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Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>","short":"C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025.","ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria.","apa":"Giannini, C. (2025). <i>Nuclear and cell surface auxin signaling in A. thaliana developmental transitions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>","chicago":"Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>.","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025."},"has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2026-04-07T11:52:16Z","_id":"20364","date_created":"2025-09-19T12:23:38Z","file":[{"embargo":"2026-09-30","file_name":"2025_Giannini_Caterina_Thesis...pdf","date_created":"2025-09-24T14:46:34Z","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","creator":"cgiannin","date_updated":"2025-09-30T14:31:29Z","relation":"main_file","file_id":"20390","checksum":"536ba1701453b0b2346be14c046b2911","file_size":14278965},{"file_name":"2025_Giannini_Caterina_Thesis...docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-09-24T14:46:35Z","relation":"source_file","creator":"cgiannin","access_level":"closed","date_updated":"2025-09-24T14:46:35Z","checksum":"192f55262f2da2ea0a59d9c23a1b8573","file_size":24499022,"file_id":"20391"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"keyword":["Auxin Signaling","Plant Development"],"type":"dissertation","corr_author":"1","status":"public","doi":"10.15479/AT-ISTA-20364","year":"2025","author":[{"full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","first_name":"Caterina"}],"page":"151","day":"19","ddc":["580"],"related_material":{"record":[{"id":"12291","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"19399"}]},"degree_awarded":"PhD","month":"09","title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions"},{"file_date_updated":"2025-08-26T10:43:30Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","publication_status":"published","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_published":"2025-08-22T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-063-3"]},"citation":{"ama":"Miranda O. 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Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025."},"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"OA_place":"publisher","language":[{"iso":"eng"}],"has_accepted_license":"1","date_updated":"2026-04-14T08:16:57Z","article_processing_charge":"No","_id":"20212","date_created":"2025-08-22T14:07:00Z","keyword":["Pten","mtor","cortical development","MADM","Mapk"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"file":[{"relation":"source_file","date_updated":"2025-08-26T09:03:50Z","creator":"omiranda","access_level":"closed","file_size":32887334,"checksum":"3331f76bbef74ff4908e2d2c9262045c","file_id":"20230","date_created":"2025-08-26T09:03:50Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx"},{"file_id":"20231","file_size":28636240,"checksum":"02509d50cff8e35c5bcbf71e8d658176","date_updated":"2025-08-26T10:43:30Z","access_level":"closed","creator":"omiranda","relation":"main_file","embargo":"2026-08-26","content_type":"application/pdf","date_created":"2025-08-26T09:05:55Z","embargo_to":"open_access","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf"}],"type":"dissertation","corr_author":"1","status":"public","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"}],"author":[{"full_name":"Miranda, Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","last_name":"Miranda","first_name":"Osvaldo"}],"doi":"10.15479/AT-ISTA-20212","year":"2025","day":"22","page":"119","ddc":["570"],"degree_awarded":"PhD","related_material":{"record":[{"id":"17425","relation":"part_of_dissertation","status":"public"}]},"month":"08","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM"},{"article_processing_charge":"No","date_updated":"2026-04-14T08:16:58Z","_id":"20737","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publication_identifier":{"isbn":["978-3-99078-072-5"],"issn":["2663-337X"]},"citation":{"apa":"Casado Polanco, R. (2025). <i>Role of NOTCH signaling in radial glial progenitor lineage progression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>","mla":"Casado Polanco, Raquel. <i>Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>.","ama":"Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage progression. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>","ista":"Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria.","short":"R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression, Institute of Science and Technology Austria, 2025.","chicago":"Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>.","ieee":"R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage progression,” Institute of Science and Technology Austria, 2025."},"oa_version":"Published Version","date_published":"2025-12-09T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"acknowledgement":"I also want to thank ISTA and the Austrian Science Fund FWF SFB F78 (F7805) for financially\r\nsupporting my research.","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2025-12-11T11:18:37Z","month":"12","title":"Role of NOTCH signaling in radial glial progenitor lineage progression","ddc":["570"],"degree_awarded":"PhD","year":"2025","doi":"10.15479/AT-ISTA-20737","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"author":[{"first_name":"Raquel","last_name":"Casado Polanco","orcid":"0000-0001-8293-4568","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","full_name":"Casado Polanco, Raquel"}],"page":"133","day":"09","status":"public","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"file":[{"file_name":"2025_CasadoPolanco_Raquel_Thesis.docx","date_created":"2025-12-11T09:28:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"71e0fdf4619b0d70d03657ad7348137d","file_size":78207207,"file_id":"20793","relation":"source_file","creator":"rcasadop","access_level":"closed","date_updated":"2025-12-11T11:18:37Z"},{"checksum":"58cf2f25c33567723bc754a019c3e396","file_size":6261874,"file_id":"20794","relation":"main_file","access_level":"closed","creator":"rcasadop","date_updated":"2025-12-11T09:28:04Z","file_name":"2025_CasadoPolanco_Raquel_Thesis.pdf","content_type":"application/pdf","date_created":"2025-12-11T09:28:04Z","embargo_to":"open_access","embargo":"2026-12-01"}],"keyword":["NOTCH","radial glial progenitor","lineage progression","cortical development"],"type":"dissertation","date_created":"2025-12-09T09:04:18Z"},{"alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"file_date_updated":"2024-02-08T23:30:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2023-02-02T00:00:00Z","oa_version":"Published Version","publication_status":"published","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>."},"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"_id":"12491","date_updated":"2026-04-07T13:49:23Z","article_processing_charge":"No","type":"dissertation","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"file":[{"file_name":"PhDThesis_BettinaZens_2023_final.pdf","content_type":"application/pdf","date_created":"2023-02-07T13:07:38Z","embargo":"2024-02-07","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"file_id":"12527","relation":"main_file","creator":"bzens","access_level":"open_access","date_updated":"2024-02-08T23:30:04Z"},{"date_updated":"2024-02-08T23:30:04Z","access_level":"closed","creator":"bzens","relation":"source_file","file_id":"12528","file_size":106169509,"checksum":"8c66ed203495d6e078ed1002a866520c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2023-02-07T13:09:05Z","file_name":"PhDThesis_BettinaZens_2023_final.docx"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"date_created":"2023-02-02T14:50:20Z","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"status":"public","corr_author":"1","day":"02","page":"187","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens","first_name":"Bettina"}],"doi":"10.15479/at:ista:12491","year":"2023","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","month":"02","degree_awarded":"PhD","related_material":{"record":[{"id":"8586","status":"public","relation":"part_of_dissertation"}]},"ddc":["570"]},{"status":"public","quality_controlled":"1","type":"journal_article","oa":1,"keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"],"date_created":"2021-12-28T11:44:18Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/pcp/pcab149"}],"abstract":[{"text":"The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.","lang":"eng"}],"title":"Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density","month":"01","article_type":"original","page":"104-119","scopus_import":"1","day":"21","doi":"10.1093/pcp/pcab149","year":"2022","author":[{"first_name":"Sylwia","last_name":"Struk","full_name":"Struk, Sylwia"},{"full_name":"Braem, Lukas","first_name":"Lukas","last_name":"Braem"},{"last_name":"Matthys","first_name":"Cedrick","full_name":"Matthys, Cedrick"},{"last_name":"Walton","first_name":"Alan","full_name":"Walton, Alan"},{"full_name":"Vangheluwe, Nick","first_name":"Nick","last_name":"Vangheluwe"},{"first_name":"Stan","last_name":"Van Praet","full_name":"Van Praet, Stan"},{"full_name":"Jiang, Lingxiang","first_name":"Lingxiang","last_name":"Jiang"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster"},{"last_name":"De Cuyper","first_name":"Carolien","full_name":"De Cuyper, Carolien"},{"full_name":"Boyer, Francois-Didier","first_name":"Francois-Didier","last_name":"Boyer"},{"full_name":"Stes, Elisabeth","last_name":"Stes","first_name":"Elisabeth"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"last_name":"Goormachtig","first_name":"Sofie","full_name":"Goormachtig, Sofie"}],"volume":63,"date_published":"2022-01-21T00:00:00Z","oa_version":"Published Version","publisher":"Oxford University Press","publication_status":"published","isi":1,"acknowledgement":"The authors thank Ralf Stracke (Bielefeld University, Bielefeld, Germany) for providing the myb mutants and their colleagues Bert De Rybel for the tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique Storme for statistical help on both the RNA-seq and lateral root density, and Martine De Cock for help in preparing the manuscript.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        63","publication":"Plant & Cell Physiology","_id":"10583","article_processing_charge":"No","date_updated":"2023-08-02T13:40:43Z","issue":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"pmid":1,"publication_identifier":{"eissn":["1471-9053"],"issn":["0032-0781"]},"citation":{"apa":"Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S., … Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>","ama":"Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. 2022;63(1):104-119. doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>","mla":"Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>.","ista":"Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L, Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant &#38; Cell Physiology. 63(1), 104–119.","short":"S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L. Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K. Gevaert, S. Goormachtig, Plant &#38; Cell Physiology 63 (2022) 104–119.","chicago":"Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe, Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>.","ieee":"S. Struk <i>et al.</i>, “Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density,” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022."},"external_id":{"isi":["000877899400009"],"pmid":["34791413"]}},{"corr_author":"1","status":"public","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"date_created":"2019-05-13T08:58:35Z","file":[{"embargo":"2020-05-08","file_name":"tesisDoctoradoBC.pdf","content_type":"application/pdf","date_created":"2019-05-13T09:16:20Z","access_level":"open_access","creator":"casillas","date_updated":"2021-02-11T11:17:15Z","relation":"main_file","file_id":"6438","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","file_size":3895187},{"relation":"source_file","date_updated":"2020-07-14T12:47:30Z","access_level":"closed","creator":"casillas","file_size":7365118,"checksum":"3d221aaff7559a7060230a1ff610594f","file_id":"6439","content_type":"application/zip","date_created":"2019-05-13T09:16:20Z","embargo_to":"open_access","file_name":"tesisDoctoradoBC.zip"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"type":"dissertation","ddc":["570","006","578","592"],"related_material":{"record":[{"id":"1999","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","month":"05","title":"Collective defenses of garden ants against a fungal pathogen","doi":"10.15479/AT:ISTA:6435","year":"2019","author":[{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez"}],"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"page":"183","day":"07","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","ec_funded":1,"date_published":"2019-05-07T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2021-02-11T11:17:15Z","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"article_processing_charge":"No","date_updated":"2026-04-08T14:02:12Z","_id":"6435","department":[{"_id":"SyCr"}],"citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019."},"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["1360-0648"],"issn":["0790-0627"]},"citation":{"ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” <i>International Journal of Water Resources Development</i>, vol. 31, no. 2. Taylor &#38; Francis, pp. 174–200, 2015.","chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” <i>International Journal of Water Resources Development</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/07900627.2015.1020417\">https://doi.org/10.1080/07900627.2015.1020417</a>.","ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200.","short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200.","mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” <i>International Journal of Water Resources Development</i>, vol. 31, no. 2, Taylor &#38; Francis, 2015, pp. 174–200, doi:<a href=\"https://doi.org/10.1080/07900627.2015.1020417\">10.1080/07900627.2015.1020417</a>.","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. <i>International Journal of Water Resources Development</i>. 2015;31(2):174-200. doi:<a href=\"https://doi.org/10.1080/07900627.2015.1020417\">10.1080/07900627.2015.1020417</a>","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., &#38; Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. <i>International Journal of Water Resources Development</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/07900627.2015.1020417\">https://doi.org/10.1080/07900627.2015.1020417</a>"},"extern":"1","language":[{"iso":"eng"}],"issue":"2","_id":"12629","article_processing_charge":"No","date_updated":"2023-02-24T09:30:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        31","publication":"International Journal of Water Resources Development","publisher":"Taylor & Francis","publication_status":"published","volume":31,"date_published":"2015-04-18T00:00:00Z","oa_version":"Published Version","page":"174-200","scopus_import":"1","day":"18","doi":"10.1080/07900627.2015.1020417","year":"2015","author":[{"full_name":"Shea, J.M.","last_name":"Shea","first_name":"J.M."},{"last_name":"Wagnon","first_name":"P.","full_name":"Wagnon, P."},{"first_name":"W.W.","last_name":"Immerzeel","full_name":"Immerzeel, W.W."},{"full_name":"Biron, R.","last_name":"Biron","first_name":"R."},{"full_name":"Brun, F.","first_name":"F.","last_name":"Brun"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}],"article_type":"original","title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","month":"04","date_created":"2023-02-20T08:16:17Z","main_file_link":[{"url":"https://doi.org/10.1080/07900627.2015.1020417","open_access":"1"}],"abstract":[{"text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region.","lang":"eng"}],"type":"journal_article","oa":1,"keyword":["Water Science and Technology","Development"],"status":"public","quality_controlled":"1"},{"month":"02","title":"Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin","year":"2012","doi":"10.1659/mrd-journal-d-11-00097.1","author":[{"last_name":"Immerzeel","first_name":"Walter Willem","full_name":"Immerzeel, Walter Willem"},{"last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"Shrestha, Arun B.","last_name":"Shrestha","first_name":"Arun B."}],"page":"30-38","scopus_import":"1","day":"01","article_type":"original","quality_controlled":"1","status":"public","main_file_link":[{"url":"https://doi.org/10.1659/MRD-JOURNAL-D-11-00097.1","open_access":"1"}],"abstract":[{"text":"Accurate quantification of the spatial distribution of precipitation in mountain regions is crucial for assessments of water resources and for the understanding of high-altitude hydrology, yet it is one of the largest unknowns due to the lack of high-altitude observations. The Hunza basin in Pakistan contains very large glacier systems, which, given the melt, cannot persist unless precipitation (snow input) is much higher than what is observed at the meteorological stations, mostly located in mountain valleys. Several studies, therefore, suggest strong positive vertical precipitation lapse rates; in the present study, we quantify this lapse rate by using glaciers as a proxy. We assume a neutral mass balance for the glaciers for the period from 2001 to 2003, and we inversely model the precipitation lapse by balancing the total accumulation in the catchment area and the ablation over the glacier area for the 50 largest glacier systems in the Hunza basin in the Karakoram. Our results reveal a vertical precipitation lapse rate that equals 0.21 ± 0.12% m−1, with a maximum precipitation at an elevation of 5500 masl. We showed that the total annual basin precipitation (828 mm) is 260% higher than what is estimated based on interpolated observations (319 mm); this has major consequences for hydrological modeling and water resource assessments in general. Our results were validated by using previously published studies on individual glaciers as well as the water balance of the Hunza basin. The approach is more widely applicable in mountain ranges where precipitation measurements at high altitude are lacking.","lang":"eng"}],"date_created":"2023-02-20T08:17:52Z","oa":1,"keyword":["General Environmental Science","Development","Environmental Chemistry"],"type":"journal_article","issue":"1","article_processing_charge":"No","date_updated":"2023-02-21T08:56:29Z","_id":"12647","publication_identifier":{"eissn":["1994-7151"],"issn":["0276-4741"]},"citation":{"apa":"Immerzeel, W. W., Pellicciotti, F., &#38; Shrestha, A. B. (2012). Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. <i>Mountain Research and Development</i>. International Mountain Society. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">https://doi.org/10.1659/mrd-journal-d-11-00097.1</a>","ama":"Immerzeel WW, Pellicciotti F, Shrestha AB. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. <i>Mountain Research and Development</i>. 2012;32(1):30-38. doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">10.1659/mrd-journal-d-11-00097.1</a>","mla":"Immerzeel, Walter Willem, et al. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” <i>Mountain Research and Development</i>, vol. 32, no. 1, International Mountain Society, 2012, pp. 30–38, doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">10.1659/mrd-journal-d-11-00097.1</a>.","ista":"Immerzeel WW, Pellicciotti F, Shrestha AB. 2012. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. Mountain Research and Development. 32(1), 30–38.","short":"W.W. Immerzeel, F. Pellicciotti, A.B. Shrestha, Mountain Research and Development 32 (2012) 30–38.","chicago":"Immerzeel, Walter Willem, Francesca Pellicciotti, and Arun B. Shrestha. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” <i>Mountain Research and Development</i>. International Mountain Society, 2012. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">https://doi.org/10.1659/mrd-journal-d-11-00097.1</a>.","ieee":"W. W. Immerzeel, F. Pellicciotti, and A. B. Shrestha, “Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin,” <i>Mountain Research and Development</i>, vol. 32, no. 1. International Mountain Society, pp. 30–38, 2012."},"language":[{"iso":"eng"}],"extern":"1","publisher":"International Mountain Society","publication_status":"published","oa_version":"Published Version","date_published":"2012-02-01T00:00:00Z","volume":32,"publication":"Mountain Research and Development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        32"},{"quality_controlled":"1","status":"public","keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"],"type":"journal_article","abstract":[{"lang":"eng","text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution."}],"date_created":"2023-01-16T09:22:18Z","month":"03","title":"Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther","article_type":"original","author":[{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Dickinson, Hugh G.","first_name":"Hugh G.","last_name":"Dickinson"}],"year":"2010","doi":"10.1042/bst0380571","day":"22","scopus_import":"1","page":"571-576","oa_version":"None","volume":38,"date_published":"2010-03-22T00:00:00Z","publication_status":"published","publisher":"Portland Press Ltd.","publication":"Biochemical Society Transactions","intvolume":"        38","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-08T10:57:59Z","article_processing_charge":"No","_id":"12200","issue":"2","language":[{"iso":"eng"}],"extern":"1","external_id":{"pmid":["20298223"]},"citation":{"chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>. Portland Press Ltd., 2010. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>.","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther,” <i>Biochemical Society Transactions</i>, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>.","ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. 2010;38(2):571-576. doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>","short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.","ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. Biochemical Society Transactions. 38(2), 571–576.","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. Portland Press Ltd. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>"},"publication_identifier":{"issn":["0300-5127","1470-8752"]},"department":[{"_id":"XiFe"}],"pmid":1}]