[{"related_material":{"record":[{"id":"14656","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"11932"}]},"_id":"10077","ec_funded":1,"doi":"10.1101/2021.09.28.460602","date_created":"2021-10-04T06:23:34Z","citation":{"ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.)."},"day":"29","date_updated":"2026-06-19T22:30:37Z","article_processing_charge":"No","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","oa":1,"date_published":"2021-09-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina"}],"acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","status":"public","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"publication_status":"draft","type":"preprint","publisher":"Cold Spring Harbor Laboratory","year":"2021","oa_version":"Preprint","language":[{"iso":"eng"}],"publication":"bioRxiv"},{"file":[{"file_name":"submission_new.zip","file_size":29703124,"checksum":"86a05b430756ca12ae8107b6e6f3c1e5","date_created":"2021-11-18T12:41:46Z","content_type":"application/zip","access_level":"closed","date_updated":"2022-12-20T23:30:08Z","file_id":"10305","creator":"lschmid","embargo_to":"open_access","relation":"source_file"},{"date_created":"2021-11-18T12:59:15Z","access_level":"open_access","content_type":"application/pdf","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_size":8320985,"file_name":"thesis_new_upload.pdf","embargo":"2022-10-18","relation":"main_file","file_id":"10306","creator":"lschmid","date_updated":"2022-12-20T23:30:08Z"}],"date_published":"2021-11-17T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura"}],"status":"public","year":"2021","language":[{"iso":"eng"}],"page":"171","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9997"},{"relation":"part_of_dissertation","status":"public","id":"9402"},{"id":"2","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:10293","date_created":"2021-11-15T17:12:57Z","citation":{"ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>","mla":"Schmid, Laura. <i>Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>.","apa":"Schmid, L. (2021). <i>Evolution of cooperation via (in)direct reciprocity under imperfect information</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria."},"corr_author":"1","day":"17","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"ddc":["519","576"],"oa":1,"file_date_updated":"2022-12-20T23:30:08Z","month":"11","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","degree_awarded":"PhD","_id":"10293","ec_funded":1,"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-08T07:11:20Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"title":"Evolution of cooperation via (in)direct reciprocity under imperfect information"},{"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"_id":"9992","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"title":"Wound healing in the Arabidopsis root meristem","date_updated":"2026-04-08T07:11:47Z","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"month":"09","project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"degree_awarded":"PhD","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","citation":{"apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"date_created":"2021-09-09T07:37:20Z","day":"13","corr_author":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6943"},{"id":"8002","relation":"part_of_dissertation","status":"public"},{"id":"6351","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:9992","ddc":["575"],"abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"oa":1,"file_date_updated":"2021-09-15T22:30:26Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2021-09-13T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"Thesis_vupload.docx","file_size":25179004,"checksum":"c763064adaa720e16066c1a4f9682bbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","embargo_to":"open_access","creator":"lhoermaye","file_id":"9993","relation":"source_file"},{"content_type":"application/pdf","access_level":"open_access","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_size":6246900,"file_name":"Thesis_vfinal_pdfa.pdf","embargo":"2021-09-09","relation":"main_file","creator":"lhoermaye","file_id":"9996","date_updated":"2021-09-15T22:30:26Z"}],"author":[{"last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas"}],"page":"168","language":[{"iso":"eng"}],"year":"2021"},{"status":"public","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","volume":11,"external_id":{"pmid":["34465830"],"isi":["000692406400018"]},"author":[{"first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"},{"first_name":"Pouya","last_name":"Shati","full_name":"Shati, Pouya"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"date_published":"2021-08-31T00:00:00Z","file":[{"checksum":"19df8816cf958b272b85841565c73182","date_created":"2021-09-13T10:31:21Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_ScientificReports_Schmid.pdf","file_size":2424943,"file_id":"10006","creator":"cchlebak","relation":"main_file","date_updated":"2021-09-13T10:31:21Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","language":[{"iso":"eng"}],"publication":"Scientific Reports","year":"2021","corr_author":"1","day":"31","date_created":"2021-09-11T16:22:02Z","quality_controlled":"1","citation":{"ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>."},"scopus_import":"1","doi":"10.1038/s41598-021-96932-1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}]},"intvolume":"        11","oa":1,"file_date_updated":"2021-09-13T10:31:21Z","abstract":[{"text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.","lang":"eng"}],"ddc":["003"],"has_accepted_license":"1","article_number":"17443","article_processing_charge":"Yes","keyword":["Multidisciplinary"],"article_type":"original","month":"08","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"Springer Nature","publication_identifier":{"eissn":["2045-2322"]},"isi":1,"pmid":1,"_id":"9997","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"The evolution of indirect reciprocity under action and assessment generosity","date_updated":"2026-06-19T22:30:39Z"},{"type":"journal_article","publisher":"Springer Nature","publication_status":"published","oa_version":"Submitted Version","month":"05","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"article_type":"original","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"A unified framework of direct and indirect reciprocity","date_updated":"2026-06-19T22:30:39Z","isi":1,"publication_identifier":{"eissn":["2397-3374"]},"_id":"9402","ec_funded":1,"pmid":1,"language":[{"iso":"eng"}],"publication":"Nature Human Behaviour","page":"1292–1302","issue":"10","year":"2021","status":"public","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","file":[{"date_updated":"2023-11-07T08:27:23Z","relation":"main_file","file_id":"14496","creator":"dernst","file_size":5232761,"file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","success":1,"date_created":"2023-11-07T08:27:23Z","content_type":"application/pdf","access_level":"open_access","checksum":"34f55e173f90dc1dab731063458ac780"}],"date_published":"2021-05-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"author":[{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"abstract":[{"text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.","lang":"eng"}],"ddc":["000"],"oa":1,"file_date_updated":"2023-11-07T08:27:23Z","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <i>Nature Human Behaviour</i>, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>"},"quality_controlled":"1","date_created":"2021-05-18T16:56:57Z","scopus_import":"1","day":"13","corr_author":"1","related_material":{"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/"}]},"intvolume":"         5","doi":"10.1038/s41562-021-01114-8"},{"quality_controlled":"1","citation":{"ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. 2021;20(8):1106–1112. doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","ieee":"D. Jirovec <i>et al.</i>, “A singlet triplet hole spin qubit in planar Ge,” <i>Nature Materials</i>, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>","chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112."},"date_created":"2020-12-02T10:50:47Z","scopus_import":"1","corr_author":"1","day":"01","related_material":{"record":[{"id":"9323","status":"public","relation":"research_data"},{"id":"10058","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","relation":"press_release"}]},"intvolume":"        20","doi":"10.1038/s41563-021-01022-2","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"oa":1,"article_processing_charge":"No","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-01T00:00:00Z","volume":20,"external_id":{"pmid":["34083775"],"isi":["000657596400001"],"arxiv":["2011.13755"]},"author":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","first_name":"Daniel"},{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"first_name":"Giulio","last_name":"Tavani","full_name":"Tavani, Giulio"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","last_name":"Crippa","orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver"},{"first_name":"Frederico","orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","last_name":"Martins","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez"},{"full_name":"Borovkov, Maksim","last_name":"Borovkov","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios"}],"publication":"Nature Materials","page":"1106–1112","language":[{"iso":"eng"}],"issue":"8","year":"2021","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"isi":1,"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"_id":"8909","ec_funded":1,"pmid":1,"department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"title":"A singlet triplet hole spin qubit in planar Ge","date_updated":"2026-06-19T22:30:41Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"project":[{"call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"month":"08","article_type":"original","arxiv":1,"type":"journal_article","publisher":"Springer Nature","publication_status":"published","oa_version":"Preprint"},{"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","date_updated":"2026-04-08T07:12:06Z","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"_id":"10135","degree_awarded":"PhD","publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva"}],"month":"10","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","grant_number":"24746"}],"ddc":["570"],"abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"file_date_updated":"2022-12-20T23:30:05Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","date_created":"2021-10-13T13:42:48Z","citation":{"ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","apa":"Semerádová, H. (2021). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>."},"alternative_title":["ISTA Thesis"],"corr_author":"1","day":"13","related_material":{"record":[{"id":"9160","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/at:ista:10135","language":[{"iso":"eng"}],"year":"2021","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","file_size":28508629,"checksum":"ce7108853e6cec6224f17cd6429b51fe","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-10-27T07:45:37Z","date_updated":"2022-12-20T23:30:05Z","creator":"cziletti","embargo_to":"open_access","file_id":"10186","relation":"source_file"},{"embargo":"2022-10-28","relation":"main_file","file_id":"10187","creator":"cziletti","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z","content_type":"application/pdf","access_level":"open_access","checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_size":10623525,"file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf"}],"date_published":"2021-10-13T00:00:00Z","author":[{"first_name":"Hana","last_name":"Semerádová","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana"}]},{"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","date_updated":"2026-04-08T07:12:19Z","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"OA_place":"publisher","_id":"10058","degree_awarded":"PhD","oa_version":"Published Version","publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"keyword":["qubits","quantum computing","holes"],"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells"}],"month":"10","file_date_updated":"2022-12-20T23:30:07Z","oa":1,"ddc":["621","539"],"abstract":[{"text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term.  The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.","lang":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"corr_author":"1","day":"05","citation":{"chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>.","mla":"Jirovec, Daniel. <i>Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>.","apa":"Jirovec, D. (2021). <i>Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10058\">https://doi.org/10.15479/at:ista:10058</a>","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10058\">10.15479/at:ista:10058</a>"},"date_created":"2021-09-30T07:53:49Z","doi":"10.15479/at:ista:10058","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10066"},{"status":"public","relation":"part_of_dissertation","id":"10065"},{"relation":"part_of_dissertation","status":"public","id":"8831"},{"relation":"part_of_dissertation","status":"public","id":"8909"},{"id":"5816","status":"public","relation":"part_of_dissertation"}]},"page":"151","language":[{"iso":"eng"}],"year":"2021","status":"public","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","author":[{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"file":[{"relation":"source_file","embargo_to":"open_access","creator":"djirovec","file_id":"10061","date_updated":"2022-12-20T23:30:07Z","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2021-09-30T14:29:14Z","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_size":32397600,"file_name":"PHD_Thesis_Jirovec_Source.zip"},{"date_created":"2021-10-05T07:56:49Z","content_type":"application/pdf","access_level":"open_access","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_size":26910829,"file_name":"PHD_Thesis_pdfa2b_1.pdf","embargo":"2022-10-06","relation":"main_file","file_id":"10087","creator":"djirovec","date_updated":"2022-12-20T23:30:07Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-10-05T00:00:00Z"},{"oa":1,"title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","department":[{"_id":"GeKa"}],"abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}],"article_processing_charge":"No","article_number":"2107.12975","date_updated":"2026-06-19T22:30:41Z","day":"27","acknowledged_ssus":[{"_id":"NanoFab"}],"citation":{"mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, 2107.12975, doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>.","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>.","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2107.12975\">https://doi.org/10.48550/arXiv.2107.12975</a>","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","ieee":"B. Severin <i>et al.</i>, “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” <i>arXiv</i>. .","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2107.12975\">10.48550/arXiv.2107.12975</a>"},"date_created":"2021-10-01T12:40:22Z","doi":"10.48550/arXiv.2107.12975","_id":"10066","related_material":{"record":[{"id":"17389","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"10058"}]},"arxiv":1,"language":[{"iso":"eng"}],"publication":"arXiv","year":"2021","oa_version":"Preprint","type":"preprint","publication_status":"draft","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12975"}],"author":[{"first_name":"B.","full_name":"Severin, B.","last_name":"Severin"},{"first_name":"D. T.","last_name":"Lennon","full_name":"Lennon, D. T."},{"full_name":"Camenzind, L. C.","last_name":"Camenzind","first_name":"L. C."},{"first_name":"F.","full_name":"Vigneau, F.","last_name":"Vigneau"},{"first_name":"F.","last_name":"Fedele","full_name":"Fedele, F."},{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"last_name":"Ballabio","full_name":"Ballabio, A.","first_name":"A."},{"last_name":"Chrastina","full_name":"Chrastina, D.","first_name":"D."},{"first_name":"G.","full_name":"Isella, G.","last_name":"Isella"},{"first_name":"M. de","last_name":"Kruijf","full_name":"Kruijf, M. de"},{"first_name":"M. J.","full_name":"Carballido, M. J.","last_name":"Carballido"},{"first_name":"S.","full_name":"Svab, S.","last_name":"Svab"},{"first_name":"A. V.","full_name":"Kuhlmann, A. V.","last_name":"Kuhlmann"},{"first_name":"F. R.","last_name":"Braakman","full_name":"Braakman, F. R."},{"first_name":"S.","last_name":"Geyer","full_name":"Geyer, S."},{"last_name":"Froning","full_name":"Froning, F. N. M.","first_name":"F. N. M."},{"first_name":"H.","last_name":"Moon","full_name":"Moon, H."},{"full_name":"Osborne, M. A.","last_name":"Osborne","first_name":"M. A."},{"full_name":"Sejdinovic, D.","last_name":"Sejdinovic","first_name":"D."},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios"},{"first_name":"D. M.","last_name":"Zumbühl","full_name":"Zumbühl, D. M."},{"first_name":"G. A. D.","last_name":"Briggs","full_name":"Briggs, G. A. D."},{"first_name":"N.","full_name":"Ares, N.","last_name":"Ares"}],"external_id":{"arxiv":["2107.12975"]},"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","call_identifier":"FWF"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-27T00:00:00Z"},{"year":"2021","language":[{"iso":"eng"}],"publication":"eLife","author":[{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","first_name":"Pradeep"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"first_name":"Diego","last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego"},{"first_name":"Thorsten","full_name":"Fritzius, Thorsten","last_name":"Fritzius"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"},{"last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"first_name":"Akos","full_name":"Kulik, Akos","last_name":"Kulik"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"first_name":"Peter","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"volume":10,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-04-29T00:00:00Z","file":[{"file_size":8174719,"file_name":"2021_eLife_Bhandari.pdf","success":1,"date_created":"2021-05-31T09:43:09Z","access_level":"open_access","content_type":"application/pdf","checksum":"6ebcb79999f889766f7cd79ee134ad28","date_updated":"2021-05-31T09:43:09Z","relation":"main_file","file_id":"9440","creator":"cziletti"}],"status":"public","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","has_accepted_license":"1","article_processing_charge":"No","article_number":"e68274","file_date_updated":"2021-05-31T09:43:09Z","oa":1,"abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"ddc":["570"],"doi":"10.7554/ELIFE.68274","intvolume":"        10","related_material":{"record":[{"id":"19271","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"9562"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}]},"day":"29","scopus_import":"1","citation":{"chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>.","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>, vol. 10, e68274, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>","ieee":"P. Bhandari <i>et al.</i>, “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021)."},"date_created":"2021-05-30T22:01:23Z","quality_controlled":"1","oa_version":"Published Version","publisher":"eLife Sciences Publications","publication_status":"published","type":"journal_article","article_type":"original","month":"04","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"date_updated":"2026-06-19T22:30:42Z","department":[{"_id":"RySh"},{"_id":"PeJo"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","pmid":1,"ec_funded":1,"_id":"9437","publication_identifier":{"eissn":["2050-084X"]},"isi":1},{"doi":"10.15479/at:ista:9562","related_material":{"record":[{"id":"9756","relation":"part_of_dissertation","status":"public"},{"id":"9437","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"612"},{"id":"8532","relation":"part_of_dissertation","status":"public"}]},"day":"01","corr_author":"1","alternative_title":["ISTA Thesis"],"date_created":"2021-06-17T14:10:47Z","citation":{"mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>"},"has_accepted_license":"1","article_processing_charge":"No","oa":1,"file_date_updated":"2022-07-02T22:30:04Z","ddc":["570"],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-06-01T00:00:00Z","file":[{"file_size":77299142,"file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","content_type":"application/pdf","access_level":"open_access","checksum":"659df5518db495f679cb1df9e9bd1d94","date_updated":"2022-07-02T22:30:04Z","embargo":"2022-07-01","relation":"main_file","file_id":"9563","creator":"dkleindienst"},{"date_updated":"2022-07-02T22:30:04Z","file_id":"9564","creator":"dkleindienst","embargo_to":"open_access","relation":"source_file","file_name":"Thesis_source.zip","file_size":369804895,"checksum":"3bcf63a2b19e5b6663be051bea332748","date_created":"2021-06-17T14:04:30Z","access_level":"closed","content_type":"application/zip"}],"status":"public","year":"2021","page":"124","language":[{"iso":"eng"}],"_id":"9562","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_updated":"2026-04-08T07:12:31Z","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","department":[{"_id":"GradSch"},{"_id":"RySh"}],"month":"06","supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","degree_awarded":"PhD"},{"type":"book_chapter","publication_status":"published","publisher":"Humana","series_title":"Neuromethods","oa_version":"None","project":[{"grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1"}],"month":"07","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"place":"New York","date_updated":"2026-06-19T22:30:42Z","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","ec_funded":1,"_id":"9756","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"year":"2021","language":[{"iso":"eng"}],"page":"267-283","publication":" Receptor and Ion Channel Detection in the Brain","date_published":"2021-07-27T00:00:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"volume":169,"status":"public","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","article_processing_charge":"No","has_accepted_license":"1","abstract":[{"text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.","lang":"eng"}],"ddc":["573"],"intvolume":"       169","related_material":{"record":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"doi":"10.1007/978-1-0716-1522-5_19","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana, 2021, pp. 267–283.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:,  Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i> Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In:  Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i> Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i> Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>."},"date_created":"2021-07-30T09:34:56Z","alternative_title":["Neuromethods"],"corr_author":"1","day":"27"},{"oa":1,"file_date_updated":"2022-05-21T22:30:04Z","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"ddc":["571"],"has_accepted_license":"1","article_processing_charge":"No","day":"18","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021."},"date_created":"2021-05-17T12:31:30Z","doi":"10.15479/at:ista:9397","language":[{"iso":"eng"}],"page":"101","year":"2021","status":"public","author":[{"first_name":"Karla","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev"}],"date_published":"2021-05-18T00:00:00Z","file":[{"date_updated":"2022-05-21T22:30:04Z","relation":"source_file","file_id":"9398","creator":"khuljev","embargo_to":"open_access","file_size":47799741,"file_name":"KHuljev_Thesis_corrections.docx","date_created":"2021-05-17T12:29:12Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"7f98532f5324a0b2f3fa8de2967baa19"},{"date_updated":"2022-05-21T22:30:04Z","file_id":"9401","creator":"khuljev","embargo":"2022-05-20","relation":"main_file","file_name":"new_KHuljev_Thesis_corrections.pdf","file_size":16542131,"checksum":"bf512f8a1e572a543778fc4b227c01ba","date_created":"2021-05-18T14:50:28Z","access_level":"open_access","content_type":"application/pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"date_updated":"2026-04-08T07:12:51Z","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","_id":"9397","degree_awarded":"PhD","oa_version":"Published Version","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"month":"05"},{"day":"18","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"date_created":"2021-11-18T15:05:06Z","doi":"10.15479/at:ista:10307","related_material":{"record":[{"id":"10316","relation":"part_of_dissertation","status":"public"}]},"oa":1,"file_date_updated":"2022-12-20T23:30:05Z","abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","status":"public","author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin"}],"date_published":"2021-11-18T00:00:00Z","file":[{"file_id":"10308","creator":"ktomasek","embargo":"2022-11-18","relation":"main_file","date_updated":"2022-12-20T23:30:05Z","checksum":"b39c9e0ef18d0484d537a67551effd02","date_created":"2021-11-18T15:07:31Z","content_type":"application/pdf","access_level":"open_access","file_name":"ThesisTomasekKathrin.pdf","file_size":13266088},{"date_created":"2021-11-18T15:07:46Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_size":7539509,"file_name":"ThesisTomasekKathrin.docx","relation":"source_file","file_id":"10309","embargo_to":"open_access","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"page":"73","year":"2021","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"_id":"10307","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"title":"Pathogenic Escherichia coli hijack the host immune response","date_updated":"2026-04-08T07:14:01Z","supervisor":[{"orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"month":"11","degree_awarded":"PhD","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","type":"dissertation","publication_status":"published"},{"date_published":"2021-10-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F"},{"first_name":"Ivana","full_name":"Glatzová, Ivana","last_name":"Glatzová","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d"},{"first_name":"Michael S.","full_name":"Lukesch, Michael S.","last_name":"Lukesch"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","first_name":"Michael K"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","status":"public","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"publication_status":"draft","type":"preprint","publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","year":"2021","language":[{"iso":"eng"}],"publication":"bioRxiv","_id":"10316","related_material":{"record":[{"status":"public","relation":"later_version","id":"11843"},{"id":"10307","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"doi":"10.1101/2021.10.18.464770","date_created":"2021-11-19T12:24:16Z","citation":{"short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"day":"18","corr_author":"1","date_updated":"2026-06-19T22:30:43Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"department":[{"_id":"CaGu"},{"_id":"MiSi"}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","oa":1},{"oa_version":"Published Version","type":"dissertation","publication_status":"published","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812"}],"month":"09","supervisor":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"date_updated":"2026-04-08T07:19:09Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","_id":"9962","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","year":"2021","language":[{"iso":"eng"}],"page":"182","author":[{"first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen"}],"date_published":"2021-09-02T00:00:00Z","file":[{"file_name":"Thesis_Hansen.docx","file_size":10629190,"checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2021-08-30T09:17:39Z","date_updated":"2022-09-03T22:30:04Z","embargo_to":"open_access","creator":"ahansen","file_id":"9971","relation":"source_file"},{"creator":"ahansen","file_id":"9972","embargo":"2022-09-02","relation":"main_file","date_updated":"2022-09-03T22:30:04Z","checksum":"204fa40321a1c6289b68c473634c4bf3","content_type":"application/pdf","access_level":"open_access","date_created":"2021-08-30T09:29:44Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","file_size":13457469}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","has_accepted_license":"1","article_processing_charge":"No","oa":1,"file_date_updated":"2022-09-03T22:30:04Z","ddc":["570"],"abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"doi":"10.15479/at:ista:9962","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8569"},{"id":"960","relation":"part_of_dissertation","status":"public"}]},"corr_author":"1","day":"02","alternative_title":["ISTA Thesis"],"citation":{"ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>.","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria."},"date_created":"2021-08-29T12:36:50Z"},{"article_number":"e106862","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"ddc":["580"],"oa":1,"file_date_updated":"2021-02-11T12:28:29Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release"}]},"intvolume":"        40","doi":"10.15252/embj.2020106862","date_created":"2021-01-17T23:01:12Z","quality_controlled":"1","citation":{"ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>."},"scopus_import":"1","corr_author":"1","day":"01","year":"2021","publication":"EMBO Journal","language":[{"iso":"eng"}],"issue":"3","file":[{"file_id":"9110","creator":"dernst","relation":"main_file","date_updated":"2021-02-11T12:28:29Z","checksum":"dc55c900f3b061d6c2790b8813d759a3","date_created":"2021-02-11T12:28:29Z","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Embo_Otvos.pdf","success":1,"file_size":2358617}],"date_published":"2021-02-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":40,"external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"full_name":"O’Brien, Jose","last_name":"O’Brien","first_name":"Jose"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","first_name":"Rashed"},{"last_name":"Antonielli","full_name":"Antonielli, Livio","first_name":"Livio"},{"first_name":"Juan C","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuzhou","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","first_name":"Candela"},{"first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","full_name":"Artner, Christina"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez"},{"first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","status":"public","date_updated":"2026-06-19T22:30:47Z","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"9010","pmid":1,"acknowledged_ssus":[{"_id":"Bio"}],"isi":1,"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"type":"journal_article","publication_status":"published","publisher":"Embo Press","oa_version":"Published Version","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","grant_number":"I 1774-B16"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"month":"02","article_type":"original"},{"date_published":"2021-09-06T00:00:00Z","file":[{"relation":"main_file","creator":"cchlebak","file_id":"10090","date_updated":"2021-10-05T13:36:42Z","access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-05T13:36:42Z","checksum":"750de03dc3b715c37090126c1548ba13","file_size":3144854,"success":1,"file_name":"2021_EmboR_Vega.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":22,"external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"author":[{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"first_name":"Isabel","full_name":"Fredes, Isabel","last_name":"Fredes"},{"first_name":"José","full_name":"O’Brien, José","last_name":"O’Brien"},{"first_name":"Zhouxin","last_name":"Shen","full_name":"Shen, Zhouxin"},{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","first_name":"Krisztina"},{"orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"first_name":"Steven P.","last_name":"Briggs","full_name":"Briggs, Steven P."},{"full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez","first_name":"Rodrigo A."}],"acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","status":"public","year":"2021","language":[{"iso":"eng"}],"publication":"EMBO Reports","issue":"9","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"intvolume":"        22","doi":"10.15252/embr.202051813","date_created":"2021-08-15T22:01:30Z","quality_controlled":"1","citation":{"ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813."},"scopus_import":"1","day":"06","article_number":"e51813","article_processing_charge":"Yes","has_accepted_license":"1","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"ddc":["580"],"oa":1,"file_date_updated":"2021-10-05T13:36:42Z","month":"09","article_type":"original","publisher":"Wiley","type":"journal_article","publication_status":"published","oa_version":"Published Version","_id":"9913","pmid":1,"isi":1,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"date_updated":"2026-06-19T22:30:47Z","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"EvBe"},{"_id":"GradSch"}]},{"_id":"10303","OA_place":"publisher","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-08T07:20:07Z","title":"Role of hormones in nitrate regulated growth","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"month":"11","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","publication_status":"published","oa_version":"Published Version","degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"47"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"relation":"part_of_dissertation","status":"public","id":"9010"}]},"doi":"10.15479/at:ista:10303","date_created":"2021-11-18T11:20:59Z","citation":{"ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria."},"corr_author":"1","day":"22","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"ddc":["580","581"],"oa":1,"file_date_updated":"2022-12-20T23:30:06Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-11-22T00:00:00Z","file":[{"checksum":"dea38b98aa4da1cea03dcd0f10862818","date_created":"2021-11-22T14:48:21Z","content_type":"application/pdf","access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf","file_size":28005730,"file_id":"10331","creator":"rabualia","embargo":"2022-11-23","relation":"main_file","date_updated":"2022-12-20T23:30:06Z"},{"file_name":"AbualiaPhDthesisfinalv3.docx","file_size":62841883,"checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","date_created":"2021-11-22T14:48:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2022-12-20T23:30:06Z","file_id":"10332","embargo_to":"open_access","creator":"rabualia","relation":"source_file"}],"author":[{"last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","first_name":"Rashed"}],"status":"public","year":"2021","language":[{"iso":"eng"}],"page":"139"},{"year":"2021","publication":"Nature Communications","language":[{"iso":"eng"}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-05-24T00:00:00Z","file":[{"checksum":"337e0f7959c35ec959984cacdcb472ba","date_created":"2021-05-28T12:39:43Z","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NatureCommunications_Morandell.pdf","success":1,"file_size":9358599,"file_id":"9430","creator":"kschuh","relation":"main_file","date_updated":"2021-05-28T12:39:43Z"}],"external_id":{"isi":["000658769900010"]},"author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","full_name":"Morandell, Jasmin","first_name":"Jasmin"},{"full_name":"Schwarz, Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A"},{"first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","first_name":"Saren"},{"first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"volume":12,"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","status":"public","article_processing_charge":"No","article_number":"3058","has_accepted_license":"1","ddc":["572"],"abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"file_date_updated":"2021-05-28T12:39:43Z","oa":1,"intvolume":"        12","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19557"},{"relation":"earlier_version","status":"public","id":"7800"},{"id":"12401","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}]},"doi":"10.1038/s41467-021-23123-x","scopus_import":"1","date_created":"2021-05-28T11:49:46Z","citation":{"ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>."},"quality_controlled":"1","day":"24","corr_author":"1","publisher":"Springer Nature","type":"journal_article","publication_status":"published","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","grant_number":"F7807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"month":"05","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2026-06-19T22:31:00Z","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"ec_funded":1,"_id":"9429","acknowledged_ssus":[{"_id":"PreCl"}],"isi":1,"publication_identifier":{"eissn":["2041-1723"]}}]