[{"author":[{"last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","month":"05","year":"2025","citation":{"short":"G. Yalniz, Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.","ista":"Yalniz G. 2025. Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","mla":"Yalniz, Gökhan. <i>Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>.","ieee":"G. Yalniz, “Transition to turbulence : Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","ama":"Yalniz G. Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>","chicago":"Yalniz, Gökhan. “Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>.","apa":"Yalniz, G. (2025). <i>Transition to turbulence : Data-, solution-, and pattern-driven approaches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>"},"article_processing_charge":"No","date_published":"2025-05-13T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"19684","date_updated":"2026-04-07T11:47:06Z","date_created":"2025-05-12T15:12:28Z","oa":1,"supervisor":[{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"alternative_title":["ISTA Thesis"],"project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"}],"related_material":{"record":[{"id":"7563","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9558"},{"id":"12105","relation":"part_of_dissertation","status":"public"},{"id":"13274","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14466","relation":"part_of_dissertation"}]},"page":"155","status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","ddc":["514","519","532","004"],"day":"13","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-19684","file_date_updated":"2025-05-12T15:43:28Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file":[{"creator":"gyalniz","success":1,"access_level":"open_access","content_type":"application/pdf","date_created":"2025-05-12T15:13:28Z","checksum":"0e452642b79f13633f1595bde71a67e3","file_name":"Gökhan Yalnız - PhD thesis.pdf","date_updated":"2025-05-12T15:13:28Z","file_size":20058169,"relation":"main_file","file_id":"19685"},{"file_size":37763743,"title":"Chapter 2 - Movie 2A.1","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","relation":"supplementary_material","file_id":"19686","creator":"gyalniz","access_level":"open_access","content_type":"video/mp4","checksum":"921099d76adab2df784ce12ce41cfb22","file_name":"Movie 2A.1.mp4","date_created":"2025-05-12T15:15:59Z","date_updated":"2025-05-12T15:43:28Z"},{"checksum":"0ae5ac7d9896003c0c4207dd746808dc","file_name":"Movie 3A.1.mp4","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:09Z","access_level":"open_access","creator":"gyalniz","file_id":"19687","relation":"supplementary_material","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.1","file_size":3902655},{"title":"Chapter 3 - Movie 3A.2","file_size":7043169,"description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","file_id":"19688","relation":"supplementary_material","creator":"gyalniz","date_created":"2025-05-12T15:16:21Z","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","file_name":"Movie 3A.2.mp4","access_level":"open_access"},{"date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 3A.3.mp4","date_created":"2025-05-12T15:16:36Z","checksum":"7ed871f428100d6827ac9b0e8ca8e985","content_type":"video/mp4","access_level":"open_access","creator":"gyalniz","file_id":"19689","relation":"supplementary_material","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.3","file_size":7748659},{"description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.4","file_size":5873052,"file_id":"19690","relation":"supplementary_material","creator":"gyalniz","file_name":"Movie 3A.4.mp4","checksum":"dd5a252e1da00c8f303588e22e2baeef","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:50Z","access_level":"open_access"},{"access_level":"open_access","content_type":"video/mp4","date_created":"2025-05-12T15:17:11Z","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 4A.1.mp4","checksum":"5ac58b86810698db28cbfc28f351ff70","creator":"gyalniz","relation":"supplementary_material","file_id":"19691","file_size":9209327,"title":"Chapter 4 - Movie 4A.1","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit."},{"title":"Chapter 5 - Movie 5A.1","file_size":5893993,"description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_id":"19692","relation":"supplementary_material","creator":"gyalniz","content_type":"video/mp4","checksum":"ac877f1e1ef39439911bf37cb1793b8e","file_name":"Movie 5A.1.mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:43Z","access_level":"open_access"},{"creator":"gyalniz","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","checksum":"fd17eabb70129ceaa414e40924d1d2fe","file_name":"Movie 5A.2.mp4","date_created":"2025-05-12T15:17:49Z","access_level":"open_access","title":"Chapter 5 - Movie 5A.2","file_size":3990352,"description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_id":"19693","relation":"supplementary_material"},{"file_id":"19694","relation":"supplementary_material","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain.","title":"Chapter 5 - Movie 5A.3","file_size":5171009,"content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:58Z","file_name":"Movie 5A.3.mp4","checksum":"32f904497ab0bbee38f0788d96b91454","access_level":"open_access","creator":"gyalniz"},{"file_size":18991996,"file_id":"19695","relation":"source_file","creator":"gyalniz","checksum":"f313261b9bb12dfb943fead8318954c6","content_type":"application/x-zip-compressed","file_name":"Gökhan Yalnız - PhD thesis.zip","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:27:10Z","access_level":"closed"}],"degree_awarded":"PhD","type":"dissertation","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.","lang":"eng"}]},{"has_accepted_license":"1","corr_author":"1","abstract":[{"text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.","lang":"eng"}],"volume":5,"scopus_import":"1","quality_controlled":"1","type":"journal_article","ec_funded":1,"file":[{"file_size":7238179,"relation":"main_file","file_id":"19802","success":1,"creator":"dernst","access_level":"open_access","checksum":"4018c833f25a3ad3b57e3577fed70334","date_updated":"2025-06-10T07:24:46Z","date_created":"2025-06-10T07:24:46Z","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"OA_place":"publisher","file_date_updated":"2025-06-10T07:24:46Z","OA_type":"gold","doi":"10.1016/j.bpr.2025.100211","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"11","acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","publication":"Biophysical Reports","ddc":["570"],"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","issue":"2","status":"public","publication_identifier":{"eissn":["2667-0747"]},"language":[{"iso":"eng"}],"project":[{"name":"CryoMinflux-guided in-situ molecular census and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057"}],"related_material":{"record":[{"id":"20206","relation":"dissertation_contains","status":"public"}]},"article_number":"100211","intvolume":"         5","DOAJ_listed":"1","date_updated":"2026-04-07T11:48:07Z","date_created":"2025-06-08T22:01:22Z","oa":1,"date_published":"2025-06-11T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"_id":"19795","article_processing_charge":"Yes","citation":{"short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Elsevier, 2025.","mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>.","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>."},"article_type":"original","year":"2025","oa_version":"Published Version","publisher":"Elsevier","month":"06","author":[{"last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501"},{"full_name":"Semenov, Nikolai","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b","first_name":"Nikolai","last_name":"Semenov"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"},{"orcid":"0000-0003-2311-2112","full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239"},{"full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854"},{"id":"EE8452B8-C26A-11E9-B157-E80CE6697425","first_name":"Marek","last_name":"Suplata","full_name":"Suplata, Marek"},{"orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lyudchik, Julia","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"last_name":"Wartak","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","first_name":"Andreas","full_name":"Wartak, Andreas"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","full_name":"Schur, Florian Km","orcid":"0000-0003-4790-8078"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}]},{"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file":[{"file_size":11899491,"relation":"source_file","file_id":"18983","creator":"odragano","access_level":"closed","content_type":"application/zip","file_name":"Thesis.zip","date_updated":"2025-01-31T16:58:30Z","checksum":"af6567e5d35e5eb330b8925ae37f1998","date_created":"2025-01-31T16:58:30Z"},{"file_name":"Thesis.pdf","date_updated":"2025-02-04T16:22:07Z","content_type":"application/pdf","checksum":"c3fef68e35b9dc2020b2ca6006da6343","date_created":"2025-02-04T16:22:07Z","access_level":"open_access","creator":"odragano","file_id":"19000","relation":"main_file","file_size":8857514}],"doi":"10.15479/at:ista:18979","file_date_updated":"2025-02-04T16:22:07Z","acknowledgement":"The research presented in this thesis was funded with the Wittgenstein Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n","day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","ddc":["514","004"],"title":"Structures and computations in topological data analysis","abstract":[{"text":"Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe describe a construction of a chromatic alpha complex, which enables  efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot.","lang":"eng"}],"corr_author":"1","has_accepted_license":"1","keyword":["topological data analysis","chromatic point set","alpha complex","persistent homology","six pack","sheaf","microlocal discrete Morse","injective resolution","collapse","knot","discrete Morse theory"],"type":"dissertation","degree_awarded":"PhD","oa":1,"date_created":"2025-01-31T17:04:40Z","date_updated":"2026-04-07T11:47:30Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"article_processing_charge":"No","citation":{"short":"O. Draganov, Structures and Computations in Topological Data Analysis, Institute of Science and Technology Austria, 2025.","ista":"Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria.","ama":"Draganov O. Structures and computations in topological data analysis. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18979\">10.15479/at:ista:18979</a>","mla":"Draganov, Ondrej. <i>Structures and Computations in Topological Data Analysis</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18979\">10.15479/at:ista:18979</a>.","ieee":"O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025.","apa":"Draganov, O. (2025). <i>Structures and computations in topological data analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18979\">https://doi.org/10.15479/at:ista:18979</a>","chicago":"Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18979\">https://doi.org/10.15479/at:ista:18979</a>."},"_id":"18979","date_published":"2025-02-03T00:00:00Z","year":"2025","author":[{"first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","orcid":"0000-0003-0464-3823","full_name":"Draganov, Ondrej"}],"oa_version":"Published Version","month":"02","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"page":"140","related_material":{"record":[{"relation":"part_of_dissertation","id":"15091","status":"public"},{"status":"public","id":"18981","relation":"part_of_dissertation"}]},"project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}]},{"file":[{"file_size":39735535,"file_id":"20228","relation":"source_file","creator":"jvorlauf","date_updated":"2025-08-25T13:49:55Z","checksum":"191db3367c19c9b32b65f4bc3a7c19de","date_created":"2025-08-25T13:49:55Z","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"file_size":10947446,"file_id":"20229","relation":"main_file","success":1,"creator":"jvorlauf","date_updated":"2025-08-25T13:49:56Z","file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","date_created":"2025-08-25T13:49:56Z","content_type":"application/pdf","checksum":"104400e6036921569610230c1d4899dc","access_level":"open_access"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"OA_place":"publisher","file_date_updated":"2025-08-25T13:49:56Z","doi":"10.15479/AT-ISTA-20206","publication_status":"published","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"25","acknowledgement":"The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. ","ddc":["621","535"],"title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n"}],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"date_created":"2025-08-22T08:12:55Z","date_updated":"2026-04-07T11:48:07Z","oa":1,"date_published":"2025-08-25T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"_id":"20206","article_processing_charge":"No","citation":{"apa":"Vorlaufer, J. (2025). <i>Construction of a cryo-super-resolution microscope to guide in situ structure analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>","chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20206\">https://doi.org/10.15479/AT-ISTA-20206</a>.","ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>","mla":"Vorlaufer, Jakob. <i>Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20206\">10.15479/AT-ISTA-20206</a>.","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria.","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025."},"year":"2025","month":"08","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"project":[{"grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination"}],"related_material":{"record":[{"status":"public","id":"19795","relation":"part_of_dissertation"}]},"page":"107","alternative_title":["ISTA Thesis"]},{"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"19398","relation":"part_of_dissertation"},{"status":"public","id":"19399","relation":"part_of_dissertation"},{"id":"12291","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14826","relation":"part_of_dissertation"}]},"page":"160","publication_identifier":{"eisbn":["978-3-99078-054-1"],"eissn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"year":"2025","author":[{"full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"03","date_updated":"2026-04-07T11:48:32Z","date_created":"2025-03-12T14:25:42Z","oa":1,"supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"citation":{"chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>.","apa":"Monzer, A. (2025). <i>Cell-Surface Auxin Signaling: Linking molecular pathways to plant development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>","mla":"Monzer, Aline. <i>Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>.","ieee":"A. Monzer, “Cell-Surface Auxin Signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","ama":"Monzer A. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>","ista":"Monzer A. 2025. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","date_published":"2025-03-13T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"_id":"19395","type":"dissertation","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood.","lang":"eng"}],"acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research.","day":"13","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Cell-Surface Auxin Signaling: Linking molecular pathways to plant development","ddc":["580"],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file":[{"file_size":13119670,"file_id":"19396","relation":"main_file","success":1,"creator":"amonzer","content_type":"application/pdf","checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7","file_name":"Final Thesis Aline Monzer.pdf","date_updated":"2025-03-12T14:14:49Z","date_created":"2025-03-12T14:14:49Z","access_level":"open_access"},{"creator":"amonzer","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis Aline.docx","checksum":"a353ce1ee2eabce37bca35499e76dbf1","date_created":"2025-03-12T14:15:19Z","date_updated":"2025-04-01T07:55:27Z","file_size":13774837,"relation":"source_file","file_id":"19397"}],"doi":"10.15479/AT-ISTA-19395","file_date_updated":"2025-04-01T07:55:27Z"},{"year":"2025","oa_version":"Published Version","publisher":"Cold Spring Harbor Laboratory","month":"03","author":[{"first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","full_name":"Monzer, Aline"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"full_name":"Zou, Minxia","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou"},{"full_name":"Smejkal, Michael","first_name":"Michael","id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9","last_name":"Smejkal"},{"full_name":"Cervenova, Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f","first_name":"Ema","last_name":"Cervenova"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"date_updated":"2026-04-07T11:48:31Z","date_created":"2025-03-12T14:28:53Z","oa":1,"date_published":"2025-03-02T00:00:00Z","_id":"19398","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"No","citation":{"ista":"Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","short":"A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.).","chicago":"Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>.","apa":"Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>","mla":"Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","ieee":"A. Monzer <i>et al.</i>, “TMK interacting network of receptor like kinases for auxin canalization and beyond,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ama":"Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>"},"related_material":{"record":[{"status":"public","id":"19395","relation":"dissertation_contains"}]},"status":"public","language":[{"iso":"eng"}],"publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"02","acknowledgement":"We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance.","publication":"bioRxiv","title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"OA_place":"repository","OA_type":"green","doi":"10.1101/2025.02.28.640727","type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2025.02.28.640727","open_access":"1"}],"corr_author":"1","has_accepted_license":"1","abstract":[{"text":"Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.","lang":"eng"}]},{"abstract":[{"text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies.","lang":"eng"}],"corr_author":"1","has_accepted_license":"1","type":"dissertation","degree_awarded":"PhD","file":[{"date_updated":"2025-03-12T12:56:46Z","checksum":"d3ab25782c7ea38ce9910e57d25f6733","date_created":"2025-03-12T12:56:46Z","file_name":"thesis_final.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"vkarle","file_id":"19394","relation":"main_file","file_size":10625143},{"relation":"source_file","file_id":"19400","file_size":23119202,"access_level":"closed","checksum":"3ccfb0aeba4d860d71e18347913034e4","content_type":"application/zip","file_name":"thesis.zip","date_updated":"2025-03-20T08:02:35Z","date_created":"2025-03-13T13:15:10Z","creator":"vkarle"}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"OA_place":"publisher","file_date_updated":"2025-03-20T08:02:35Z","OA_type":"gold","doi":"10.15479/AT-ISTA-19393","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","day":"13","title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","ddc":["530"],"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"14851","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12788","status":"public"},{"id":"19425","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9903","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15004"}]},"page":"192","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko"}],"oa":1,"date_created":"2025-03-12T13:04:59Z","date_updated":"2026-04-07T11:48:53Z","_id":"19393","date_published":"2025-03-13T00:00:00Z","article_processing_charge":"No","citation":{"ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025.","apa":"Karle, V. (2025). <i>Non-equilibrium topological phases with periodically driven molecules and quantum rotors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19393\">https://doi.org/10.15479/AT-ISTA-19393</a>.","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025.","mla":"Karle, Volker. <i>Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19393\">10.15479/AT-ISTA-19393</a>."},"year":"2025","oa_version":"Published Version","month":"03","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","full_name":"Karle, Volker","orcid":"0000-0002-6963-0129"}]},{"ec_funded":1,"file":[{"creator":"jsvoboda","success":1,"access_level":"open_access","date_updated":"2025-08-14T09:54:43Z","date_created":"2025-08-14T09:54:43Z","checksum":"c6c4df9777f4537940de7ab392ad57e2","content_type":"application/pdf","file_name":"2025_Svoboda_Jakub_Thesis.pdf","file_size":5927291,"relation":"main_file","file_id":"20177"},{"creator":"jsvoboda","access_level":"closed","content_type":"application/zip","checksum":"485e9f9822821bc03666d245d80aaa08","date_updated":"2025-08-21T11:48:39Z","file_name":"2025_Svoboda_Jakub_Thesis.zip","date_created":"2025-08-14T09:55:20Z","file_size":6731815,"relation":"source_file","file_id":"20178"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"OA_place":"publisher","file_date_updated":"2025-08-21T11:48:39Z","doi":"10.15479/AT-ISTA-20138","publication_status":"published","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n","day":"05","ddc":["000","519"],"title":"Structural properties of games on graphs","has_accepted_license":"1","corr_author":"1","abstract":[{"text":"The evolution shapes the world around us.\r\nNot only in biology, where the fittest individuals spread their genes but also in physics and social dynamics, the evolutionary forces determine the development of a state of matter or public opinions.\r\nMany models describe these dynamics.\r\nThis thesis examines the role of the structure in the models of selection.\r\nThe population structure is represented as a graph or a network, and each vertex is occupied by one individual.\r\nEvery individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors.\r\nThe evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness.\r\n\r\n\r\n\r\nThe role of the networks is widely examined in the literature.\r\nThe structures that promote the spread of the desired type compared to the structureless case are called amplifiers.\r\nThe existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified.\r\nMoreover, there are other important questions about the number of steps until one type spreads over the whole network (fixation time), the computational complexity, and the questions about the robustness of these processes.\r\n\r\n\r\nThis thesis explores the role of structure in evolution from many perspectives.\r\nFirst, it introduces different models and various choices that can be made in the models of evolution.\r\nIt highlights the role of the structure in the real world and how this is reflected in these models.\r\nThen, it describes the previous results and open problems.\r\nSecond, the thesis describes an amplifier for two variants of the Moran process: one with a constant birth rate and the other with a constant death rate.\r\nThis is an important contribution to the robustness of the amplification.\r\nThird, the thesis determines the complexity of spatial games.\r\nThese are processes where the fitness comes from a game, and the strength of selection is high.\r\nIt shows that determining the fate of cooperation in these games is a PSPACE-complete problem.\r\nFourth, the thesis describes the amplifier of cooperation for spatial games.\r\nThis is the first amplifier in this setting.\r\nFifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity.\r\nIn this setting, the fitness depends not only on the type of the individual but also on the occupied vertex.\r\nThe chapter determines the relationship between the interactions of vertices of different types and the coexistence time.\r\nSixth, the thesis examines the social balance on networks and proposes a stochastic dynamic partially aware of the state of the graph, which reaches a balanced position quickly.\r\nFinally, the thesis presents conclusions and outlines the directions for future work.\r\n\r\n\r\n","lang":"eng"}],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"date_created":"2025-08-05T14:33:59Z","date_updated":"2026-04-07T11:49:12Z","oa":1,"date_published":"2025-08-05T00:00:00Z","_id":"20138","article_processing_charge":"No","citation":{"ista":"Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria.","short":"J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025.","apa":"Svoboda, J. (2025). <i>Structural properties of games on graphs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20138\">https://doi.org/10.15479/AT-ISTA-20138</a>","chicago":"Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20138\">https://doi.org/10.15479/AT-ISTA-20138</a>.","ama":"Svoboda J. Structural properties of games on graphs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20138\">10.15479/AT-ISTA-20138</a>","ieee":"J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025.","mla":"Svoboda, Jakub. <i>Structural Properties of Games on Graphs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20138\">10.15479/AT-ISTA-20138</a>."},"year":"2025","publisher":"Institute of Science and Technology Austria","month":"08","oa_version":"Published Version","author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"}],"status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"related_material":{"record":[{"id":"12787","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"12101","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"12257"},{"id":"15297","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18703","relation":"part_of_dissertation"}]},"page":"167","alternative_title":["ISTA Thesis"]},{"supervisor":[{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"date_updated":"2026-04-07T11:49:34Z","date_created":"2025-08-04T15:24:21Z","_id":"20117","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_published":"2025-08-04T00:00:00Z","citation":{"ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>."},"article_processing_charge":"No","year":"2025","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"08","author":[{"id":"82F537F2-B517-11E9-84D7-6433E6697425","first_name":"Yiqun","last_name":"Wang","full_name":"Wang, Yiqun"}],"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18063"}]},"page":"108","alternative_title":["ISTA Thesis"],"file":[{"access_level":"closed","date_created":"2025-08-22T08:22:10Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"36b87c17d12c7bf5955d6d812acb8d77","file_name":"2025_Wang_Yiqun_Thesis.docx","date_updated":"2025-08-22T08:53:46Z","creator":"yiqwang","relation":"source_file","file_id":"20209","file_size":25798848},{"file_size":12628313,"embargo_to":"open_access","relation":"main_file","file_id":"20211","creator":"yiqwang","embargo":"2026-09-03","access_level":"closed","checksum":"8d7a2383f66377da675d379ec30ea0fe","content_type":"application/pdf","file_name":"2025_Wang_Yiqun_Thesis.pdf","date_created":"2025-08-22T10:32:30Z","date_updated":"2025-09-03T09:36:52Z"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2025-09-03T09:36:52Z","doi":"10.15479/AT-ISTA-20117","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","day":"04","ddc":["580"],"title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","has_accepted_license":"1","corr_author":"1","type":"dissertation","degree_awarded":"PhD"},{"status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"15039","status":"public"},{"status":"public","id":"18874","relation":"part_of_dissertation"},{"id":"17426","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11839"}]},"page":"84","date_updated":"2026-04-07T11:49:52Z","date_created":"2025-05-28T16:20:48Z","oa":1,"supervisor":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"article_processing_charge":"No","citation":{"ama":"Prach B. Robust image classification with 1-Lipschitz networks. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>","ieee":"B. Prach, “Robust image classification with 1-Lipschitz networks,” Institute of Science and Technology Austria, 2025.","mla":"Prach, Bernd. <i>Robust Image Classification with 1-Lipschitz Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>.","apa":"Prach, B. (2025). <i>Robust image classification with 1-Lipschitz networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>","chicago":"Prach, Bernd. “Robust Image Classification with 1-Lipschitz Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>.","short":"B. Prach, Robust Image Classification with 1-Lipschitz Networks, Institute of Science and Technology Austria, 2025.","ista":"Prach B. 2025. Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria."},"date_published":"2025-05-30T00:00:00Z","_id":"19759","year":"2025","author":[{"full_name":"Prach, Bernd","first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach"}],"month":"05","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"Despite generating remarkable results in various computer vision tasks, deep learning comes\r\nwith some surprising shortcomings. For example, tiny perturbations, often imperceptible to\r\nthe human eye, can completely change the predictions of image classifiers. Despite a decade\r\nof research, the field has made limited progress in developing image classifiers that are both\r\naccurate and robust. This thesis aims to address this gap.\r\nAs our first contribution, we aim to simplify the process of training certifiably robust image\r\nclassifiers. We do this by designing a convolutional layer that does not require executing an\r\niterative procedure in every forward pass, but relies on an explicit bound instead. We also\r\npropose a loss function that allows optimizing for a particular margin more precisely.\r\nNext, we provide an overview and comparison of various methods that create robust image\r\nclassifiers by constraining the Lipschitz constant. This is important since generally longer\r\ntraining times and more parameters improve the performance of robust classifiers, making it\r\nchallenging to determine the most practical and effective methods from existing literature.\r\nIn 1-Lipschitz classification, the performance of current methods is still much worse than what\r\nwe expect on the simple tasks we consider. Therefore, we next investigate potential causes of\r\nthis shortcoming. We first consider the role of the activation function. We prove a theoretical\r\nshortcoming of the commonly used activation function, and provide an alternative without it.\r\nHowever this theoretical improvement does barely translate to the empirical performance of\r\nrobust classifiers, suggesting a different bottleneck.\r\nTherefore, in the final chapter, we study how the performance depends on the amount of\r\ntraining data. We prove that in the worst case, we might require far more data to train a\r\nrobust classifier compared to a normal one. We furthermore find that the amount of training\r\ndata is a key determinant of the performance current methods achieve on popular datasets.\r\nAdditionally, we show that linear subspaces exist with tiny data variance, and yet we can\r\nstill train very accurate classifiers after projecting into those subspaces. This shows that on\r\nthe datasets considered, enforcing robustness in classification makes the task strictly more\r\nchallenging.\r\n\r\n-----------------“In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of [name of university or educational entity]’s products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.”\r\n"}],"type":"dissertation","degree_awarded":"PhD","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file":[{"relation":"main_file","file_id":"19829","file_size":3578077,"access_level":"open_access","checksum":"e5108e759014e2a9020c973c778fafc9","content_type":"application/pdf","file_name":"ThesisFinal.pdf","date_created":"2025-06-10T18:11:05Z","date_updated":"2025-06-10T18:11:05Z","creator":"bprach"},{"access_level":"closed","date_updated":"2025-06-10T18:14:03Z","date_created":"2025-06-10T18:14:03Z","content_type":"application/x-zip-compressed","file_name":"ThesisFinal.zip","checksum":"51bf6c11fb6d8a9f8010b458c600a83f","creator":"bprach","relation":"source_file","file_id":"19830","file_size":74894357}],"doi":"10.15479/10.15479/at-ista-19759","file_date_updated":"2025-06-10T18:14:03Z","day":"30","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["000"],"title":"Robust image classification with 1-Lipschitz networks"},{"degree_awarded":"PhD","type":"dissertation","has_accepted_license":"1","corr_author":"1","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","day":"13","acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","file_date_updated":"2025-09-18T14:12:29Z","doi":"10.15479/AT-ISTA-20167","file":[{"creator":"hschoen","file_name":"2025_Schoen_Hanna_Thesis.docx","checksum":"b40c74404b8d9593802dabf57bfdf10f","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-09T08:57:04Z","date_created":"2025-09-08T14:33:50Z","access_level":"closed","file_size":78812587,"file_id":"20311","relation":"source_file"},{"embargo_to":"open_access","file_size":9667057,"file_id":"20347","relation":"main_file","creator":"hschoen","date_updated":"2025-09-18T14:12:29Z","date_created":"2025-09-11T14:20:59Z","content_type":"application/pdf","checksum":"16abc3ff66396ce2457fe07ffa8bed90","file_name":"2025_Schoen_Hanna_Thesis.pdf","embargo":"2026-09-15","access_level":"closed"}],"department":[{"_id":"GradSch"},{"_id":"MaDe"}],"OA_place":"publisher","page":"171","project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"name":"Control of gene expression at the endoplasmic reticulum","grant_number":"ALTF 302-2019","_id":"23813290-32DE-11EA-91FC-C7463DDC885E"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"isbn":["978-3-99078-061-9"],"issn":["2663-337X"]},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","month":"08","author":[{"last_name":"Schön","first_name":"Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","full_name":"Schön, Hanna"}],"year":"2025","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"20167","date_published":"2025-08-13T00:00:00Z","article_processing_charge":"No","citation":{"mla":"Schön, Hanna. <i>The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>","chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>.","apa":"Schön, H. (2025). <i>The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>","short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria."},"supervisor":[{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"date_created":"2025-08-13T11:13:13Z","date_updated":"2026-04-07T11:50:26Z"},{"corr_author":"1","has_accepted_license":"1","abstract":[{"text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.","lang":"eng"}],"volume":123,"scopus_import":"1","quality_controlled":"1","type":"journal_article","file_date_updated":"2025-09-01T14:09:31Z","pmid":1,"OA_type":"hybrid","doi":"10.1111/tpj.70396","file":[{"file_size":5791111,"file_id":"20264","relation":"main_file","creator":"dernst","success":1,"date_created":"2025-09-01T14:09:31Z","content_type":"application/pdf","date_updated":"2025-09-01T14:09:31Z","checksum":"1cdc3341d2d23101abca72521f1f23cb","file_name":"2025_PlantJournal_Babic.pdf","access_level":"open_access"}],"OA_place":"publisher","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"publication":"Plant Journal","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","ddc":["580"],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"status":"public","PlanS_conform":"1","language":[{"iso":"eng"}],"issue":"3","external_id":{"isi":["001547884300001"],"pmid":["40782342"]},"article_number":"e70396","intvolume":"       123","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}],"related_material":{"record":[{"status":"public","id":"20362","relation":"dissertation_contains"}]},"date_published":"2025-08-01T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"_id":"20187","citation":{"ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>.","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>."},"article_processing_charge":"Yes (via OA deal)","date_created":"2025-08-17T22:01:36Z","date_updated":"2026-04-07T11:52:02Z","oa":1,"oa_version":"Published Version","publisher":"Wiley","month":"08","author":[{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","last_name":"Babic","full_name":"Babic, David"},{"orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia"},{"last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"full_name":"Tellier, Frédérique","last_name":"Tellier","first_name":"Frédérique"},{"last_name":"Smoljan","id":"cced8a85-223e-11ed-af04-b0596c55053b","first_name":"Adrijana","full_name":"Smoljan, Adrijana"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA"},{"last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Valošek, Petr"},{"full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Faure","first_name":"Jean Denis","full_name":"Faure, Jean Denis"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_type":"original","isi":1,"year":"2025"},{"author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","last_name":"Babic"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"09","year":"2025","article_processing_charge":"No","citation":{"ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>.","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"20362","date_published":"2025-09-18T00:00:00Z","date_updated":"2026-04-07T11:52:02Z","date_created":"2025-09-17T13:28:01Z","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"alternative_title":["ISTA Thesis"],"page":"116","related_material":{"record":[{"relation":"part_of_dissertation","id":"20187","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","ddc":["580"],"title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","doi":"10.15479/AT-ISTA-20362","file_date_updated":"2025-09-26T07:29:11Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"file":[{"embargo":"2026-09-25","access_level":"closed","checksum":"5ecf274281a54a41e0288bc79edf7492","file_name":"2025_David_Babic_Thesis.pdf","content_type":"application/pdf","date_updated":"2025-09-26T07:29:11Z","date_created":"2025-09-24T13:43:14Z","creator":"dbabic","relation":"main_file","file_id":"20388","embargo_to":"open_access","file_size":7501548},{"creator":"dbabic","access_level":"closed","date_created":"2025-09-24T13:43:14Z","checksum":"2703e548390de0a1af7a707137e8ab3b","date_updated":"2025-09-26T07:29:11Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Babic_draft.docx","file_size":23206052,"relation":"source_file","file_id":"20389"}],"degree_awarded":"PhD","type":"dissertation","corr_author":"1","has_accepted_license":"1"},{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Cell surface receptor complexes for auxin signaling in plants","_id":"26060676-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 985-2016"}],"related_material":{"record":[{"relation":"later_version","id":"20656","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19395"},{"status":"public","id":"20364","relation":"dissertation_contains"}]},"status":"public","language":[{"iso":"eng"}],"year":"2025","oa_version":"Published Version","publisher":"Cold Spring Harbor Laboratory","month":"02","author":[{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"full_name":"Zou, Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia"},{"full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii","last_name":"Vladimirtsev","full_name":"Vladimirtsev, Dmitrii"},{"full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch"},{"last_name":"Yu","first_name":"Yongfan","full_name":"Yu, Yongfan"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","last_name":"Gelová"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"full_name":"Chen, Meng","last_name":"Chen","first_name":"Meng"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan"},{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Marques-Bueno, Maria Mar","last_name":"Marques-Bueno","first_name":"Maria Mar"},{"full_name":"Quddoos, Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","first_name":"Zainab","last_name":"Quddoos"},{"first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"full_name":"Jaillais, Yvon","first_name":"Yvon","last_name":"Jaillais"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"date_created":"2025-03-13T08:36:48Z","date_updated":"2026-04-07T11:52:15Z","oa":1,"date_published":"2025-02-20T00:00:00Z","_id":"19399","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"citation":{"ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.).","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>."},"article_processing_charge":"No","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"corr_author":"1","abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.","lang":"eng"}],"publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","acknowledgement":"We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).","publication":"bioRxiv","title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","ec_funded":1,"OA_place":"repository","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"OA_type":"green","doi":"10.1101/2022.11.30.518503"},{"author":[{"last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","month":"10","year":"2025","citation":{"chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>.","apa":"Lee, S. (2025). <i>Nanoparticle-based precursors toward advanced crystalline inorganic solids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>","mla":"Lee, Seungho. <i>Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>.","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","date_published":"2025-10-01T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"_id":"20415","date_updated":"2026-04-07T11:52:32Z","date_created":"2025-10-01T09:04:00Z","supervisor":[{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Protesescu, Loredana","last_name":"Protesescu","first_name":"Loredana"},{"last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"alternative_title":["ISTA Thesis"],"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"related_material":{"record":[{"id":"15357","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12237","status":"public"}]},"page":"144","publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"ddc":["540"],"title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids","day":"01","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-20415","file_date_updated":"2025-10-07T08:57:14Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"file":[{"access_level":"closed","date_updated":"2025-10-07T08:57:14Z","file_name":"2025_Lee_Seungho_Thesis.docx","checksum":"fa6d5946feb37b678ee1c6dffb4fa167","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-10-03T12:29:43Z","creator":"slee","relation":"source_file","file_id":"20420","file_size":88706648},{"creator":"slee","access_level":"closed","embargo":"2026-10-03","date_updated":"2025-10-03T12:29:25Z","file_name":"2025_Lee_Seungho_Thesis__.pdf","date_created":"2025-10-03T12:29:25Z","checksum":"c5ba6d464113ad0c5812a9d24b539b86","content_type":"application/pdf","file_size":14587276,"embargo_to":"open_access","relation":"main_file","file_id":"20421"}],"degree_awarded":"PhD","type":"dissertation","has_accepted_license":"1","corr_author":"1"},{"date_published":"2025-09-19T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"_id":"20364","article_processing_charge":"No","citation":{"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.","ama":"Giannini C. 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>","mla":"Giannini, Caterina. <i>Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">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.","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>."},"supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"date_updated":"2026-04-07T11:52:16Z","date_created":"2025-09-19T12:23:38Z","publisher":"Institute of Science and Technology Austria","month":"09","oa_version":"Published Version","author":[{"full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"}],"year":"2025","status":"public","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"12291","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"19399","relation":"part_of_dissertation"}]},"page":"151","alternative_title":["ISTA Thesis"],"file_date_updated":"2025-09-30T14:31:29Z","doi":"10.15479/AT-ISTA-20364","file":[{"embargo_to":"open_access","file_size":14278965,"relation":"main_file","file_id":"20390","creator":"cgiannin","embargo":"2026-09-30","access_level":"closed","content_type":"application/pdf","checksum":"536ba1701453b0b2346be14c046b2911","file_name":"2025_Giannini_Caterina_Thesis...pdf","date_created":"2025-09-24T14:46:34Z","date_updated":"2025-09-30T14:31:29Z"},{"creator":"cgiannin","date_updated":"2025-09-24T14:46:35Z","date_created":"2025-09-24T14:46:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_Giannini_Caterina_Thesis...docx","checksum":"192f55262f2da2ea0a59d9c23a1b8573","access_level":"closed","file_size":24499022,"file_id":"20391","relation":"source_file"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","ddc":["580"],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"Plant Facility,\r\nProtein Service Facility","day":"19","keyword":["Auxin Signaling","Plant Development"],"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","type":"dissertation"},{"file":[{"access_level":"open_access","date_updated":"2025-10-28T13:10:08Z","date_created":"2025-10-28T13:10:08Z","file_name":"Thesis_PDFA_.pdf","checksum":"2892f04d4a5c18677871c3e06ac1244a","content_type":"application/pdf","success":1,"creator":"snaik","relation":"main_file","file_id":"20567","file_size":6846189},{"relation":"source_file","file_id":"20568","file_size":8839300,"access_level":"open_access","file_name":"Thesis.zip","date_updated":"2025-10-28T13:10:26Z","checksum":"15934d4465cd0e9b7c32678da9a33a2f","content_type":"application/zip","date_created":"2025-10-28T13:10:26Z","creator":"snaik"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2025-10-28T13:10:26Z","doi":"10.15479/AT-ISTA-20441","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"day":"12","acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","ddc":["596","597","532"],"title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","has_accepted_license":"1","corr_author":"1","abstract":[{"text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium.","lang":"eng"}],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"date_updated":"2026-04-07T11:58:57Z","date_created":"2025-10-10T14:58:30Z","oa":1,"date_published":"2025-10-12T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"20441","citation":{"ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.","apa":"Naik, S. (2025). <i>Keratins act as global coordinators of tissue spreading through mechanosensitive feedback</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>","chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>.","ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>","mla":"Naik, Suyash. <i>Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>.","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025."},"article_processing_charge":"No","year":"2025","month":"10","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash","last_name":"Naik"}],"status":"public","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-069-5"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"25AA5F24-B435-11E9-9278-68D0E5697425","grant_number":"W 1250-B20"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"20465","status":"public"}]},"page":"105","alternative_title":["ISTA Thesis"]},{"ddc":["570"],"title":"Dissecting gap junction biology using the C. elegans nervous system","day":"23","acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","doi":"10.15479/AT-ISTA-20485","file_date_updated":"2025-11-06T11:08:06Z","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"OA_place":"publisher","file":[{"file_size":75070995,"file_id":"20518","relation":"source_file","creator":"mmisova","file_name":"2025-Misova-Michaela-Thesis.docx","date_created":"2025-10-23T08:22:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"e042ea314e7e13fce76c6c95e126779a","date_updated":"2025-11-06T11:08:06Z","access_level":"closed"},{"date_updated":"2025-10-23T08:21:21Z","file_name":"2025-Misova-Michaela-Thesis.pdf","date_created":"2025-10-23T08:21:21Z","checksum":"fcd8973d6a025256eb0eb1a82c02172c","content_type":"application/pdf","embargo":"2026-10-23","access_level":"closed","creator":"mmisova","file_id":"20519","relation":"main_file","file_size":10974630,"embargo_to":"open_access"}],"ec_funded":1,"degree_awarded":"PhD","type":"dissertation","has_accepted_license":"1","corr_author":"1","author":[{"full_name":"Misova, Michaela","orcid":"0000-0003-2427-6856","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","first_name":"Michaela","last_name":"Misova"}],"month":"10","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","year":"2025","article_processing_charge":"No","citation":{"apa":"Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans nervous system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20485\">https://doi.org/10.15479/AT-ISTA-20485</a>.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025.","mla":"Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20485\">10.15479/AT-ISTA-20485</a>.","ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria.","short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025."},"_id":"20485","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_published":"2025-10-23T00:00:00Z","date_updated":"2026-04-07T11:54:00Z","date_created":"2025-10-17T16:15:09Z","supervisor":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"}],"alternative_title":["ISTA Thesis"],"page":"155","project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-068-8"],"issn":["2663-337X"]},"status":"public"},{"status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2025.02.14.638262","open_access":"1"}],"language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"text":"For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"20441","relation":"dissertation_contains"}]},"type":"preprint","license":"https://creativecommons.org/licenses/by-nd/4.0/","OA_place":"repository","date_updated":"2026-04-07T11:58:57Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"date_created":"2025-10-14T07:25:27Z","oa":1,"date_published":"2025-02-17T00:00:00Z","_id":"20465","article_processing_charge":"No","citation":{"apa":"Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &#38; Heisenberg, C.-P. J. (n.d.). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>","chicago":"Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo, Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>.","ama":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>","mla":"Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>.","ieee":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P. J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>.","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, BioRxiv (n.d.)."},"doi":"10.1101/2025.02.14.638262","publication_status":"draft","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"day":"17","year":"2025","month":"02","publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","author":[{"id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash","last_name":"Naik","full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508"},{"last_name":"Keta","first_name":"Yann-Edwin","full_name":"Keta, Yann-Edwin"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henkes","first_name":"Silke","full_name":"Henkes, Silke"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"publication":"bioRxiv"},{"keyword":["asteroseismology","stellar physics","red giant","magnetism","suppressed"],"has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"The internal dynamical properties of red giant stars have been explored extensively in recent\r\nyears as a result of the increase in high precision data availability from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been\r\ndiscovered that some of these stars are not behaving as expected. Red giants are stars that have\r\nevolved off of the main sequence after having completed fusing hydrogen into helium in their\r\ncore. Observational data shows that the cores are rotating significantly slower than models can\r\nrecreate consistently across evolutionary stages. This discrepancy has prompted investigation\r\ninto the efficiency of angular momentum transport mechanisms and mixing processes including\r\nmeridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc., to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only\r\nway in which the deep stellar interior can be probed and subsequently characterized; this is\r\npossible as global oscillations modulating the stellar surface are effected by internal processes.\r\nFor red giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes; resonating in the radiative interior) couple to create mixed modes. These\r\nmixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two\r\ndifferent power laws, respectively. And the other being a reduced visibility of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted; one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of\r\ntheir power spectra rather than across the entire spectra, will be the subject of this study as\r\nthe respective mode amplitudes are still visible at high frequencies.\r\nAs such, this study will search for asymmetric frequency shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the aim here is to investigate if both\r\nmode suppression and magnetic shifting of dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038,\r\na target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its\r\nmagnetic parameters. I present a novel method to model the stellar power spectra of\r\npartially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With the results of this study I aim at constraining\r\nthe cause of this partial dipole mode amplitude suppression, allowing for more detailed\r\nstudies regarding their astrophysical nature. Furthermore, the long term hope for the method\r\nused in this study will be to expand the sample of partially suppressed red giants and fit their\r\nasteroseismic parameters accordingly."}],"degree_awarded":"MS","type":"dissertation","file_date_updated":"2025-10-09T14:38:57Z","doi":"10.15479/AT-ISTA-19853","file":[{"file_id":"20434","relation":"source_file","file_size":8263624,"date_created":"2025-10-08T08:01:42Z","file_name":"2025_Smith_Kanah_Thesis.zip","content_type":"application/zip","checksum":"80d241d11b69af771c1fab0998be4f19","date_updated":"2025-10-08T09:45:33Z","access_level":"closed","creator":"ksmith"},{"file_size":9748339,"relation":"main_file","file_id":"20439","creator":"ksmith","success":1,"access_level":"open_access","file_name":"2025_Smith_Kanah_Thesis.pdf","date_created":"2025-10-09T14:38:57Z","checksum":"13cb48cc98e00fdfe32f3ff66f17aa26","content_type":"application/pdf","date_updated":"2025-10-09T14:38:57Z"}],"department":[{"_id":"GradSch"},{"_id":"LiBu"}],"OA_place":"publisher","ddc":["520"],"title":"Exploring internal magnetism in partially suppressed red giant stars","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"08","acknowledgement":"I would like to give thanks to myself for my hard work on this document. This paper includes data collected by the Kepler mission and obtained from the MAST data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is operated by the Association of\r\nUniversities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.\r\n","status":"public","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"page":"38","alternative_title":["ISTA Master's Thesis"],"date_published":"2025-10-08T00:00:00Z","_id":"19853","article_processing_charge":"No","citation":{"ista":"Smith K. 2025. Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria.","short":"K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant Stars, Institute of Science and Technology Austria, 2025.","chicago":"Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red Giant Stars.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>.","apa":"Smith, K. (2025). <i>Exploring internal magnetism in partially suppressed red giant stars</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19853\">https://doi.org/10.15479/AT-ISTA-19853</a>","ieee":"K. Smith, “Exploring internal magnetism in partially suppressed red giant stars,” Institute of Science and Technology Austria, 2025.","mla":"Smith, Kanah. <i>Exploring Internal Magnetism in Partially Suppressed Red Giant Stars</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>.","ama":"Smith K. Exploring internal magnetism in partially suppressed red giant stars. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19853\">10.15479/AT-ISTA-19853</a>"},"supervisor":[{"orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet"}],"date_created":"2025-06-20T13:27:08Z","date_updated":"2026-04-07T12:01:37Z","oa":1,"publisher":"Institute of Science and Technology Austria","month":"10","oa_version":"Published Version","author":[{"id":"7703505d-3211-11ee-a6a9-a2ab9d936c15","first_name":"Kanah","last_name":"Smith","full_name":"Smith, Kanah"}],"year":"2025"}]