publication status: public - id: '14280' relation: used_in_publication status: public status: public title: In vitro reconstitution of Escherichia coli divisome activation 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) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11373' abstract: - lang: eng text: The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_number: '2635' article_processing_charge: No article_type: original author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Maria D full_name: Lopez Pelegrin, Maria D id: 319AA9CE-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Pelegrin - first_name: David full_name: Michalik, David id: B9577E20-AA38-11E9-AC9A-0930E6697425 last_name: Michalik - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 2022;13. doi:10.1038/s41467-022-30301-y apa: Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., & Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-30301-y chicago: Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30301-y. ieee: P. Radler et al., “In vitro reconstitution of Escherichia coli divisome activation,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635. mla: Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications, vol. 13, 2635, Springer Nature, 2022, doi:10.1038/s41467-022-30301-y. short: P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022). corr_author: '1' date_created: 2022-05-13T09:06:28Z date_published: 2022-05-12T00:00:00Z date_updated: 2026-04-03T22:30:04Z day: '12' ddc: - '570' department: - _id: MaLo doi: 10.1038/s41467-022-30301-y ec_funded: 1 external_id: isi: - '000795171100037' file: - access_level: open_access checksum: 5af863ee1b95a0710f6ee864d68dc7a6 content_type: application/pdf creator: dernst date_created: 2022-05-13T09:10:51Z date_updated: 2022-05-13T09:10:51Z file_id: '11374' file_name: 2022_NatureCommunications_Radler.pdf file_size: 6945191 relation: main_file success: 1 file_date_updated: 2022-05-13T09:10:51Z has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: In vitro reconstitution of bacterial cell division publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-022-34485-1 record: - id: '10934' relation: research_data status: public - id: '14280' relation: dissertation_contains status: public scopus_import: '1' status: public title: In vitro reconstitution of Escherichia coli divisome activation 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) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '11879' abstract: - lang: eng text: "As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: SSU acknowledgement: I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner citation: ama: Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879 apa: Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879 chicago: Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879. ieee: C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022. ista: Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. mla: Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879. short: C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-08-17T07:58:53Z date_published: 2022-08-17T00:00:00Z date_updated: 2025-04-15T06:37:15Z day: '17' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:11879 file: - access_level: open_access checksum: a2c2fdc28002538840490bfa6a08b2cb content_type: application/pdf creator: cartner date_created: 2022-08-17T12:08:49Z date_updated: 2023-09-09T22:30:03Z embargo: 2023-09-08 file_id: '11907' file_name: ChristinaArtner_PhD_Thesis_2022.pdf file_size: 11113608 relation: main_file - access_level: closed checksum: 66b461c074b815fbe63481b3f46a9f43 content_type: application/octet-stream creator: cartner date_created: 2022-08-17T12:08:59Z date_updated: 2023-09-09T22:30:03Z embargo_to: open_access file_id: '11908' file_name: ChristinaArtner_PhD_Thesis_2022.7z file_size: 19097730 relation: source_file file_date_updated: 2023-09-09T22:30:03Z has_accepted_license: '1' keyword: - high ambient temperature - auxin - PINs - Zinc-Finger proteins - thermomorphogenesis - stress language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '128' project: - _id: 2685A872-B435-11E9-9278-68D0E5697425 name: Hormonal regulation of plant adaptive responses to environmental signals publication_identifier: isbn: - 978-3-99078-022-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11160' abstract: - lang: eng text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com. article_number: '110615' article_processing_charge: Yes article_type: original author: - first_name: Carlo Emanuele full_name: Villa, Carlo Emanuele last_name: Villa - first_name: Cristina full_name: Cheroni, Cristina last_name: Cheroni - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Alejandro full_name: López-Tóbon, Alejandro last_name: López-Tóbon - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Aysan Çerağ full_name: Yahya, Aysan Çerağ id: 365A65F8-F248-11E8-B48F-1D18A9856A87 last_name: Yahya - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Michele full_name: Gabriele, Michele last_name: Gabriele - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Mariano full_name: Gabitto, Mariano last_name: Gabitto - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Giuseppe full_name: Testa, Giuseppe last_name: Testa - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 2022;39(1). doi:10.1016/j.celrep.2022.110615 apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615 chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615. ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” Cell Reports, vol. 39, no. 1. Elsevier, 2022. ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615. mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol. 39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615. short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022). corr_author: '1' date_created: 2022-04-15T09:03:10Z date_published: 2022-04-05T00:00:00Z date_updated: 2026-04-03T22:30:14Z day: '05' ddc: - '570' department: - _id: JoDa - _id: GaNo doi: 10.1016/j.celrep.2022.110615 ec_funded: 1 external_id: isi: - '000785983900003' pmid: - '35385734' file: - access_level: open_access checksum: b4e8d68f0268dec499af333e6fd5d8e1 content_type: application/pdf creator: dernst date_created: 2022-04-15T09:06:25Z date_updated: 2022-04-15T09:06:25Z file_id: '11164' file_name: 2022_CellReports_Villa.pdf file_size: '7808644' relation: main_file success: 1 file_date_updated: 2022-04-15T09:06:25Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2690FEAC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I04205 name: Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy publication: Cell Reports publication_identifier: issn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '18674' relation: dissertation_contains status: public - id: '18681' relation: dissertation_contains status: public - id: '12364' relation: dissertation_contains status: public scopus_import: '1' status: public title: CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2022' ... --- _id: '12244' abstract: - lang: eng 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. acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp 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 article_type: original author: - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Lida full_name: Kanari, Lida last_name: Kanari - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X - first_name: Martina full_name: Scolamiero, Martina last_name: Scolamiero - first_name: Jens full_name: Agerberg, Jens last_name: Agerberg - first_name: Hansruedi full_name: Mathys, Hansruedi last_name: Mathys - first_name: Li-Huei full_name: Tsai, Li-Huei last_name: Tsai - first_name: Wojciech full_name: Chachólski, Wojciech last_name: Chachólski - first_name: Kathryn full_name: Hess, Kathryn last_name: Hess - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 2022;25(10):1379-1393. doi:10.1038/s41593-022-01167-6 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. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-022-01167-6 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.” Nature Neuroscience. Springer Nature, 2022. https://doi.org/10.1038/s41593-022-01167-6. ieee: G. Colombo et al., “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” Nature Neuroscience, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022. 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.” Nature Neuroscience, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:10.1038/s41593-022-01167-6. 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. corr_author: '1' date_created: 2023-01-16T09:53:07Z date_published: 2022-10-01T00:00:00Z date_updated: 2026-04-03T22:30:16Z day: '01' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41593-022-01167-6 ec_funded: 1 external_id: isi: - '000862214700001' pmid: - '36180790' file: - access_level: open_access checksum: 28431146873096f52e0107b534f178c9 content_type: application/pdf creator: dernst date_created: 2023-01-30T08:06:56Z date_updated: 2023-01-30T08:06:56Z file_id: '12437' file_name: 2022_NatureNeuroscience_Colombo.pdf file_size: 23789835 relation: main_file success: 1 file_date_updated: 2023-01-30T08:06:56Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '10' keyword: - General Neuroscience language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1379-1393 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25D4A630-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715571' name: Microglia action towards neuronal circuit formation and function in health and disease publication: Nature Neuroscience publication_identifier: eissn: - 1546-1726 issn: - 1097-6256 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/ record: - id: '12378' relation: dissertation_contains status: public scopus_import: '1' status: public title: A tool for mapping microglial morphology, morphOMICs, 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) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2022' ... --- _id: '12378' 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\x02automatic 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\x02like 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." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 citation: ama: Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378 apa: Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378 chicago: Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378. ieee: 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. mla: Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378. short: G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2023-01-25T14:27:43Z date_published: 2022-11-11T00:00:00Z date_updated: 2025-04-15T07:23:15Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/at:ista:12378 ec_funded: 1 file: - access_level: closed checksum: 8cd3ddfe9b53381dcf086023d8d8893a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-01-25T14:31:32Z date_updated: 2023-04-12T22:30:03Z embargo_to: open_access file_id: '12379' file_name: Gloria_Colombo_Thesis.docx file_size: 23890382 relation: source_file - access_level: open_access checksum: 8af4319c18b516e8758e9a6cb02b103b content_type: application/pdf creator: cchlebak date_created: 2023-01-25T14:31:36Z date_updated: 2023-04-12T22:30:03Z embargo: 2023-04-11 file_id: '12380' file_name: Gloria_Colombo_Thesis.pdf file_size: 13802421 relation: main_file file_date_updated: 2023-04-12T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '142' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12244' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 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) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '10703' abstract: - lang: eng text: 'When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes.' acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687. article_processing_charge: No article_type: original author: - first_name: Florian full_name: Gaertner, Florian last_name: Gaertner - first_name: Patricia full_name: Dos Reis Rodrigues, Patricia id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F last_name: Dos Reis Rodrigues orcid: 0000-0003-1681-508X - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Juan full_name: Aguilera, Juan last_name: Aguilera - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden orcid: 0000-0002-9438-4783 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Gaertner F, Dos Reis Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 2022;57(1):47-62.e9. doi:10.1016/j.devcel.2021.11.024 apa: Gaertner, F., Dos Reis Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2021.11.024 chicago: Gaertner, Florian, Patricia Dos Reis Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell. Cell Press, 2022. https://doi.org/10.1016/j.devcel.2021.11.024. ieee: F. Gaertner et al., “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” Developmental Cell, vol. 57, no. 1. Cell Press, p. 47–62.e9, 2022. ista: Gaertner F, Dos Reis Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9. mla: Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell, vol. 57, no. 1, Cell Press, 2022, p. 47–62.e9, doi:10.1016/j.devcel.2021.11.024. short: F. Gaertner, P. Dos Reis Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9. corr_author: '1' date_created: 2022-01-30T23:01:33Z date_published: 2022-01-10T00:00:00Z date_updated: 2026-04-03T22:30:19Z day: '10' ddc: - '570' department: - _id: MiSi - _id: EM-Fac - _id: NanoFab - _id: BjHo doi: 10.1016/j.devcel.2021.11.024 ec_funded: 1 external_id: isi: - '000768933800005' pmid: - '34919802' intvolume: ' 57' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.sciencedirect.com/science/article/pii/S1534580721009497 month: '01' oa: 1 oa_version: Published Version page: 47-62.e9 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular Navigation Along Spatial Gradients publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '12726' relation: dissertation_contains status: public - id: '14530' relation: dissertation_contains status: public - id: '20149' relation: dissertation_contains status: public - id: '12401' relation: dissertation_contains status: public scopus_import: '1' status: public title: WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 57 year: '2022' ... --- _id: '10565' abstract: - lang: eng text: 'Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).' acknowledged_ssus: - _id: Bio acknowledgement: This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support. article_number: '101012' article_processing_charge: Yes article_type: original author: - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012 apa: Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2021.101012 chicago: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier, 2021. https://doi.org/10.1016/j.xpro.2021.101012. ieee: A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier, 2021. ista: Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012. mla: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier, 2021, doi:10.1016/j.xpro.2021.101012. short: A. Venturino, S. Siegert, STAR Protocols 2 (2021). date_created: 2021-12-19T23:01:32Z date_published: 2021-12-17T00:00:00Z date_updated: 2025-05-14T11:26:30Z day: '17' ddc: - '573' department: - _id: SaSi doi: 10.1016/j.xpro.2021.101012 ec_funded: 1 file: - access_level: open_access checksum: 9ea2501056c5df99e84726b845e9b976 content_type: application/pdf creator: cchlebak date_created: 2021-12-20T08:58:40Z date_updated: 2021-12-20T08:58:40Z file_id: '10570' file_name: 2021_STARProt_Venturino.pdf file_size: 6207060 relation: main_file success: 1 file_date_updated: 2021-12-20T08:58:40Z has_accepted_license: '1' intvolume: ' 2' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25D4A630-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715571' name: Microglia action towards neuronal circuit formation and function in health and disease publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '10606' abstract: - lang: eng text: Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s). acknowledged_ssus: - _id: NanoFab - _id: Bio acknowledgement: 'We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR ''MorCell'': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).' article_number: e75639 article_processing_charge: No article_type: original author: - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Remi full_name: Dumollard, Remi last_name: Dumollard - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Alex full_name: Mcdougall, Alex last_name: Mcdougall citation: ama: Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 2021;10. doi:10.7554/eLife.75639 apa: Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., & Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.75639 chicago: Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.75639. ieee: B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639. mla: Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife, vol. 10, e75639, eLife Sciences Publications, 2021, doi:10.7554/eLife.75639. short: B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021). corr_author: '1' date_created: 2022-01-09T23:01:26Z date_published: 2021-12-21T00:00:00Z date_updated: 2025-04-14T12:59:47Z day: '21' ddc: - '570' department: - _id: CaHe doi: 10.7554/eLife.75639 external_id: isi: - '000733610100001' pmid: - '34889186' file: - access_level: open_access checksum: 759c7a873d554c48a6639e6350746ca6 content_type: application/pdf creator: alisjak date_created: 2022-01-10T09:40:37Z date_updated: 2022-01-10T09:40:37Z file_id: '10611' file_name: 2021_eLife_Godard.pdf file_size: 7769934 relation: main_file success: 1 file_date_updated: 2022-01-10T09:40:37Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2646861A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03601 name: Control of embryonic cleavage pattern publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Combined effect of cell geometry and polarity domains determines the orientation of unequal division 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2021' ... --- _id: '10655' abstract: - lang: eng text: "Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n" acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript. article_processing_charge: Yes article_type: original author: - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Gabriele M. full_name: Wögenstein, Gabriele M. last_name: Wögenstein - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Raquel full_name: Casado Polanco, Raquel id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd last_name: Casado Polanco orcid: 0000-0001-8293-4568 - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006 apa: Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006 chicago: Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006. ieee: M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021. ista: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224. mla: Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006. short: M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224. corr_author: '1' date_created: 2022-01-23T23:01:28Z date_published: 2021-12-10T00:00:00Z date_updated: 2025-04-14T07:41:46Z day: '10' ddc: - '570' department: - _id: SaSi - _id: SiHi doi: 10.1016/j.omtm.2021.09.006 ec_funded: 1 external_id: isi: - '000748748500019' file: - access_level: open_access checksum: 77dc540e8011c5475031bdf6ccef20a6 content_type: application/pdf creator: cchlebak date_created: 2022-01-24T07:43:09Z date_updated: 2022-01-24T07:43:09Z file_id: '10657' file_name: 2021_MolTherMethodsClinDev_Maes.pdf file_size: 4794147 relation: main_file success: 1 file_date_updated: 2022-01-24T07:43:09Z has_accepted_license: '1' intvolume: ' 23' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 210-224 project: - _id: 25D4A630-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715571' name: Microglia action towards neuronal circuit formation and function in health and disease publication: Molecular Therapy - Methods and Clinical Development publication_identifier: eissn: - 2329-0501 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2021' ... --- _id: '10223' abstract: - lang: eng text: Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments. acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: Bio acknowledgement: We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C. article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Koji full_name: Takahashi, Koji last_name: Takahashi - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Jian full_name: Chen, Jian last_name: Chen - first_name: Lana full_name: Shabala, Lana last_name: Shabala - first_name: Wouter full_name: Smet, Wouter last_name: Smet - first_name: Hong full_name: Ren, Hong last_name: Ren - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Sergey full_name: Shabala, Sergey last_name: Shabala - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Toshinori full_name: Kinoshita, Toshinori last_name: Kinoshita - first_name: William M. full_name: Gray, William M. last_name: Gray - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6 apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6 chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6. ieee: L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021. ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277. mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6. short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277. corr_author: '1' date_created: 2021-11-07T23:01:25Z date_published: 2021-11-11T00:00:00Z date_updated: 2025-07-10T11:49:46Z day: '11' department: - _id: JiFr - _id: NanoFab doi: 10.1038/s41586-021-04037-6 ec_funded: 1 external_id: isi: - '000713338100006' pmid: - '34707283' intvolume: ' 599' isi: 1 issue: '7884' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.21203/rs.3.rs-266395/v3 month: '11' oa: 1 oa_version: Preprint page: 273-277 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/stop-and-grow/ record: - id: '10095' relation: earlier_version status: public scopus_import: '1' status: public title: Cell surface and intracellular auxin signalling for H+ fluxes in root growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 599 year: '2021' ... --- _id: '10268' abstract: - lang: eng text: The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments. acknowledged_ssus: - _id: Bio acknowledgement: We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 citation: ama: 'Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6' apa: Hörmayer, L., Friml, J., & Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In Plant Cell Division (Vol. 2382, pp. 105–114). Humana Press. https://doi.org/10.1007/978-1-0716-1744-1_6 chicago: Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021. https://doi.org/10.1007/978-1-0716-1744-1_6. ieee: L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–114. ista: 'Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.' mla: Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6. short: L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114. date_created: 2021-11-11T10:03:30Z date_published: 2021-10-28T00:00:00Z date_updated: 2022-06-03T06:47:06Z day: '28' department: - _id: JiFr doi: 10.1007/978-1-0716-1744-1_6 external_id: pmid: - '34705235' intvolume: ' 2382' language: - iso: eng month: '10' oa_version: None page: 105-114 pmid: 1 publication: Plant Cell Division publication_identifier: eisbn: - 978-1-0716-1744-1 eissn: - 1940-6029 isbn: - 978-1-0716-1743-4 issn: - 1064-3745 publication_status: published publisher: Humana Press quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2382 year: '2021' ... --- _id: '10290' abstract: - lang: eng text: A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: 'This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.' article_number: '107808' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Behnam full_name: Amiri, Behnam last_name: Amiri - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Martin full_name: Falcke, Martin last_name: Falcke - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808 apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808 chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808. ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021. ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808. mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808. short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021). corr_author: '1' date_created: 2021-11-15T12:21:42Z date_published: 2021-11-03T00:00:00Z date_updated: 2025-04-15T08:25:41Z day: '03' ddc: - '572' department: - _id: FlSc doi: 10.1016/j.jsb.2021.107808 external_id: isi: - '000720259500002' file: - access_level: open_access checksum: 6b209e4d44775d4e02b50f78982c15fa content_type: application/pdf creator: cchlebak date_created: 2021-11-15T13:11:27Z date_updated: 2021-11-15T13:11:27Z file_id: '10291' file_name: 2021_JournalStructBiol_Dimchev.pdf file_size: 16818304 relation: main_file success: 1 file_date_updated: 2021-11-15T13:11:27Z has_accepted_license: '1' intvolume: ' 213' isi: 1 issue: '4' keyword: - Structural Biology language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex - _id: 2674F658-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02495 name: Protein structure and function in filopodia across scales publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' related_material: record: - id: '14502' relation: software status: public scopus_import: '1' status: public title: Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 213 year: '2021' ... --- _id: '10321' abstract: - lang: eng text: Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021). acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H. article_number: '100939' article_processing_charge: Yes article_type: original author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939 apa: Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939 chicago: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939. ieee: N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021. ista: Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939. mla: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939. short: N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021). corr_author: '1' date_created: 2021-11-21T23:01:28Z date_published: 2021-11-10T00:00:00Z date_updated: 2025-04-15T08:23:07Z day: '10' ddc: - '573' department: - _id: SiHi doi: 10.1016/j.xpro.2021.100939 ec_funded: 1 file: - access_level: open_access checksum: 9e3f6d06bf583e7a8b6a9e9a60500a28 content_type: application/pdf creator: cchlebak date_created: 2021-11-22T08:23:58Z date_updated: 2021-11-22T08:23:58Z file_id: '10329' file_name: 2021_STARProtocols_Amberg.pdf file_size: 7309464 relation: main_file success: 1 file_date_updated: 2021-11-22T08:23:58Z has_accepted_license: '1' intvolume: ' 2' issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T01031 name: Role of Eed in neural stem cell lineage progression - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '8582' 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." acknowledged_ssus: - _id: Bio 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Daniel full_name: von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Nasser full_name: Darwish-Miranda, Nasser id: 39CD9926-F248-11E8-B48F-1D18A9856A87 last_name: Darwish-Miranda orcid: 0000-0002-8821-8236 - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Riet full_name: de Rycke, Riet last_name: de Rycke - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Daniel J full_name: Gütl, Daniel J id: 381929CE-F248-11E8-B48F-1D18A9856A87 last_name: Gütl - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Meiyu full_name: Ke, Meiyu last_name: Ke - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Jan full_name: Dettmer, Jan last_name: Dettmer - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 2021;229(1):351-369. doi:10.1111/nph.16887 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. New Phytologist. Wiley. https://doi.org/10.1111/nph.16887 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.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16887. ieee: H. Li et al., “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 1. Wiley, pp. 351–369, 2021. ista: Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369. mla: Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:10.1111/nph.16887. 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. date_created: 2020-09-28T08:59:28Z date_published: 2021-01-01T00:00:00Z date_updated: 2025-06-12T06:32:24Z day: '01' ddc: - '580' department: - _id: JiFr - _id: EM-Fac - _id: Bio - _id: EvBe doi: 10.1111/nph.16887 ec_funded: 1 external_id: isi: - '000570187900001' pmid: - '32810889' file: - access_level: open_access checksum: b45621607b4cab97eeb1605ab58e896e content_type: application/pdf creator: dernst date_created: 2021-02-04T09:44:17Z date_updated: 2021-02-04T09:44:17Z file_id: '9084' file_name: 2021_NewPhytologist_Li.pdf file_size: 4061962 relation: main_file success: 1 file_date_updated: 2021-02-04T09:44:17Z has_accepted_license: '1' intvolume: ' 229' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 351-369 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 229 year: '2021' ... --- _id: '8988' 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. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: EM-Fac 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. " article_number: e2010054118 article_processing_charge: No article_type: original author: - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Albert full_name: Auer, Albert id: 3018E8C2-F248-11E8-B48F-1D18A9856A87 last_name: Auer orcid: 0000-0002-3580-2906 - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 - first_name: Katrin full_name: Loibl, Katrin id: 3760F32C-F248-11E8-B48F-1D18A9856A87 last_name: Loibl orcid: 0000-0002-2429-7668 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 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. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(1). doi:10.1073/pnas.2010054118 apa: Düllberg, C. F., 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. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118 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.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2010054118. 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,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1. National Academy of Sciences, 2021. 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. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118. mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118. short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021). corr_author: '1' date_created: 2021-01-03T23:01:23Z date_published: 2021-01-05T00:00:00Z date_updated: 2025-05-14T10:59:29Z day: '05' department: - _id: MaLo - _id: MiSi doi: 10.1073/pnas.2010054118 external_id: isi: - '000607270100018' pmid: - '33443153' intvolume: ' 118' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2010054118 month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2599F062-B435-11E9-9278-68D0E5697425 grant_number: RGY0083/2016 name: Reconstitution of cell polarity and axis determination in a cell-free system publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2021' ...