[{"month":"10","issue":"19","file_date_updated":"2024-01-10T12:41:13Z","article_processing_charge":"Yes (via OA deal)","isi":1,"language":[{"iso":"eng"}],"volume":150,"quality_controlled":"1","ddc":["570"],"year":"2023","has_accepted_license":"1","intvolume":"       150","publication_status":"published","publisher":"Company of Biologists","type":"journal_article","citation":{"mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. Company of Biologists, 2023.","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559."},"abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"doi":"10.1242/dev.201559","article_type":"original","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","department":[{"_id":"AnKi"}],"day":"01","author":[{"id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","full_name":"Harish, Rohit K","last_name":"Harish","first_name":"Rohit K"},{"full_name":"Gupta, Mansi","first_name":"Mansi","last_name":"Gupta"},{"full_name":"Zöller, Daniela","first_name":"Daniela","last_name":"Zöller"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"full_name":"Machate, Anja","last_name":"Machate","first_name":"Anja"},{"last_name":"Hans","first_name":"Stefan","full_name":"Hans, Stefan"},{"last_name":"Brand","first_name":"Michael","full_name":"Brand, Michael"}],"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Developmental Biology","Molecular Biology"],"date_updated":"2026-08-12T09:59:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Development","file":[{"file_id":"14790","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2024-01-10T12:41:13Z","file_size":12836306,"date_created":"2024-01-10T12:41:13Z","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","relation":"main_file","file_name":"2023_Development_Harish.pdf","creator":"dernst"}],"article_number":"dev201559","oa_version":"Published Version","date_created":"2024-01-10T09:18:54Z","pmid":1,"_id":"14774","external_id":{"isi":["001097449100002"],"pmid":["37665167"]},"oa":1,"date_published":"2023-10-01T00:00:00Z","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]}},{"intvolume":"        20","has_accepted_license":"1","publisher":"Royal Society","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident."}],"citation":{"apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., &#38; Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>","mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society Interface</i>, vol. 20, no. 208, 20230355, Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>.","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” <i>Journal of the Royal Society Interface</i>, vol. 20, no. 208. Royal Society, 2023.","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface. 20(208), 20230355.","chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2023. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>.","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society Interface</i>. 2023;20(208). doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society Interface 20 (2023)."},"doi":"10.1098/rsif.2023.0355","scopus_import":"1","issue":"208","file_date_updated":"2023-12-11T11:10:32Z","month":"11","isi":1,"article_processing_charge":"Yes (in subscription journal)","volume":20,"language":[{"iso":"eng"}],"ddc":["000","570"],"year":"2023","quality_controlled":"1","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2023-12-11T11:10:32Z","file_id":"14673","file_name":"2023_RoyalInterface_Tkadlec.pdf","creator":"dernst","file_size":1720243,"checksum":"2eefab13127c7786dbd33303c482a004","date_created":"2023-12-11T11:10:32Z","relation":"main_file"}],"publication":"Journal of the Royal Society Interface","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"pmid":1,"_id":"14657","article_number":"20230355","oa_version":"Published Version","date_created":"2023-12-10T23:00:58Z","external_id":{"pmid":["38016637"],"isi":["001124419300002"]},"oa":1,"publication_identifier":{"eissn":["1742-5662"]},"date_published":"2023-11-29T00:00:00Z","department":[{"_id":"KrCh"}],"day":"29","ec_funded":1,"article_type":"original","acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","title":"Evolutionary dynamics of mutants that modify population structure","author":[{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T14:05:25Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"No","page":"89","file_date_updated":"2024-10-29T23:31:04Z","month":"08","ddc":["570","577"],"year":"2023","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","has_accepted_license":"1","doi":"10.15479/at:ista:13984","abstract":[{"lang":"eng","text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection."}],"citation":{"apa":"Franschitz, A. (2023). <i>Individual and social immunity against viral infections in ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>","mla":"Franschitz, Anna. <i>Individual and Social Immunity against Viral Infections in Ants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023."},"alternative_title":["ISTA Thesis"],"title":"Individual and social immunity against viral infections in ants","author":[{"id":"480826C8-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Franschitz","full_name":"Franschitz, Anna"}],"day":"08","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"OA_place":"publisher","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:51:29Z","status":"public","_id":"13984","oa_version":"Published Version","date_created":"2023-08-08T15:33:29Z","file":[{"file_id":"15044","content_type":"application/pdf","date_updated":"2024-10-29T23:31:04Z","access_level":"open_access","title":"Combined Version of original Thesis and Addendum","relation":"main_file","file_size":10416761,"date_created":"2024-03-01T08:56:06Z","checksum":"55c876b73d49db15228a7f571592ec77","embargo_to":"open_access","creator":"cchlebak","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf"},{"file_name":"Thesis_AnnaFranschitz_202308.pdf","embargo":"2024-08-08","creator":"afransch","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","date_created":"2023-08-08T18:01:28Z","file_size":10797612,"relation":"main_file","access_level":"open_access","date_updated":"2024-08-09T22:30:03Z","content_type":"application/pdf","file_id":"13986"},{"file_id":"13987","access_level":"closed","date_updated":"2024-08-09T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"40abf7ccca14a3893f72dc7fb88585d6","date_created":"2023-08-08T18:02:25Z","file_size":2619085,"relation":"source_file","file_name":"Thesis_AnnaFranschitz_202308.docx","creator":"afransch","embargo_to":"open_access"},{"embargo":"2024-08-08","file_name":"Addendum_AnnaFranschitz202402.pdf","creator":"cchlebak","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","date_created":"2024-03-01T08:37:15Z","file_size":85956,"relation":"main_file","title":"Addendum","access_level":"open_access","date_updated":"2024-10-29T23:31:04Z","description":"Minor modifications and clarifications - Feb 2024","content_type":"application/pdf","file_id":"15042"},{"creator":"cchlebak","embargo_to":"open_access","file_name":"Addendum_AnnaFranschitz202402.docx","title":"Addendum - source file","relation":"source_file","checksum":"66745aa01f960f17472c024875c049ed","date_created":"2024-03-01T08:39:20Z","file_size":11818,"date_updated":"2024-08-09T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"15043"}],"publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663-337X"]},"date_published":"2023-08-08T00:00:00Z","oa":1},{"page":"187","file_date_updated":"2024-02-08T23:30:04Z","month":"02","article_processing_charge":"No","language":[{"iso":"eng"}],"ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"citation":{"chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>"},"related_material":{"record":[{"status":"public","id":"8586","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:12491","day":"02","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"OA_place":"publisher","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"date_updated":"2026-04-07T13:49:23Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"12527","access_level":"open_access","date_updated":"2024-02-08T23:30:04Z","content_type":"application/pdf","date_created":"2023-02-07T13:07:38Z","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"relation":"main_file","embargo":"2024-02-07","file_name":"PhDThesis_BettinaZens_2023_final.pdf","creator":"bzens"},{"file_id":"12528","date_updated":"2024-02-08T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"8c66ed203495d6e078ed1002a866520c","date_created":"2023-02-07T13:09:05Z","file_size":106169509,"creator":"bzens","embargo_to":"open_access","file_name":"PhDThesis_BettinaZens_2023_final.docx"}],"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"_id":"12491","oa_version":"Published Version","date_created":"2023-02-02T14:50:20Z","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"date_published":"2023-02-02T00:00:00Z"},{"article_processing_charge":"No","month":"05","page":"146","file_date_updated":"2024-05-18T22:30:03Z","year":"2023","ddc":["530"],"language":[{"iso":"eng"}],"publication_status":"published","supervisor":[{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","corr_author":"1","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"8602","status":"public"}]},"doi":"10.15479/at:ista:12964","citation":{"mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>."},"abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"author":[{"full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"title":"Mechanochemical pattern formation across biological scales","OA_place":"publisher","degree_awarded":"PhD","day":"17","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_updated":"2026-04-07T13:52:57Z","oa_version":"Published Version","date_created":"2023-05-15T14:52:36Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"_id":"12964","file":[{"date_updated":"2024-05-18T22:30:03Z","content_type":"application/pdf","access_level":"open_access","file_id":"12988","creator":"dboocock","file_name":"thesis_boocock.pdf","embargo":"2024-05-17","relation":"main_file","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","date_created":"2023-05-17T13:39:54Z","file_size":40414730},{"file_id":"12989","date_updated":"2024-05-18T22:30:03Z","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"581a2313ffeb40fe77e8a122a25a7795","date_created":"2023-05-17T13:39:53Z","file_size":34338567,"embargo_to":"open_access","creator":"dboocock","file_name":"thesis_boocock.zip"}],"date_published":"2023-05-17T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"oa":1},{"citation":{"mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>."},"abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"doi":"10.15479/at:ista:12897","related_material":{"record":[{"status":"public","id":"9817","relation":"part_of_dissertation"},{"status":"public","id":"13188","relation":"dissertation_contains"},{"status":"public","id":"7117","relation":"part_of_dissertation"}]},"has_accepted_license":"1","publication_status":"published","type":"dissertation","corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"year":"2023","ddc":["516","004","518","531"],"month":"05","file_date_updated":"2023-12-08T23:30:04Z","page":"180","article_processing_charge":"No","oa":1,"date_published":"2023-05-05T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-031-2"]},"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-12-08T23:30:04Z","file_id":"12942","embargo":"2023-12-07","file_name":"thesis-hafner-2023may11-a2b.pdf","creator":"chafner","file_size":50714445,"date_created":"2023-05-11T10:43:20Z","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","relation":"main_file"},{"file_id":"12943","date_updated":"2023-12-08T23:30:04Z","content_type":"application/pdf","access_level":"closed","relation":"source_file","date_created":"2023-05-11T10:43:44Z","checksum":"a6b51334be2b81672357b1549afab40c","file_size":265319,"creator":"chafner","embargo_to":"open_access","file_name":"thesis-release-form.pdf"}],"date_created":"2023-05-05T10:40:14Z","oa_version":"Published Version","_id":"12897","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"status":"public","date_updated":"2025-04-15T07:16:15Z","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","degree_awarded":"PhD","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"BeBi"}],"day":"05","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian","full_name":"Hafner, Christian"}],"alternative_title":["ISTA Thesis"]},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"year":"2023","ddc":["570"],"month":"04","page":"115","file_date_updated":"2024-04-08T22:30:03Z","article_processing_charge":"No","citation":{"mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>"},"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"doi":"10.15479/at:ista:12809","has_accepted_license":"1","publication_status":"published","supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","corr_author":"1","status":"public","date_updated":"2026-04-07T13:53:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RySh"}],"day":"06","alternative_title":["ISTA Thesis"],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","first_name":"Catarina","last_name":"Alcarva","full_name":"Alcarva, 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Example","relation":"supplementary_material","checksum":"71b00712b489ada2cd9815910ee180a9","date_created":"2023-07-04T07:47:10Z","file_size":25790,"creator":"chafner","file_name":"matlab-submission.zip","file_id":"13193","date_updated":"2023-07-04T07:47:10Z","content_type":"application/x-zip-compressed","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","keyword":["Computer Graphics","Computational Design","Computational Geometry","Shape Modeling"],"date_updated":"2026-08-12T22:30:05Z","title":"The design space of Kirchhoff rods","author":[{"full_name":"Hafner, Christian","first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Julian Fischer for his help in proving Proposition 1. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 715767).","article_type":"original","ec_funded":1,"day":"20","department":[{"_id":"BeBi"}],"scopus_import":"1","doi":"10.1145/3606033","related_material":{"record":[{"relation":"part_of_dissertation","id":"12897","status":"public"}]},"citation":{"chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>.","ista":"Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions on Graphics. 42(5), 171.","ieee":"C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).","ama":"Hafner C, Bickel B. The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>","apa":"Hafner, C., &#38; Bickel, B. (2023). The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 171, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>."},"abstract":[{"lang":"eng","text":"The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.\r\nWe also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics."}],"publication_status":"published","corr_author":"1","type":"journal_article","publisher":"Association for Computing Machinery","has_accepted_license":"1","intvolume":"        42","acknowledged_ssus":[{"_id":"M-Shop"}],"quality_controlled":"1","ddc":["516"],"year":"2023","language":[{"iso":"eng"}],"volume":42,"article_processing_charge":"No","isi":1,"month":"09","file_date_updated":"2023-07-04T08:11:28Z","issue":"5"},{"article_processing_charge":"No","month":"09","page":"156","file_date_updated":"2024-10-05T22:30:03Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["572"],"year":"2023","language":[{"iso":"eng"}],"publication_status":"published","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"corr_author":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","id":"10934","status":"public"},{"status":"public","id":"11373","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7387","status":"public"}]},"doi":"10.15479/at:ista:14280","citation":{"apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>"},"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"alternative_title":["ISTA Thesis"],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","author":[{"last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","degree_awarded":"PhD","day":"25","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"date_updated":"2026-04-07T14:06:05Z","oa_version":"Published Version","date_created":"2023-09-06T10:58:25Z","project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall synthesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"_id":"14280","file":[{"date_created":"2023-10-04T10:11:53Z","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_size":114932847,"relation":"source_file","file_name":"PhD Thesis_Philipp Radler_20231004.docx","creator":"pradler","embargo_to":"open_access","file_id":"14390","access_level":"closed","date_updated":"2024-10-05T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","date_updated":"2024-10-05T22:30:03Z","access_level":"open_access","file_id":"14391","creator":"pradler","embargo":"2024-10-04","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","relation":"main_file","file_size":37838778,"checksum":"3253e099b7126469d941fd9419d68b4f","date_created":"2023-10-04T10:11:21Z"}],"date_published":"2023-09-25T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"oa":1},{"citation":{"ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>."},"abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:12781","has_accepted_license":"1","publication_status":"published","supervisor":[{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","corr_author":"1","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["570","572"],"year":"2023","month":"03","page":"127","file_date_updated":"2024-04-22T22:30:06Z","article_processing_charge":"No","oa":1,"date_published":"2023-03-23T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"file":[{"file_id":"12852","access_level":"open_access","date_updated":"2024-04-22T22:30:06Z","content_type":"application/pdf","checksum":"5ebb6345cb4119f93460c81310265a6d","date_created":"2023-04-19T14:33:41Z","file_size":6071553,"relation":"main_file","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo":"2024-04-20","creator":"vkravchu"},{"file_id":"12853","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-04-22T22:30:06Z","access_level":"open_access","relation":"source_file","file_size":19468766,"checksum":"c12055c48411d030d2afa51de2166221","date_created":"2023-04-19T14:33:52Z","creator":"vkravchu","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","embargo":"2024-04-20"}],"oa_version":"Published Version","date_created":"2023-03-31T12:24:42Z","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697"}],"_id":"12781","status":"public","date_updated":"2026-04-07T14:10:40Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","degree_awarded":"PhD","day":"23","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"ec_funded":1,"alternative_title":["ISTA Thesis"],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","author":[{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","first_name":"Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}]},{"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"day":"05","ec_funded":1,"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"author":[{"orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"}],"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","date_updated":"2025-06-12T06:56:58Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_size":31434230,"date_created":"2023-05-05T13:01:14Z","checksum":"59b0303dc483f40a96a610a90aab7ee9","creator":"aschauer","embargo":"2024-05-05","file_name":"Thesis_Schauer_final.pdf","file_id":"12907","content_type":"application/pdf","date_updated":"2024-05-06T22:30:03Z","access_level":"open_access"},{"creator":"aschauer","embargo_to":"open_access","file_name":"Thesis_Schauer_final.docx","relation":"source_file","file_size":43809109,"date_created":"2023-05-05T13:04:15Z","checksum":"25f54e12479b6adaabd129a20568e6c1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-05-06T22:30:03Z","access_level":"closed","file_id":"12908"}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"_id":"12891","oa_version":"Published Version","date_created":"2023-05-05T08:48:20Z","oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-05-05T00:00:00Z","page":"190","file_date_updated":"2024-05-06T22:30:03Z","month":"05","article_processing_charge":"No","language":[{"iso":"eng"}],"ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"citation":{"apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023."},"related_material":{"record":[{"status":"public","id":"7888","relation":"part_of_dissertation"},{"status":"public","id":"8966","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:12891"},{"year":"2023","ddc":["570"],"quality_controlled":"1","volume":120,"language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"No","issue":"25","file_date_updated":"2023-12-13T23:30:03Z","month":"06","doi":"10.1073/pnas.2221313120","scopus_import":"1","abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"citation":{"apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"publisher":"National Academy of Sciences","type":"journal_article","publication_status":"published","intvolume":"       120","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2023-12-13T23:30:04Z","status":"public","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","author":[{"full_name":"Wang, Yalu","last_name":"Wang","first_name":"Yalu"},{"first_name":"Zhi","last_name":"Yuan","full_name":"Yuan, Zhi"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"last_name":"Guo","first_name":"Yan","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"}],"day":"12","department":[{"_id":"JiFr"}],"article_type":"original","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_published":"2023-06-12T00:00:00Z","external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"oa":1,"pmid":1,"_id":"13201","oa_version":"Published Version","article_number":"e2221313120","date_created":"2023-07-09T22:01:12Z","file":[{"access_level":"open_access","date_updated":"2023-12-13T23:30:03Z","content_type":"application/pdf","file_id":"13204","embargo":"2023-12-12","file_name":"2023_PNAS_Wang.pdf","creator":"alisjak","date_created":"2023-07-10T08:48:40Z","checksum":"d800e06252eaefba28531fa9440f23f0","file_size":5244581,"relation":"main_file"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"file_date_updated":"2024-02-09T23:30:03Z","page":"46","month":"02","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2023","ddc":["570"],"has_accepted_license":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","supervisor":[{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"citation":{"ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>"},"doi":"10.15479/at:ista:12531","day":"08","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"degree_awarded":"MS","OA_place":"publisher","title":"Panoramic functional gradients across the mouse retina","author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","full_name":"Kirillova, Kseniia","first_name":"Kseniia","last_name":"Kirillova"}],"alternative_title":["ISTA Master's Thesis"],"date_updated":"2026-04-07T14:06:26Z","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"12532","content_type":"application/pdf","date_updated":"2024-02-09T23:30:03Z","access_level":"open_access","relation":"main_file","file_size":8369317,"checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_created":"2023-02-09T08:03:32Z","creator":"cchlebak","embargo":"2024-02-08","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf"},{"relation":"source_file","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","date_created":"2023-02-10T09:32:06Z","file_size":11204408,"creator":"cchlebak","embargo_to":"open_access","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","file_id":"12535","date_updated":"2024-02-09T23:30:03Z","content_type":"application/x-zip-compressed","access_level":"closed"}],"_id":"12531","date_created":"2023-02-09T07:45:05Z","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["2791-4585"]},"date_published":"2023-02-08T00:00:00Z"},{"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"date_published":"2023-12-20T00:00:00Z","file":[{"relation":"main_file","date_created":"2023-12-20T09:35:34Z","checksum":"457927165d5d556305d3086f6b83e5c7","file_size":51585778,"creator":"jstopp","embargo":"2024-12-20","file_name":"Thesis.pdf","file_id":"14699","date_updated":"2024-12-20T23:30:04Z","content_type":"application/pdf","access_level":"open_access"},{"access_level":"closed","date_updated":"2024-12-20T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14700","file_name":"Thesis.docx","embargo_to":"open_access","creator":"jstopp","date_created":"2023-12-20T09:35:35Z","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"relation":"source_file"}],"_id":"14697","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_created":"2023-12-18T19:14:28Z","oa_version":"Published Version","date_updated":"2026-06-18T17:34:48Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"day":"20","degree_awarded":"PhD","OA_place":"publisher","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","author":[{"last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies."}],"citation":{"chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>."},"doi":"10.15479/at:ista:14697","related_material":{"record":[{"status":"public","id":"14360","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"12272"},{"status":"public","id":"6328","relation":"part_of_dissertation"},{"id":"7885","relation":"part_of_dissertation","status":"public"},{"id":"14274","relation":"part_of_dissertation","status":"public"}]},"has_accepted_license":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","supervisor":[{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","language":[{"iso":"eng"}],"ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2024-12-20T23:30:04Z","page":"226","month":"12","article_processing_charge":"No"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T22:30:14Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"ec_funded":1,"article_type":"original","acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","author":[{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","full_name":"Singh, Amrita","last_name":"Singh","first_name":"Amrita"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P","last_name":"Zagórski"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna"}],"external_id":{"pmid":["37456593"],"isi":["000964029300003"]},"oa":1,"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"date_published":"2023-07-01T00:00:00Z","file":[{"file_name":"2023_NaturePhysics_Boncanegra.pdf","creator":"dernst","checksum":"858225a4205b74406e5045006cdd853f","date_created":"2023-10-04T11:13:28Z","file_size":5532285,"relation":"main_file","access_level":"open_access","date_updated":"2023-10-04T11:13:28Z","content_type":"application/pdf","success":1,"file_id":"14392"}],"publication":"Nature Physics","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"pmid":1,"_id":"12837","oa_version":"Published Version","date_created":"2023-04-16T22:01:09Z","volume":19,"language":[{"iso":"eng"}],"ddc":["570"],"year":"2023","quality_controlled":"1","page":"1050-1058","file_date_updated":"2023-10-04T11:13:28Z","month":"07","isi":1,"article_processing_charge":"No","abstract":[{"text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.","lang":"eng"}],"citation":{"ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. 2023;19:1050-1058. doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1050–1058, 2023.","ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058.","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>.","apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., &#38; Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>"},"related_material":{"record":[{"status":"public","id":"13081","relation":"dissertation_contains"}]},"doi":"10.1038/s41567-023-01977-w","scopus_import":"1","intvolume":"        19","has_accepted_license":"1","publisher":"Springer Nature","corr_author":"1","type":"journal_article","publication_status":"published"},{"author":[{"first_name":"Ewa","last_name":"Sitarska","full_name":"Sitarska, Ewa"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"full_name":"Beckwith, Marianne Sandvold","last_name":"Beckwith","first_name":"Marianne Sandvold"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"full_name":"Czuchnowski, Jakub","last_name":"Czuchnowski","first_name":"Jakub"},{"full_name":"Siggel, Marc","first_name":"Marc","last_name":"Siggel"},{"last_name":"Roessner","first_name":"Rita","full_name":"Roessner, Rita"},{"first_name":"Aline","last_name":"Tschanz","full_name":"Tschanz, Aline"},{"first_name":"Christer","last_name":"Ejsing","full_name":"Ejsing, Christer"},{"first_name":"Yannick","last_name":"Schwab","full_name":"Schwab, Yannick"},{"last_name":"Kosinski","first_name":"Jan","full_name":"Kosinski, Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Kreshuk, Anna","first_name":"Anna","last_name":"Kreshuk"},{"full_name":"Erzberger, Anna","first_name":"Anna","last_name":"Erzberger"},{"first_name":"Alba","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba"}],"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","day":"13","department":[{"_id":"MiSi"}],"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T22:30:13Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","_id":"14360","pmid":1,"date_created":"2023-09-24T22:01:10Z","oa_version":"Published Version","article_number":"5644","file":[{"relation":"main_file","file_size":2725421,"date_created":"2023-09-25T08:22:58Z","checksum":"ad670e3b3c64fc585675948370f6b149","creator":"dernst","file_name":"2023_NatureComm_Sitarska.pdf","file_id":"14365","content_type":"application/pdf","success":1,"date_updated":"2023-09-25T08:22:58Z","access_level":"open_access"}],"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"date_published":"2023-09-13T00:00:00Z","oa":1,"external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"isi":1,"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-09-25T08:22:58Z","month":"09","year":"2023","ddc":["570"],"quality_controlled":"1","volume":14,"language":[{"iso":"eng"}],"type":"journal_article","publisher":"Springer Nature","publication_status":"published","intvolume":"        14","has_accepted_license":"1","doi":"10.1038/s41467-023-41173-1","related_material":{"record":[{"relation":"dissertation_contains","id":"14697","status":"public"}]},"scopus_import":"1","abstract":[{"text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.","lang":"eng"}],"citation":{"apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."}},{"title":"Epithelial dynamics during mouse neural tube development","author":[{"last_name":"Bocanegra","first_name":"Laura","full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"day":"23","degree_awarded":"PhD","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-14T09:50:54Z","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","_id":"13081","date_created":"2023-05-23T19:10:42Z","oa_version":"Published Version","file":[{"file_id":"13089","access_level":"closed","date_updated":"2024-06-01T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-05-25T06:32:12Z","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_size":25615534,"relation":"source_file","file_name":"Thesis_final_LauraBocanegra.docx","embargo_to":"open_access","creator":"lbocaneg"},{"embargo":"2024-05-31","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","creator":"lbocaneg","file_size":12386046,"checksum":"c6cdef6323eacfb4b7a8af20f32eae97","date_created":"2023-05-25T06:32:16Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-06-01T22:30:04Z","file_id":"13090"}],"publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-05-23T00:00:00Z","oa":1,"article_processing_charge":"No","file_date_updated":"2024-06-01T22:30:04Z","page":"93","month":"05","ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"type":"dissertation","corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","has_accepted_license":"1","doi":"10.15479/at:ista:13081","related_material":{"record":[{"id":"9349","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"12837","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling.  Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis."}],"citation":{"mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>.","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>"}},{"ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","page":"151","file_date_updated":"2025-03-13T23:30:05Z","month":"09","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7883"}]},"doi":"10.15479/at:ista:14323","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"citation":{"mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>."},"supervisor":[{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2026-04-14T09:50:54Z","status":"public","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"}],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","day":"13","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"OA_place":"publisher","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-09-13T00:00:00Z","oa":1,"project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"_id":"14323","oa_version":"Published 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Mara","first_name":"Mara","last_name":"Julseth"}],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","alternative_title":["ISTA Master's Thesis"],"degree_awarded":"MS","OA_place":"publisher","day":"05","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_updated":"2026-04-07T14:01:51Z","publication_status":"published","corr_author":"1","publisher":"Institute of Science and Technology Austria","type":"dissertation","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.15479/at:ista:12800","citation":{"mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023."},"abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"article_processing_charge":"No","month":"04","file_date_updated":"2023-06-02T22:30:04Z","page":"21","ddc":["576"],"year":"2023","language":[{"iso":"eng"}]},{"scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17465"}]},"citation":{"short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:31151-31209.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:31151–209. ML Research Press, 2023.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 31151–209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., &#38; Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press."},"abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}],"publication_status":"published","publisher":"ML Research Press","type":"conference","corr_author":"1","intvolume":"       202","quality_controlled":"1","year":"2023","conference":{"location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29","name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23"},"language":[{"iso":"eng"}],"volume":202,"article_processing_charge":"No","month":"07","page":"31151-31209","date_published":"2023-07-30T00:00:00Z","arxiv":1,"publication_identifier":{"eissn":["2640-3498"]},"oa":1,"external_id":{"arxiv":["2212.13468"]},"date_created":"2023-10-29T23:01:17Z","oa_version":"Preprint","_id":"14459","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"publication":"Proceedings of the 40th International Conference on Machine Learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-08-12T22:30:15Z","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","author":[{"last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Kögler, Kevin","last_name":"Kögler","first_name":"Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"alternative_title":["PMLR"],"acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","day":"30","department":[{"_id":"MaMo"},{"_id":"DaAl"}]}]