[{"has_accepted_license":"1","issue":"12","scopus_import":"1","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}],"citation":{"chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>.","ieee":"X. Contreras <i>et al.</i>, “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” <i>Cell Reports</i>, vol. 35, no. 12. Cell Press, 2021.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>, vol. 35, no. 12, 109274, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. 2021;35(12). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>"},"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"external_id":{"isi":["000664463600016"]},"file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","date_updated":"2021-06-28T14:06:24Z","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","date_created":"2021-06-28T14:06:24Z","file_id":"9613","file_size":7653149,"file_name":"2021_CellReports_Contreras.pdf"}],"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","publication":"Cell Reports","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"status":"public","date_updated":"2023-08-10T13:55:00Z","ec_funded":1,"abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","day":"22","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"        35","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"article_processing_charge":"No","file_date_updated":"2021-06-28T14:06:24Z","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., 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":"109274","date_created":"2021-06-27T22:01:48Z","volume":35,"article_type":"original","isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["22111247"]},"month":"06","type":"journal_article","publisher":"Cell Press","year":"2021","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2021.109274","date_published":"2021-06-22T00:00:00Z","oa":1,"_id":"9603","author":[{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425","first_name":"Amarbayasgalan","full_name":"Davaatseren, Amarbayasgalan"},{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H"},{"first_name":"Johanna","full_name":"Sonntag, Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag"},{"last_name":"Andersen","first_name":"Lill","full_name":"Andersen, Lill"},{"last_name":"Bernthaler","first_name":"Tina","full_name":"Bernthaler, Tina"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"first_name":"Anna-Magdalena","full_name":"Heger, Anna-Magdalena","last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Randy L.","full_name":"Johnson, Randy L."},{"last_name":"Schwarz","full_name":"Schwarz, Lindsay A.","first_name":"Lindsay A."},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon"}]},{"type":"dissertation","publisher":"Institute of Science and Technology Austria","year":"2021","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","oa":1,"_id":"9623","author":[{"first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"file_date_updated":"2022-07-02T22:30:06Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"date_created":"2021-07-01T14:50:17Z","supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"month":"07","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"status":"public","date_updated":"2023-09-07T13:33:27Z","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","page":"111","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","citation":{"ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria."},"related_material":{"record":[{"status":"public","id":"9750","relation":"part_of_dissertation"},{"status":"public","id":"9006","relation":"part_of_dissertation"}]},"file":[{"creator":"scaballe","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"PhDThesis_SCM.docx","file_size":131946790,"checksum":"e039225a47ef32666d59bf35ddd30ecf","date_created":"2021-07-01T14:48:54Z","file_id":"9624","embargo_to":"open_access","date_updated":"2022-07-02T22:30:06Z"},{"date_created":"2021-07-01T14:46:25Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","date_updated":"2022-07-02T22:30:06Z","file_name":"PhDThesis_SCM.pdf","file_size":17094958,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","embargo":"2022-07-01","creator":"scaballe"}],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes"},{"date_created":"2021-07-11T22:01:16Z","article_number":"109313","department":[{"_id":"SaSi"}],"acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","pmid":1,"file_date_updated":"2021-07-19T13:32:17Z","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"intvolume":"        36","month":"07","publication_identifier":{"eissn":["22111247"]},"quality_controlled":"1","isi":1,"article_type":"original","volume":36,"doi":"10.1016/j.celrep.2021.109313","language":[{"iso":"eng"}],"year":"2021","publisher":"Elsevier","type":"journal_article","author":[{"full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403"},{"full_name":"Schulz, Rouven","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","orcid":"0000-0001-5297-733X"},{"first_name":"Héctor","full_name":"De Jesús-Cortés, Héctor","last_name":"De Jesús-Cortés"},{"last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"first_name":"Balint","full_name":"Nagy, Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","last_name":"Nagy"},{"last_name":"Reilly-Andújar","first_name":"Francis","full_name":"Reilly-Andújar, Francis"},{"first_name":"Gloria","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cubero, Ryan J","first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E"},{"first_name":"Mark F.","full_name":"Bear, Mark F.","last_name":"Bear"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra"}],"_id":"9642","oa":1,"date_published":"2021-07-06T00:00:00Z","citation":{"ieee":"A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>.","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313."},"project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","issue":"1","has_accepted_license":"1","publication":"Cell Reports","file":[{"file_size":56388540,"file_name":"2021_CellReports_Venturino.pdf","date_updated":"2021-07-19T13:32:17Z","success":1,"date_created":"2021-07-19T13:32:17Z","file_id":"9693","checksum":"f056255f6d01fd9a86b5387635928173","creator":"cziletti","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/"}]},"date_updated":"2023-08-10T14:09:39Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"day":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"ec_funded":1},{"abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots 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 phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. 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 alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"09","publication_status":"accepted","oa_version":"Preprint","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"date_updated":"2024-10-29T10:22:44Z","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"},{"id":"10223","status":"public","relation":"later_version"}]},"publication":"Research Square","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"citation":{"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.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","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. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","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, Research Square (n.d.).","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>"},"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"date_published":"2021-09-09T00:00:00Z","_id":"10095","oa":1,"author":[{"first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia"},{"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"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"}],"type":"preprint","year":"2021","doi":"10.21203/rs.3.rs-266395/v3","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2693-5015"]},"month":"09","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge 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) 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.), the 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 the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","article_number":"266395","date_created":"2021-10-06T08:56:22Z"},{"type":"journal_article","year":"2021","publisher":"Springer Nature","doi":"10.1038/s41586-021-04037-6","language":[{"iso":"eng"}],"date_published":"2021-11-11T00:00:00Z","_id":"10223","oa":1,"author":[{"full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X"},{"first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","full_name":"Ren, Hong","last_name":"Ren"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Sergey","full_name":"Shabala, Sergey","last_name":"Shabala"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"full_name":"Kinoshita, Toshinori","first_name":"Toshinori","last_name":"Kinoshita"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"intvolume":"       599","keyword":["Multidisciplinary"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"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.","pmid":1,"date_created":"2021-11-07T23:01:25Z","article_type":"original","volume":599,"isi":1,"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"quality_controlled":"1","month":"11","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"date_updated":"2024-10-29T10:22:45Z","abstract":[{"text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.","lang":"eng"}],"ec_funded":1,"day":"11","oa_version":"Preprint","page":"273-277","publication_status":"published","scopus_import":"1","issue":"7884","citation":{"ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>.","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.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>."},"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351"}],"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/stop-and-grow/"}],"record":[{"relation":"earlier_version","id":"10095","status":"public"}]},"publication":"Nature","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}]},{"status":"public","acknowledged_ssus":[{"_id":"Bio"}],"date_updated":"2022-06-03T06:47:06Z","day":"28","oa_version":"None","page":"105-114","publication_status":"published","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"citation":{"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 <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>.","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 <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","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.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","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: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>"},"series_title":"MIMB","publication":"Plant Cell Division","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","external_id":{"pmid":["34705235"]},"type":"book_chapter","doi":"10.1007/978-1-0716-1744-1_6","language":[{"iso":"eng"}],"year":"2021","publisher":"Humana Press","date_published":"2021-10-28T00:00:00Z","author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Matous","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783"}],"_id":"10268","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"      2382","date_created":"2021-11-11T10:03:30Z","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.","department":[{"_id":"JiFr"}],"pmid":1,"volume":2382,"month":"10","publication_identifier":{"eissn":["1940-6029"],"isbn":["978-1-0716-1743-4"],"eisbn":["978-1-0716-1744-1"],"issn":["1064-3745"]},"quality_controlled":"1"},{"volume":213,"article_type":"original","isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1047-8477"]},"month":"11","keyword":["Structural Biology"],"intvolume":"       213","ddc":["572"],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-11-15T13:11:27Z","department":[{"_id":"FlSc"}],"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.","date_created":"2021-11-15T12:21:42Z","article_number":"107808","date_published":"2021-11-03T00:00:00Z","oa":1,"_id":"10290","author":[{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","first_name":"Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"first_name":"Florian","full_name":"Fäßler, Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","publisher":"Elsevier ","year":"2021","language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2021.107808","external_id":{"isi":["000720259500002"]},"related_material":{"record":[{"relation":"software","id":"14502","status":"public"}]},"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"cchlebak","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","file_id":"10291","date_updated":"2021-11-15T13:11:27Z","success":1,"file_name":"2021_JournalStructBiol_Dimchev.pdf","file_size":16818304}],"publication":"Journal of Structural Biology","has_accepted_license":"1","issue":"4","scopus_import":"1","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","call_identifier":"FWF"}],"citation":{"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.” <i>Journal of Structural Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (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.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>"},"abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized 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.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"status":"public","date_updated":"2023-11-21T08:36:02Z"},{"author":[{"full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"}],"_id":"10303","oa":1,"date_published":"2021-11-22T00:00:00Z","doi":"10.15479/at:ista:10303","language":[{"iso":"eng"}],"year":"2021","publisher":"Institute of Science and Technology Austria","type":"dissertation","month":"11","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"date_created":"2021-11-18T11:20:59Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:06Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["580","581"],"article_processing_charge":"No","degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"22","publication_status":"published","page":"139","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"date_updated":"2023-09-19T14:42:45Z","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"file_name":"AbualiaPhDthesisfinalv3.pdf","file_size":28005730,"date_created":"2021-11-22T14:48:21Z","checksum":"dea38b98aa4da1cea03dcd0f10862818","file_id":"10331","date_updated":"2022-12-20T23:30:06Z","embargo":"2022-11-23","creator":"rabualia","access_level":"open_access","content_type":"application/pdf","relation":"main_file"},{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"rabualia","date_created":"2021-11-22T14:48:34Z","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_id":"10332","embargo_to":"open_access","date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.docx","file_size":62841883}],"title":"Role of hormones in nitrate regulated growth","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"status":"public","id":"9913","relation":"part_of_dissertation"},{"status":"public","id":"47","relation":"part_of_dissertation"}]},"citation":{"ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021."},"has_accepted_license":"1","alternative_title":["ISTA Thesis"]},{"_id":"10307","oa":1,"author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","first_name":"Kathrin"}],"date_published":"2021-11-18T00:00:00Z","year":"2021","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:10307","language":[{"iso":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"month":"11","supervisor":[{"first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C"}],"department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"date_created":"2021-11-18T15:05:06Z","file_date_updated":"2022-12-20T23:30:05Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"day":"18","publication_status":"published","oa_version":"Published Version","page":"73","date_updated":"2023-09-07T13:34:38Z","status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"title":"Pathogenic Escherichia coli hijack the host immune response","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2022-11-18","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_id":"10308","checksum":"b39c9e0ef18d0484d537a67551effd02","date_created":"2021-11-18T15:07:31Z","file_size":13266088,"file_name":"ThesisTomasekKathrin.pdf"},{"file_size":7539509,"file_name":"ThesisTomasekKathrin.docx","embargo_to":"open_access","date_updated":"2022-12-20T23:30:05Z","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","date_created":"2021-11-18T15:07:46Z","file_id":"10309","creator":"ktomasek","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10316","status":"public"}]},"citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>."},"has_accepted_license":"1","alternative_title":["ISTA Thesis"]},{"date_created":"2021-11-19T12:24:16Z","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373"},{"name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","call_identifier":"FWF"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"citation":{"chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","month":"10","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"publication":"bioRxiv","related_material":{"record":[{"status":"public","id":"11843","relation":"later_version"},{"status":"public","id":"10307","relation":"dissertation_contains"}]},"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","language":[{"iso":"eng"}],"doi":"10.1101/2021.10.18.464770","date_updated":"2024-03-25T23:30:19Z","publisher":"Cold Spring Harbor Laboratory","year":"2021","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"status":"public","type":"preprint","author":[{"first_name":"Kathrin","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X"},{"first_name":"Alexander F","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner"},{"first_name":"Ivana","full_name":"Glatzová, Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","last_name":"Glatzová"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Michael K","full_name":"Sixt, Michael K"}],"oa":1,"_id":"10316","date_published":"2021-10-18T00:00:00Z","publication_status":"submitted","oa_version":"Preprint","day":"18","ec_funded":1,"abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}]},{"article_type":"original","volume":2,"publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","month":"11","intvolume":"         2","file_date_updated":"2021-11-22T08:23:58Z","ddc":["573"],"article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"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","date_created":"2021-11-21T23:01:28Z","date_published":"2021-11-10T00:00:00Z","_id":"10321","oa":1,"author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"type":"journal_article","year":"2021","publisher":"Cell Press","doi":"10.1016/j.xpro.2021.100939","language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2021_STARProtocols_Amberg.pdf","file_size":7309464,"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","file_id":"10329","date_created":"2021-11-22T08:23:58Z","date_updated":"2021-11-22T08:23:58Z","success":1}],"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","publication":"STAR Protocols","has_accepted_license":"1","scopus_import":"1","issue":"4","citation":{"apa":"Amberg, N., &#38; Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 2, no. 4, 100939, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>.","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.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>.","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 2, no. 4. Cell Press, 2021."},"project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","call_identifier":"FWF"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"}],"abstract":[{"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).","lang":"eng"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"10","oa_version":"Published Version","publication_status":"published","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_updated":"2023-11-16T13:08:03Z"},{"ec_funded":1,"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)."}],"oa_version":"Published Version","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"17","date_updated":"2023-11-16T13:11:04Z","acknowledged_ssus":[{"_id":"Bio"}],"status":"public","file":[{"success":1,"date_updated":"2021-12-20T08:58:40Z","checksum":"9ea2501056c5df99e84726b845e9b976","file_id":"10570","date_created":"2021-12-20T08:58:40Z","file_size":6207060,"file_name":"2021_STARProt_Venturino.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"cchlebak"}],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","publication":"STAR Protocols","project":[{"call_identifier":"H2020","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"citation":{"ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>.","apa":"Venturino, A., &#38; Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. Elsevier ; Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>","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.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” <i>STAR Protocols</i>, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>. Elsevier ; Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>."},"has_accepted_license":"1","issue":"4","scopus_import":"1","oa":1,"_id":"10565","author":[{"full_name":"Venturino, Alessandro","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","orcid":"0000-0003-2356-9403"},{"full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"}],"date_published":"2021-12-17T00:00:00Z","publisher":"Elsevier ; Cell Press","year":"2021","language":[{"iso":"eng"}],"doi":"10.1016/j.xpro.2021.101012","type":"journal_article","quality_controlled":"1","publication_identifier":{"eissn":["2666-1667"]},"month":"12","volume":2,"article_type":"original","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.","department":[{"_id":"SaSi"}],"date_created":"2021-12-19T23:01:32Z","article_number":"101012","intvolume":"         2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","ddc":["573"],"file_date_updated":"2021-12-20T08:58:40Z"},{"intvolume":"        10","file_date_updated":"2022-01-10T09:40:37Z","ddc":["570"],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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).","department":[{"_id":"CaHe"}],"date_created":"2022-01-09T23:01:26Z","article_number":"e75639","volume":10,"article_type":"original","isi":1,"publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","month":"12","type":"journal_article","year":"2021","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.75639","language":[{"iso":"eng"}],"date_published":"2021-12-21T00:00:00Z","_id":"10606","oa":1,"author":[{"id":"33280250-F248-11E8-B48F-1D18A9856A87","last_name":"Godard","first_name":"Benoit G","full_name":"Godard, Benoit G"},{"full_name":"Dumollard, Remi","first_name":"Remi","last_name":"Dumollard"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"full_name":"Mcdougall, Alex","first_name":"Alex","last_name":"Mcdougall"}],"has_accepted_license":"1","scopus_import":"1","citation":{"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,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","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.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.75639\">https://doi.org/10.7554/eLife.75639</a>.","ama":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.75639\">10.7554/eLife.75639</a>","short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","apa":"Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., &#38; Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.75639\">https://doi.org/10.7554/eLife.75639</a>","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.” <i>ELife</i>, vol. 10, e75639, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.75639\">10.7554/eLife.75639</a>."},"project":[{"call_identifier":"FWF","grant_number":"I03601","name":"Control of embryonic cleavage pattern","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division","file":[{"file_size":7769934,"file_name":"2021_eLife_Godard.pdf","date_updated":"2022-01-10T09:40:37Z","success":1,"file_id":"10611","checksum":"759c7a873d554c48a6639e6350746ca6","date_created":"2022-01-10T09:40:37Z","creator":"alisjak","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"external_id":{"isi":["000733610100001"]},"publication":"eLife","status":"public","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"date_updated":"2023-08-17T06:32:44Z","abstract":[{"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).","lang":"eng"}],"day":"21","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","publication_status":"published"},{"month":"12","quality_controlled":"1","publication_identifier":{"eissn":["2329-0501"]},"isi":1,"article_type":"original","volume":23,"date_created":"2022-01-23T23:01:28Z","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.","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","ddc":["570"],"file_date_updated":"2022-01-24T07:43:09Z","intvolume":"        23","author":[{"full_name":"Maes, Margaret E","first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes"},{"full_name":"Wögenstein, Gabriele M.","first_name":"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"},{"orcid":"0000-0001-8293-4568","last_name":"Casado Polanco","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","first_name":"Raquel","full_name":"Casado Polanco, Raquel"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra"}],"oa":1,"_id":"10655","date_published":"2021-12-10T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1016/j.omtm.2021.09.006","publisher":"Elsevier","year":"2021","type":"journal_article","publication":"Molecular Therapy - Methods and Clinical Development","external_id":{"isi":["000748748500019"]},"title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","file":[{"creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","file_size":4794147,"checksum":"77dc540e8011c5475031bdf6ccef20a6","date_created":"2022-01-24T07:43:09Z","file_id":"10657","success":1,"date_updated":"2022-01-24T07:43:09Z"}],"project":[{"call_identifier":"H2020","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"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. <i>Molecular Therapy - Methods and Clinical Development</i>. 2021;23:210-224. doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., &#38; Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>","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.” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23, Elsevier, 2021, pp. 210–24, doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","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,” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23. Elsevier, pp. 210–224, 2021.","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.” <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>."},"scopus_import":"1","has_accepted_license":"1","oa_version":"Published Version","page":"210-224","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"10","ec_funded":1,"abstract":[{"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","lang":"eng"}],"date_updated":"2023-11-16T13:12:03Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"status":"public"},{"status":"public","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2024-02-19T11:06:09Z","day":"14","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"issue":"51","has_accepted_license":"1","citation":{"ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51. National Academy of Sciences, 2021."},"project":[{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the National Academy of Sciences","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","file":[{"creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2021_PNAS_Johnson.pdf","file_size":2757340,"file_id":"10546","date_created":"2021-12-15T08:59:40Z","checksum":"8d01e72e22c4fb1584e72d8601947069","success":1,"date_updated":"2021-12-15T08:59:40Z"}],"external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14510"},{"status":"public","id":"14988","relation":"research_data"}]},"type":"journal_article","doi":"10.1073/pnas.2113046118","language":[{"iso":"eng"}],"year":"2021","publisher":"National Academy of Sciences","date_published":"2021-12-14T00:00:00Z","author":[{"full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"first_name":"Vanessa","full_name":"Zheden, Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"last_name":"Mahou","first_name":"Pierre","full_name":"Mahou, Pierre"},{"last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","first_name":"Mónika"},{"last_name":"Wang","first_name":"Jie","full_name":"Wang, Jie"},{"orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","full_name":"Aguilera Servin, Juan L"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"last_name":"Beaurepaire","first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin"},{"last_name":"Bednarek","first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"_id":"9887","oa":1,"file_date_updated":"2021-12-15T08:59:40Z","ddc":["580"],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       118","article_number":"e2113046118","date_created":"2021-08-11T14:11:43Z","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"pmid":1,"isi":1,"volume":118,"article_type":"original","month":"12","publication_identifier":{"eissn":["1091-6490"]},"quality_controlled":"1"},{"abstract":[{"text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. ","lang":"eng"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication_status":"published","oa_version":"Published Version","date_updated":"2023-08-11T10:34:44Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file":[{"creator":"asandaue","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","file_size":6132410,"checksum":"a4bc06e9a2c803ceff5a91f10b174054","date_created":"2021-08-16T09:35:56Z","file_id":"9923","success":1,"date_updated":"2021-08-16T09:35:56Z"}],"title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"publication":"International Journal of Molecular Sciences","citation":{"ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021."},"project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020"}],"has_accepted_license":"1","scopus_import":"1","issue":"15","_id":"9907","oa":1,"author":[{"last_name":"Labajová","first_name":"Naďa","full_name":"Labajová, Naďa"},{"full_name":"Baranova, Natalia S.","first_name":"Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"full_name":"Jurásek, Miroslav","first_name":"Miroslav","last_name":"Jurásek"},{"last_name":"Vácha","first_name":"Robert","full_name":"Vácha, Robert"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin"},{"last_name":"Barák","full_name":"Barák, Imrich","first_name":"Imrich"}],"date_published":"2021-08-01T00:00:00Z","year":"2021","publisher":"MDPI","doi":"10.3390/ijms22158350","language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"quality_controlled":"1","month":"08","volume":22,"article_type":"original","isi":1,"department":[{"_id":"MaLo"}],"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","pmid":1,"date_created":"2021-08-15T22:01:27Z","article_number":"8350","intvolume":"        22","file_date_updated":"2021-08-16T09:35:56Z","article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"]},{"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2023-09-07T13:38:33Z","abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"ec_funded":1,"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"13","page":"168","oa_version":"Published Version","publication_status":"published","degree_awarded":"PhD","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"citation":{"ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>."},"project":[{"call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"},{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file":[{"creator":"lhoermaye","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_vupload.docx","file_size":25179004,"checksum":"c763064adaa720e16066c1a4f9682bbb","file_id":"9993","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","embargo_to":"open_access"},{"creator":"lhoermaye","embargo":"2021-09-09","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Thesis_vfinal_pdfa.pdf","file_size":6246900,"file_id":"9996","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","date_updated":"2021-09-15T22:30:26Z"}],"title":"Wound healing in the Arabidopsis root meristem","related_material":{"record":[{"status":"public","id":"6351","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6943"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"type":"dissertation","year":"2021","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:9992","language":[{"iso":"eng"}],"date_published":"2021-09-13T00:00:00Z","_id":"9992","oa":1,"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"}],"file_date_updated":"2021-09-15T22:30:26Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["575"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_created":"2021-09-09T07:37:20Z","supervisor":[{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"publisher":"Springer Nature","year":"2020","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-15895-5","type":"journal_article","oa":1,"_id":"7805","author":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","orcid":"0000-0003-3638-1426","first_name":"Andrej","full_name":"Hurny, Andrej"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","first_name":"Candela"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola","full_name":"Cavallari, Nicola"},{"full_name":"Ötvös, Krisztina","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","orcid":"0000-0002-5503-4983"},{"last_name":"Duclercq","first_name":"Jerome","full_name":"Duclercq, Jerome"},{"last_name":"Dokládal","full_name":"Dokládal, Ladislav","first_name":"Ladislav"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","orcid":"0000-0001-9179-6099","first_name":"Juan C","full_name":"Montesinos López, Juan C"},{"orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","full_name":"Gallemi, Marçal","first_name":"Marçal"},{"last_name":"Semeradova","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semeradova, Hana","first_name":"Hana"},{"full_name":"Rauter, Thomas","first_name":"Thomas","id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","last_name":"Rauter"},{"last_name":"Stenzel","first_name":"Irene","full_name":"Stenzel, Irene"},{"last_name":"Persiau","full_name":"Persiau, Geert","first_name":"Geert"},{"first_name":"Freia","full_name":"Benade, Freia","last_name":"Benade"},{"last_name":"Bhalearo","first_name":"Rishikesh","full_name":"Bhalearo, Rishikesh"},{"full_name":"Sýkorová, Eva","first_name":"Eva","last_name":"Sýkorová"},{"last_name":"Gorzsás","full_name":"Gorzsás, András","first_name":"András"},{"first_name":"Julien","full_name":"Sechet, Julien","last_name":"Sechet"},{"last_name":"Mouille","full_name":"Mouille, Gregory","first_name":"Gregory"},{"first_name":"Ingo","full_name":"Heilmann, Ingo","last_name":"Heilmann"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"last_name":"Ludwig-Müller","full_name":"Ludwig-Müller, Jutta","first_name":"Jutta"},{"first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"date_published":"2020-05-01T00:00:00Z","pmid":1,"department":[{"_id":"EvBe"}],"acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","article_number":"2170","date_created":"2020-05-10T22:00:48Z","intvolume":"        11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"article_processing_charge":"No","file_date_updated":"2020-10-06T07:47:53Z","quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"month":"05","volume":11,"article_type":"original","isi":1,"date_updated":"2023-08-21T06:21:56Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","ec_funded":1,"abstract":[{"lang":"eng","text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens."}],"oa_version":"Published Version","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","project":[{"call_identifier":"FWF","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"citation":{"chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-15895-5\">https://doi.org/10.1038/s41467-020-15895-5</a>.","ieee":"A. Hurny <i>et al.</i>, “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.","short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” <i>Nature Communications</i>, vol. 11, 2170, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-15895-5\">10.1038/s41467-020-15895-5</a>.","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-15895-5\">https://doi.org/10.1038/s41467-020-15895-5</a>","ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-15895-5\">10.1038/s41467-020-15895-5</a>"},"has_accepted_license":"1","scopus_import":"1","external_id":{"isi":["000531425900012"],"pmid":["32358503"]},"title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2020-10-06T07:47:53Z","success":1,"checksum":"2cba327c9e9416d75cb96be54b0fb441","date_created":"2020-10-06T07:47:53Z","file_id":"8614","file_size":4743576,"file_name":"2020_NatureComm_Hurny.pdf"}],"publication":"Nature Communications"},{"publication":"Frontiers in Education","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1402146,"file_name":"2020_FrontiersEduc_Beattie.pdf","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-11T11:34:08Z","file_id":"7818","checksum":"a24ec24e38d843341ae620ec76c53688"}],"title":"SCOPES: Sparking curiosity through Open-Source platforms in education and science","has_accepted_license":"1","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","call_identifier":"FWF"},{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"citation":{"short":"R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020).","ista":"Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 5, 48.","apa":"Beattie, R. J., Hippenmeyer, S., &#38; Pauler, F. (2020). SCOPES: Sparking curiosity through Open-Source platforms in education and science. <i>Frontiers in Education</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/feduc.2020.00048\">https://doi.org/10.3389/feduc.2020.00048</a>","mla":"Beattie, Robert J., et al. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” <i>Frontiers in Education</i>, vol. 5, 48, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/feduc.2020.00048\">10.3389/feduc.2020.00048</a>.","ama":"Beattie RJ, Hippenmeyer S, Pauler F. SCOPES: Sparking curiosity through Open-Source platforms in education and science. <i>Frontiers in Education</i>. 2020;5. doi:<a href=\"https://doi.org/10.3389/feduc.2020.00048\">10.3389/feduc.2020.00048</a>","chicago":"Beattie, Robert J, Simon Hippenmeyer, and Florian Pauler. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” <i>Frontiers in Education</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/feduc.2020.00048\">https://doi.org/10.3389/feduc.2020.00048</a>.","ieee":"R. J. Beattie, S. Hippenmeyer, and F. Pauler, “SCOPES: Sparking curiosity through Open-Source platforms in education and science,” <i>Frontiers in Education</i>, vol. 5. Frontiers Media, 2020."},"oa_version":"Published Version","publication_status":"published","day":"08","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"abstract":[{"text":"Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"status":"public","date_updated":"2021-01-12T08:15:42Z","article_type":"original","volume":5,"month":"05","quality_controlled":"1","publication_identifier":{"issn":["2504-284X"]},"ddc":["570"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:48:03Z","intvolume":"         5","date_created":"2020-05-11T08:18:48Z","article_number":"48","department":[{"_id":"SiHi"}],"date_published":"2020-05-08T00:00:00Z","author":[{"last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian"}],"oa":1,"_id":"7814","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3389/feduc.2020.00048","publisher":"Frontiers Media","year":"2020"},{"publication_identifier":{"issn":["1940-087X"]},"quality_controlled":"1","month":"05","article_type":"original","isi":1,"department":[{"_id":"SiHi"}],"article_number":"e61147","date_created":"2020-05-11T08:31:20Z","file_date_updated":"2020-07-14T12:48:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","_id":"7815","oa":1,"author":[{"first_name":"Robert J","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen"},{"full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H","first_name":"Andi H"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"date_published":"2020-05-08T00:00:00Z","year":"2020","publisher":"MyJove Corporation","doi":"10.3791/61147","language":[{"iso":"eng"}],"type":"journal_article","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","file":[{"creator":"rbeattie","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1352186,"file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","date_updated":"2020-07-14T12:48:03Z","file_id":"7816","checksum":"3154ea7f90b9fb45e084cd1c2770597d","date_created":"2020-05-11T08:28:38Z"}],"external_id":{"isi":["000546406600043"]},"related_material":{"record":[{"status":"public","id":"7902","relation":"part_of_dissertation"}]},"publication":"Journal of Visual Experiments","citation":{"chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>. MyJove Corporation, 2020. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>.","ieee":"R. J. Beattie <i>et al.</i>, “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” <i>Journal of Visual Experiments</i>, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., &#38; Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>, no. 159, e61147, MyJove Corporation, 2020, doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. 2020;(159). doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>"},"project":[{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"has_accepted_license":"1","scopus_import":"1","issue":"159","abstract":[{"lang":"eng","text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present."}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"08","publication_status":"published","oa_version":"Published Version","date_updated":"2024-03-25T23:30:23Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}]}]