[{"year":"2026","das_tickbox":"0","intvolume":"      3049","file":[{"success":1,"access_level":"open_access","date_created":"2026-09-17T07:28:53Z","date_updated":"2026-09-17T07:28:53Z","file_id":"22938","file_name":"2026_MIMB_Vijatovic.pdf","checksum":"e7a075a9ee1b91d5824f8f2b9b1f3c9b","file_size":1004024,"relation":"main_file","content_type":"application/pdf","creator":"dernst"}],"alternative_title":["Methods in Molecular Biology"],"researchdata_availability":"no","citation":{"apa":"Vijatovic, D., Papadopoulos, S., Dalla Vecchia, M., &#38; Sweeney, L. B. (2026). Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In C. W. Beck (Ed.), <i>Xenopus</i> (Vol. 3049, pp. 245–259). Springer. <a href=\"https://doi.org/10.1007/978-1-0716-5360-9_11\">https://doi.org/10.1007/978-1-0716-5360-9_11</a>","ieee":"D. Vijatovic, S. Papadopoulos, M. Dalla Vecchia, and L. B. Sweeney, “Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections,” in <i>Xenopus</i>, vol. 3049, C. W. Beck, Ed. Springer, 2026, pp. 245–259.","ista":"Vijatovic D, Papadopoulos S, Dalla Vecchia M, Sweeney LB. 2026.Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In: Xenopus. Methods in Molecular Biology, vol. 3049, 245–259.","short":"D. Vijatovic, S. Papadopoulos, M. Dalla Vecchia, L.B. Sweeney, in:, C.W. Beck (Ed.), Xenopus, Springer, 2026, pp. 245–259.","chicago":"Vijatovic, David, Stavros Papadopoulos, Marco Dalla Vecchia, and Lora B. Sweeney. “Fluorescent in Situ MRNA Hybridization (FISH) Using Hybridization Chain Reaction (HCR) in Xenopus Cryosections.” In <i>Xenopus</i>, edited by Caroline W. Beck, 3049:245–59. MIMB. Springer, 2026. <a href=\"https://doi.org/10.1007/978-1-0716-5360-9_11\">https://doi.org/10.1007/978-1-0716-5360-9_11</a>.","mla":"Vijatovic, David, et al. “Fluorescent in Situ MRNA Hybridization (FISH) Using Hybridization Chain Reaction (HCR) in Xenopus Cryosections.” <i>Xenopus</i>, edited by Caroline W. Beck, vol. 3049, Springer, 2026, pp. 245–59, doi:<a href=\"https://doi.org/10.1007/978-1-0716-5360-9_11\">10.1007/978-1-0716-5360-9_11</a>.","ama":"Vijatovic D, Papadopoulos S, Dalla Vecchia M, Sweeney LB. Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In: Beck CW, ed. <i>Xenopus</i>. Vol 3049. MIMB. Springer; 2026:245-259. doi:<a href=\"https://doi.org/10.1007/978-1-0716-5360-9_11\">10.1007/978-1-0716-5360-9_11</a>"},"date_updated":"2026-09-17T07:31:16Z","status":"public","type":"book_chapter","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"doi":"10.1007/978-1-0716-5360-9_11","date_published":"2026-09-02T00:00:00Z","_id":"22925","volume":3049,"series_title":"MIMB","oa":1,"publication_identifier":{"eissn":["1940-6029"]},"title":"Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections","file_date_updated":"2026-09-17T07:28:53Z","OA_place":"publisher","OA_type":"hybrid","external_id":{"pmid":["42681228"]},"abstract":[{"lang":"eng","text":"Hybridization Chain Reaction (HCR) enables highly sensitive and multiplexed detection of mRNA with subcellular spatial resolution. It employs fluorophore-tagged DNA hairpins that self-assemble on target-bound probe pairs, amplifying the signal without enzymatic reactions. Here, we describe a protocol for performing HCR fluorescence in situ hybridization (FISH) on Xenopus tissue sections. We also outline a semi-automated image analysis pipeline that enables per-cell quantification of probe expression and co-localization. This method provides a robust and quantitative approach for visualizing gene expression patterns in situ."}],"date_created":"2026-09-13T22:01:55Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"245-259","corr_author":"1","author":[{"first_name":"David","full_name":"Vijatovic, David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","orcid":"0000-0002-5494-0941","last_name":"Vijatovic"},{"full_name":"Papadopoulos, Stavros","first_name":"Stavros","id":"40606b92-f128-11eb-9611-bf66a98cfa5c","last_name":"Papadopoulos"},{"full_name":"Dalla Vecchia, Marco","first_name":"Marco","last_name":"Dalla Vecchia","id":"02a7a869-ff06-11ed-a87f-86649d6077e5"},{"orcid":"0000-0001-9242-5601","last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger"}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.1007/978-1-0716-5360-9_11","quality_controlled":"1","month":"09","supplementarymaterial":"no","oa_version":"Published Version","keyword":["mRNA FISH","Hybridization chain reaction","In situ hybridization","Fluorescence microscopy"],"article_processing_charge":"No","editor":[{"last_name":"Beck","full_name":"Beck, Caroline W.","first_name":"Caroline W."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"ddc":["570"],"publication":"Xenopus","scopus_import":"1","project":[{"name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","grant_number":"F7814"},{"_id":"cf428362-b037-11f1-b015-8277a8a2f63d","name":"Neuronal circuits in health and disease (Sweeney)","grant_number":"COE16"},{"grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis"},{"_id":"907b765e-16d5-11f0-9cad-fef108a945b1","name":"A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb transition of Xenopus metamorphosis","grant_number":"27229"}],"acknowledgement":"This work was supported by a Horizon Europe ERC Starting Grant\r\nNumber 101041551 (L.B.S., D.V., S.P.), Special Research Program\r\n(SFB) of the Austrian Science Fund (FWF) F7814-B (L.B.S., S.P.),\r\nAustrian Science Fund (FWF) 10.55776/COE16 (L.B.S.), FTI\r\nStrategy Lower Austria Dissertation Grant Number FT121-D-046\r\n(D.V.), and Austrian Academy of Sciences DOC Fellowship 27229\r\n(S.P.). We also thank the Imaging & Optics and Scientific Computing Facilities at ISTA for their support in developing the quantification pipeline.","publisher":"Springer","day":"02","department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"IAS"}],"pmid":1},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"day":"10","degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"ddc":["570"],"language":[{"iso":"eng"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"11","fulldoi":"https://doi.org/10.15479/at:ista:14510","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"article_processing_charge":"No","oa_version":"Published Version","has_accepted_license":"1","author":[{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"}],"date_created":"2023-11-10T09:10:06Z","page":"180","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. "}],"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","file_date_updated":"2024-11-23T23:30:38Z","oa":1,"OA_place":"publisher","related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"status":"public","type":"dissertation","date_updated":"2026-10-10T22:30:52Z","_id":"14510","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)"},"doi":"10.15479/at:ista:14510","date_published":"2023-11-10T00:00:00Z","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>."},"ec_funded":1,"alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":20824903,"creator":"ngnyliuk","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_updated":"2024-11-23T23:30:38Z","embargo_to":"open_access","access_level":"closed","date_created":"2023-11-20T09:18:51Z"},{"creator":"ngnyliuk","content_type":"application/pdf","relation":"main_file","file_size":24871844,"checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","file_id":"14568","date_updated":"2024-11-23T23:30:38Z","date_created":"2023-11-20T09:23:11Z","access_level":"open_access"}],"year":"2023"}]