[{"corr_author":"1","external_id":{"arxiv":["2012.00322"]},"doi":"10.48550/arXiv.2012.00322","has_accepted_license":"1","author":[{"full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal","orcid":"0000-0001-9985-9293","first_name":"Kushagra"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"first_name":"Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"first_name":"Amir","last_name":"Sammak","full_name":"Sammak, Amir"},{"last_name":"Botifoll","full_name":"Botifoll, Marc","first_name":"Marc"},{"full_name":"Marti-Sanchez, Sara","last_name":"Marti-Sanchez","first_name":"Sara"},{"first_name":"Menno","full_name":"Veldhorst, Menno","last_name":"Veldhorst"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"title":"Enhancement of proximity induced superconductivity in planar Germanium","abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"ec_funded":1,"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"oa_version":"Submitted Version","file_date_updated":"2020-12-02T10:42:31Z","article_processing_charge":"No","_id":"8831","date_published":"2020-12-02T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"citation":{"ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2012.00322\">10.48550/arXiv.2012.00322</a>","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2012.00322\">https://doi.org/10.48550/arXiv.2012.00322</a>","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, 2012.00322, doi:<a href=\"https://doi.org/10.48550/arXiv.2012.00322\">10.48550/arXiv.2012.00322</a>.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2012.00322\">https://doi.org/10.48550/arXiv.2012.00322</a>.","ieee":"K. Aggarwal <i>et al.</i>, “Enhancement of proximity induced superconductivity in planar Germanium,” <i>arXiv</i>. .","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.)."},"date_created":"2020-12-02T10:42:53Z","publication":"arXiv","status":"public","arxiv":1,"related_material":{"record":[{"status":"public","id":"10559","relation":"later_version"},{"status":"public","id":"8834","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"10058"}]},"ddc":["530"],"article_number":"2012.00322","day":"02","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","type":"preprint","file":[{"access_level":"open_access","file_size":1697939,"date_updated":"2020-12-02T10:42:31Z","relation":"main_file","creator":"gkatsaro","checksum":"22a612e206232fa94b138b2c2f957582","date_created":"2020-12-02T10:42:31Z","file_name":"Superconducting_2D_Ge.pdf","file_id":"8832","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-07-23T22:30:35Z","month":"12","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","department":[{"_id":"GeKa"}]},{"acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"12","language":[{"iso":"eng"}],"date_updated":"2026-07-23T22:30:37Z","oa":1,"isi":1,"pmid":1,"department":[{"_id":"JiFr"}],"publication_status":"published","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"day":"11","year":"2020","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2021-01-07T12:44:33Z","file_name":"2020_ScienceAdvances_Zhang.pdf","success":1,"file_id":"8994","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-01-07T12:44:33Z","file_size":10578145,"relation":"main_file","creator":"dernst","checksum":"5ac2500b191c08ef6dab5327f40ff663"}],"article_number":"eabc8895","publication":"Science Advances","status":"public","date_created":"2021-01-03T23:01:23Z","ddc":["580"],"related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"volume":6,"article_processing_charge":"No","publisher":"AAAS","publication_identifier":{"eissn":["2375-2548"]},"citation":{"ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. 2020;6(50). doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., &#38; Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” <i>Science Advances</i>, vol. 6, no. 50. AAAS, 2020.","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>."},"date_published":"2020-12-11T00:00:00Z","_id":"8986","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","intvolume":"         6","file_date_updated":"2021-01-07T12:44:33Z","has_accepted_license":"1","author":[{"first_name":"Yuzhou","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","orcid":"0000-0002-5607-272X"},{"full_name":"Zhang, Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"doi":"10.1126/sciadv.abc8895","abstract":[{"text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.","lang":"eng"}],"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","ec_funded":1,"corr_author":"1","quality_controlled":"1","scopus_import":"1","issue":"50","external_id":{"pmid":["33310852"],"isi":["000599903600014"]}},{"_id":"8283","publisher":"MDPI","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"citation":{"ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. <i>International Journal of Molecular Sciences</i>. 2020;21(16). doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>","ieee":"H. Chen <i>et al.</i>, “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16. MDPI, 2020.","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21165727\">https://doi.org/10.3390/ijms21165727</a>.","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16, 5272, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21165727\">10.3390/ijms21165727</a>."},"date_published":"2020-08-10T00:00:00Z","article_processing_charge":"No","volume":21,"intvolume":"        21","oa_version":"Published Version","file_date_updated":"2020-08-25T09:53:50Z","abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","doi":"10.3390/ijms21165727","has_accepted_license":"1","author":[{"first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang"},{"first_name":"Linyi","full_name":"Lai, Linyi","last_name":"Lai"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"last_name":"Liu","full_name":"Liu, Liping","first_name":"Liping"},{"full_name":"Jakada, Bello Hassan","last_name":"Jakada","first_name":"Bello Hassan"},{"first_name":"Youmei","last_name":"Huang","full_name":"Huang, Youmei"},{"full_name":"He, Qing","last_name":"He","first_name":"Qing"},{"first_name":"Mengnan","full_name":"Chai, Mengnan","last_name":"Chai"},{"last_name":"Niu","full_name":"Niu, Xiaoping","first_name":"Xiaoping"},{"last_name":"Qin","full_name":"Qin, Yuan","first_name":"Yuan"}],"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"issue":"16","quality_controlled":"1","scopus_import":"1","department":[{"_id":"JiFr"}],"isi":1,"pmid":1,"month":"08","oa":1,"language":[{"iso":"eng"}],"date_updated":"2026-07-23T22:30:37Z","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","file":[{"date_created":"2020-08-25T09:53:50Z","success":1,"file_name":"2020_IntMolecSciences_Chen.pdf","content_type":"application/pdf","file_id":"8292","date_updated":"2020-08-25T09:53:50Z","access_level":"open_access","file_size":5718755,"creator":"cziletti","relation":"main_file","checksum":"03b039244e6ae80580385fd9f577e2b2"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","publication_status":"published","article_type":"original","type":"journal_article","article_number":"5272","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"ddc":["570"],"date_created":"2020-08-24T06:24:03Z","publication":"International Journal of Molecular Sciences","status":"public"},{"article_number":"100048","ddc":["580"],"related_material":{"record":[{"id":"10135","status":"public","relation":"dissertation_contains"}]},"OA_type":"gold","date_created":"2021-02-18T10:18:43Z","publication":"Plant Communications","status":"public","department":[{"_id":"EvBe"}],"isi":1,"pmid":1,"month":"05","date_updated":"2026-07-23T22:30:39Z","oa":1,"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","file":[{"relation":"main_file","creator":"dernst","checksum":"785b266d82a94b007cf40dbbe7c4847e","file_size":840289,"date_updated":"2021-02-18T10:23:59Z","access_level":"open_access","file_name":"2020_PlantComm_Semeradova.pdf","success":1,"file_id":"9161","content_type":"application/pdf","date_created":"2021-02-18T10:23:59Z"}],"OA_place":"publisher","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"year":"2020","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","day":"11","publication_status":"published","article_type":"original","type":"journal_article","abstract":[{"text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.","lang":"eng"}],"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","doi":"10.1016/j.xplc.2020.100048","DOAJ_listed":"1","has_accepted_license":"1","author":[{"first_name":"Hana","full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova"},{"first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","full_name":"Montesinos López, Juan C"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"external_id":{"isi":["000654052800010"],"pmid":["33367243"]},"issue":"3","corr_author":"1","scopus_import":"1","quality_controlled":"1","_id":"9160","publisher":"Elsevier","date_published":"2020-05-11T00:00:00Z","publication_identifier":{"issn":["2590-3462"]},"citation":{"ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. <i>Plant Communications</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">10.1016/j.xplc.2020.100048</a>","apa":"Semerádová, H., Montesinos López, J. C., &#38; Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">https://doi.org/10.1016/j.xplc.2020.100048</a>","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” <i>Plant Communications</i>, vol. 1, no. 3, 100048, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">10.1016/j.xplc.2020.100048</a>.","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” <i>Plant Communications</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">https://doi.org/10.1016/j.xplc.2020.100048</a>.","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” <i>Plant Communications</i>, vol. 1, no. 3. Elsevier, 2020.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020)."},"article_processing_charge":"No","volume":1,"oa_version":"Published Version","intvolume":"         1","file_date_updated":"2021-02-18T10:23:59Z","project":[{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}]},{"language":[{"iso":"eng"}],"oa":1,"month":"07","date_updated":"2026-07-23T22:30:43Z","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"day":"13","year":"2020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","type":"conference","file":[{"access_level":"open_access","file_size":5336380,"date_updated":"2021-03-02T15:38:14Z","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","creator":"dernst","relation":"main_file","date_created":"2021-03-02T15:38:14Z","content_type":"application/pdf","file_id":"9217","success":1,"file_name":"2020_PMLR_Shevchenko.pdf"}],"date_created":"2021-02-25T09:36:22Z","publication":"Proceedings of the 37th International Conference on Machine Learning","status":"public","ddc":["000"],"related_material":{"record":[{"id":"17465","status":"public","relation":"dissertation_contains"}]},"arxiv":1,"article_processing_charge":"No","volume":119,"_id":"9198","publisher":"ML Research Press","date_published":"2020-07-13T00:00:00Z","citation":{"ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ML Research Press; 2020:8773-8784.","apa":"Shevchenko, A., &#38; Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 8773–8784). ML Research Press.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","mla":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, ML Research Press, 2020, pp. 8773–84.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, 2020, vol. 119, pp. 8773–8784.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","chicago":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:8773–84. ML Research Press, 2020."},"page":"8773-8784","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Published Version","intvolume":"       119","file_date_updated":"2021-03-02T15:38:14Z","author":[{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"has_accepted_license":"1","title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"quality_controlled":"1","external_id":{"arxiv":["1912.10095"]}},{"scopus_import":"1","quality_controlled":"1","external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"has_accepted_license":"1","author":[{"first_name":"Tatiana","last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","first_name":"Louisa"},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"first_name":"Kseniia A.","last_name":"Palkina","full_name":"Palkina, Kseniia A."},{"last_name":"Shakhova","full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S."},{"last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I."},{"first_name":"Sofia V.","last_name":"Chekova","full_name":"Chekova, Sofia V."},{"last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","last_name":"Golubev","first_name":"Yaroslav V."},{"last_name":"Negrebetsky","full_name":"Negrebetsky, Vadim V.","first_name":"Vadim V."},{"last_name":"Dolgushin","full_name":"Dolgushin, Sergey A.","first_name":"Sergey A."},{"first_name":"Pavel V.","last_name":"Shalaev","full_name":"Shalaev, Pavel V."},{"full_name":"Shlykov, Dmitry","last_name":"Shlykov","first_name":"Dmitry"},{"first_name":"Olesya A.","last_name":"Melnik","full_name":"Melnik, Olesya A."},{"first_name":"Victoria O.","last_name":"Shipunova","full_name":"Shipunova, Victoria O."},{"last_name":"Deyev","full_name":"Deyev, Sergey M.","first_name":"Sergey M."},{"first_name":"Andrey I.","last_name":"Bubyrev","full_name":"Bubyrev, Andrey I."},{"last_name":"Pushin","full_name":"Pushin, Alexander S.","first_name":"Alexander S."},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"last_name":"Dolgov","full_name":"Dolgov, Sergey V.","first_name":"Sergey V."},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Ilia V.","full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky"},{"first_name":"Karen S.","full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan"}],"doi":"10.1038/s41587-020-0500-9","ec_funded":1,"title":"Plants with genetically encoded autoluminescence","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"page":"944-946","file_date_updated":"2021-03-02T23:30:03Z","intvolume":"        38","oa_version":"Submitted Version","volume":38,"article_processing_charge":"No","citation":{"ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. 2020;38:944-946. doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>, vol. 38, Springer Nature, 2020, pp. 944–46, doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>."},"date_published":"2020-04-27T00:00:00Z","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publisher":"Springer Nature","_id":"7889","status":"public","publication":"Nature Biotechnology","date_created":"2020-05-25T15:02:00Z","ddc":["570"],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"type":"journal_article","publication_status":"published","article_type":"original","year":"2020","day":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"embargo":"2021-03-01","checksum":"1b30467500ec6277229a875b06e196d0","relation":"main_file","creator":"dernst","file_size":1180086,"access_level":"open_access","date_updated":"2021-03-02T23:30:03Z","content_type":"application/pdf","file_id":"8316","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","date_created":"2020-08-28T08:57:07Z"}],"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:49:47Z","month":"04","pmid":1,"isi":1,"department":[{"_id":"FyKo"}]},{"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"issue":"15","quality_controlled":"1","scopus_import":"1","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.","lang":"eng"}],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","ec_funded":1,"doi":"10.1242/jcs.248062","has_accepted_license":"1","author":[{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","first_name":"Nataliia"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"orcid":"0000-0002-8600-0671","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"full_name":"Vert, G","last_name":"Vert","first_name":"G"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"intvolume":"       133","oa_version":"Published Version","file_date_updated":"2021-08-08T22:30:03Z","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"8139","publisher":"The Company of Biologists","date_published":"2020-08-06T00:00:00Z","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"citation":{"ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. 2020;133(15). doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., &#38; Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>.","ieee":"A. J. Johnson <i>et al.</i>, “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” <i>Journal of Cell Science</i>, vol. 133, no. 15. The Company of Biologists, 2020.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>."},"article_processing_charge":"No","volume":133,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"ddc":["575"],"date_created":"2020-07-21T08:58:19Z","publication":"Journal of Cell Science","status":"public","article_number":"jcs248062","file":[{"date_created":"2020-11-26T17:12:51Z","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","content_type":"application/pdf","file_id":"8815","access_level":"open_access","file_size":15150403,"date_updated":"2021-08-08T22:30:03Z","relation":"main_file","creator":"ajohnson","embargo":"2021-08-07","checksum":"2d11f79a0b4e0a380fb002b933da331a"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2020","day":"06","article_type":"original","publication_status":"published","type":"journal_article","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"isi":1,"pmid":1,"month":"08","language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-07-23T22:30:46Z","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. "},{"file_date_updated":"2021-09-11T22:30:04Z","oa_version":"None","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"page":"242","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"date_published":"2020-09-09T00:00:00Z","citation":{"mla":"Kampjut, Domen. <i>Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>.","chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>.","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>","apa":"Kampjut, D. (2020). <i>Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"EM-Fac"}],"publisher":"Institute of Science and Technology Austria","_id":"8340","degree_awarded":"PhD","article_processing_charge":"No","corr_author":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies."}],"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","author":[{"first_name":"Domen","orcid":"0000-0002-6018-3422","full_name":"Kampjut, Domen","last_name":"Kampjut","id":"37233050-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:8340","OA_place":"publisher","file":[{"date_created":"2020-09-08T13:32:06Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8345","file_name":"ThesisFull20200908.docx","date_updated":"2021-09-11T22:30:04Z","access_level":"closed","file_size":166146359,"checksum":"dd270baf82121eb4472ad19d77bf227c","embargo_to":"open_access","relation":"source_file","creator":"dkampjut"},{"file_name":"2020_Thesis_Kampjut.pdf","content_type":"application/pdf","file_id":"8393","date_created":"2020-09-14T15:02:20Z","relation":"main_file","creator":"dernst","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","embargo":"2021-09-10","file_size":13873769,"date_updated":"2021-09-11T22:30:04Z","access_level":"open_access"}],"type":"dissertation","publication_status":"published","day":"09","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2020","department":[{"_id":"LeSa"}],"acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","month":"09","date_updated":"2026-04-08T07:43:58Z","oa":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6848"}]},"alternative_title":["ISTA Thesis"],"ddc":["572"],"status":"public","date_created":"2020-09-07T18:42:23Z"},{"quality_controlled":"1","corr_author":"1","scopus_import":"1","issue":"159","external_id":{"pmid":["32449730"],"isi":["000546406600043"]},"has_accepted_license":"1","author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","full_name":"Beattie, Robert J","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"doi":"10.3791/61147","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"ec_funded":1,"project":[{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416"},{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration"},{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z","article_processing_charge":"No","publisher":"MyJove Corporation","publication_identifier":{"issn":["1940-087X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_published":"2020-05-08T00:00:00Z","citation":{"mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>, no. 159, e61147, MyJove Corporation, 2020, doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>.","ieee":"R. J. Beattie <i>et al.</i>, “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” <i>Journal of Visual Experiments</i>, no. 159. MyJove Corporation, 2020.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>. MyJove Corporation, 2020. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>.","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. 2020;(159). doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., &#38; Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>"},"_id":"7815","publication":"Journal of Visual Experiments","status":"public","date_created":"2020-05-11T08:31:20Z","related_material":{"record":[{"id":"7902","status":"public","relation":"part_of_dissertation"}]},"ddc":["570"],"article_number":"e61147","publication_status":"published","article_type":"original","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"year":"2020","day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":1352186,"access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","checksum":"3154ea7f90b9fb45e084cd1c2770597d","relation":"main_file","creator":"rbeattie","date_created":"2020-05-11T08:28:38Z","file_id":"7816","content_type":"application/pdf","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf"}],"language":[{"iso":"eng"}],"date_updated":"2026-07-23T22:30:48Z","oa":1,"month":"05","isi":1,"pmid":1,"department":[{"_id":"SiHi"}]},{"ddc":["570"],"related_material":{"record":[{"id":"28","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"7815","status":"public"},{"id":"6830","status":"public","relation":"dissertation_contains"}]},"alternative_title":["ISTA Thesis"],"status":"public","date_created":"2020-05-29T08:27:32Z","OA_place":"publisher","file":[{"date_created":"2020-06-05T08:18:08Z","file_name":"PhDThesis_Contreras.docx","file_id":"7927","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":53134142,"access_level":"closed","date_updated":"2021-06-07T22:30:03Z","creator":"xcontreras","relation":"source_file","embargo_to":"open_access","checksum":"43c172bf006c95b65992d473c7240d13"},{"creator":"xcontreras","relation":"main_file","embargo":"2021-06-06","checksum":"addfed9128271be05cae3608e03a6ec0","file_size":35117191,"access_level":"open_access","date_updated":"2021-06-07T22:30:03Z","file_name":"PhDThesis_Contreras.pdf","content_type":"application/pdf","file_id":"7928","date_created":"2020-06-05T08:18:07Z"}],"publication_status":"published","type":"dissertation","day":"05","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"date_updated":"2026-06-18T19:12:39Z","oa":1,"month":"06","corr_author":"1","abstract":[{"text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation.","lang":"eng"}],"title":"Genetic dissection of neural development in health and disease at single cell resolution","ec_funded":1,"author":[{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:7902","oa_version":"Published Version","file_date_updated":"2021-06-07T22:30:03Z","page":"214","supervisor":[{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","date_published":"2020-06-05T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"citation":{"mla":"Contreras, Ximena. <i>Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>","apa":"Contreras, X. (2020). <i>Genetic dissection of neural development in health and disease at single cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>"},"_id":"7902","degree_awarded":"PhD","article_processing_charge":"No"},{"external_id":{"isi":["000573631000004"],"pmid":["32699885"]},"scopus_import":"1","issue":"8","title":"Zena Werb (1945-2020): Cell biology in context","has_accepted_license":"1","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Anna","full_name":"Huttenlocher, Anna","last_name":"Huttenlocher"}],"doi":"10.1083/jcb.202007029","oa_version":"Published Version","intvolume":"       219","file_date_updated":"2021-02-02T23:30:03Z","publisher":"Rockefeller University Press","date_published":"2020-07-22T00:00:00Z","publication_identifier":{"eissn":["1540-8140"]},"citation":{"mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>"},"_id":"8190","volume":219,"article_processing_charge":"No","ddc":["570"],"publication":"The Journal of Cell Biology","status":"public","date_created":"2020-08-02T22:00:57Z","article_number":"e202007029","file":[{"access_level":"open_access","file_size":830725,"date_updated":"2021-02-02T23:30:03Z","embargo":"2021-02-01","checksum":"30016d778d266b8e17d01094917873b8","relation":"main_file","creator":"dernst","date_created":"2020-08-04T13:11:52Z","content_type":"application/pdf","file_id":"8200","file_name":"2020_JCB_Sixt.pdf"}],"article_type":"letter_note","publication_status":"published","type":"journal_article","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"year":"2020","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"pmid":1,"department":[{"_id":"MiSi"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_updated":"2025-06-12T07:34:40Z","oa":1,"month":"07","language":[{"iso":"eng"}]},{"status":"public","date_created":"2020-09-09T11:12:10Z","related_material":{"record":[{"status":"public","id":"7001","relation":"part_of_dissertation"},{"status":"public","id":"6508","relation":"part_of_dissertation"},{"status":"public","id":"735","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"661"}]},"alternative_title":["ISTA Thesis"],"ddc":["570"],"acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","language":[{"iso":"eng"}],"date_updated":"2025-09-11T07:08:52Z","month":"09","oa":1,"department":[{"_id":"BjHo"},{"_id":"CaHe"}],"type":"dissertation","publication_status":"published","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","file":[{"date_created":"2020-09-09T11:06:27Z","file_name":"Shayan-Thesis-Final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8351","access_level":"closed","file_size":65194814,"date_updated":"2021-09-11T22:30:05Z","creator":"sshamip","relation":"source_file","embargo_to":"open_access","checksum":"6e47871c74f85008b9876112eb3fcfa1"},{"relation":"main_file","creator":"sshamip","embargo":"2021-09-10","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","access_level":"open_access","date_updated":"2021-09-11T22:30:05Z","file_size":23729605,"file_name":"Shayan-Thesis-Final.pdf","file_id":"8352","content_type":"application/pdf","date_created":"2020-09-09T11:06:13Z"}],"author":[{"last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:8350","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"corr_author":"1","degree_awarded":"PhD","article_processing_charge":"No","date_published":"2020-09-09T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","apa":"Shamipour, S. (2020). <i>Bulk actin dynamics drive phase segregation in zebrafish oocytes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>.","mla":"Shamipour, Shayan. <i>Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes </i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>."},"publisher":"Institute of Science and Technology Austria","_id":"8350","page":"107","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"file_date_updated":"2021-09-11T22:30:05Z","oa_version":"None"},{"article_number":"jcs239020","status":"public","publication":"Journal of Cell Science","date_created":"2020-09-17T14:00:33Z","ddc":["570"],"acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","oa":1,"month":"04","date_updated":"2025-04-15T07:52:13Z","language":[{"iso":"eng"}],"pmid":1,"isi":1,"department":[{"_id":"FlSc"}],"type":"journal_article","publication_status":"published","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"09","year":"2020","file":[{"file_size":13493302,"date_updated":"2020-10-11T22:30:02Z","access_level":"open_access","checksum":"ba917e551acc4ece2884b751434df9ae","embargo":"2020-10-10","relation":"main_file","creator":"dernst","date_created":"2020-09-17T14:07:51Z","file_id":"8435","content_type":"application/pdf","file_name":"2020_JournalCellScience_Dimchev.pdf"}],"author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"full_name":"Humphries, Ashley C.","last_name":"Humphries","first_name":"Ashley C."},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"first_name":"Vanessa","last_name":"Dimchev","full_name":"Dimchev, Vanessa"},{"full_name":"Stradal, Theresia E. B.","last_name":"Stradal","first_name":"Theresia E. B."},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Krause","full_name":"Krause, Matthias","first_name":"Matthias"},{"full_name":"Way, Michael","last_name":"Way","first_name":"Michael"},{"last_name":"Falcke","full_name":"Falcke, Martin","first_name":"Martin"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"}],"has_accepted_license":"1","doi":"10.1242/jcs.239020","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","abstract":[{"lang":"eng","text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. "}],"keyword":["Cell Biology"],"scopus_import":"1","quality_controlled":"1","issue":"7","external_id":{"isi":["000534387800005"],"pmid":[" 32094266"]},"volume":133,"article_processing_charge":"No","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"date_published":"2020-04-09T00:00:00Z","citation":{"ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>."},"publisher":"The Company of Biologists","_id":"8434","project":[{"grant_number":"M02495","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"file_date_updated":"2020-10-11T22:30:02Z","oa_version":"Published Version","intvolume":"       133"},{"type":"journal_article","publication_status":"published","article_type":"original","year":"2020","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"03","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"success":1,"file_name":"2020_CurrentBiology_Tan.pdf","content_type":"application/pdf","file_id":"8555","date_created":"2020-09-22T09:51:28Z","creator":"dernst","relation":"main_file","checksum":"16f7d51fe28f91c21e4896a2028df40b","file_size":5360135,"date_updated":"2020-09-22T09:51:28Z","access_level":"open_access"}],"acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-07-23T22:30:50Z","month":"02","pmid":1,"isi":1,"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"status":"public","publication":"Current Biology","date_created":"2020-02-02T23:01:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"ddc":["580"],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis"}],"page":"381-395.e8","file_date_updated":"2020-09-22T09:51:28Z","oa_version":"Published Version","intvolume":"        30","volume":30,"article_processing_charge":"No","citation":{"mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>.","ieee":"S. Tan <i>et al.</i>, “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” <i>Current Biology</i>, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. 2020;30(3):381-395.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>"},"publication_identifier":{"issn":["09609822"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_published":"2020-02-03T00:00:00Z","publisher":"Cell Press","_id":"7427","quality_controlled":"1","scopus_import":"1","corr_author":"1","issue":"3","external_id":{"pmid":["31956021"],"isi":["000511287900018"]},"has_accepted_license":"1","author":[{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"last_name":"Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abas, Melinda F","first_name":"Melinda F"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328"},{"full_name":"Glanc, Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783"},{"full_name":"Molnar, Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub"},{"first_name":"Pavel","full_name":"Lasák, Pavel","last_name":"Lasák"},{"first_name":"Ivan","last_name":"Petřík","full_name":"Petřík, Ivan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"full_name":"Pospíšil, Jiří","last_name":"Pospíšil","first_name":"Jiří"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"doi":"10.1016/j.cub.2019.11.058","ec_funded":1,"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","abstract":[{"text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense.","lang":"eng"}]},{"scopus_import":"1","corr_author":"1","quality_controlled":"1","issue":"5","external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"author":[{"first_name":"E","full_name":"Mazur, E","last_name":"Mazur"},{"first_name":"Ivan","full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik"},{"last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"}],"has_accepted_license":"1","doi":"10.1111/nph.16446","title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","abstract":[{"text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.","lang":"eng"}],"ec_funded":1,"page":"1375-1383","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development"}],"oa_version":"Published Version","intvolume":"       226","file_date_updated":"2020-11-20T09:32:10Z","volume":226,"article_processing_charge":"No","publisher":"Wiley","date_published":"2020-06-01T00:00:00Z","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"citation":{"ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","apa":"Mazur, E., Kulik, I., Hajny, J., &#38; Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. <i>New Phytologist</i>. 2020;226(5):1375-1383. doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16446\">https://doi.org/10.1111/nph.16446</a>.","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” <i>New Phytologist</i>, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” <i>New Phytologist</i>, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:<a href=\"https://doi.org/10.1111/nph.16446\">10.1111/nph.16446</a>."},"_id":"7500","publication":"New Phytologist","status":"public","date_created":"2020-02-18T10:03:47Z","related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"ddc":["580"],"article_type":"original","publication_status":"published","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","year":"2020","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2020-11-20T09:32:10Z","file_name":"2020_NewPhytologist_Mazur.pdf","success":1,"file_id":"8781","content_type":"application/pdf","file_size":2106888,"access_level":"open_access","date_updated":"2020-11-20T09:32:10Z","relation":"main_file","creator":"dernst","checksum":"17de728b0205979feb95ce663ba918c2"}],"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","date_updated":"2026-07-23T22:30:50Z","language":[{"iso":"eng"}],"oa":1,"month":"06","isi":1,"pmid":1,"department":[{"_id":"JiFr"}]},{"oa_version":"Submitted Version","intvolume":"         4","file_date_updated":"2020-10-09T09:56:01Z","page":"612-625","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"_id":"7652","publisher":"Springer Nature","citation":{"apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., &#38; Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. 2020;4(4):612-625. doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &#38; Evolution. 4(4), 612–625.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology &#38; Evolution 4 (2020) 612–625.","ieee":"I. Tomanek <i>et al.</i>, “Gene amplification as a form of population-level gene expression regulation,” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>."},"date_published":"2020-04-01T00:00:00Z","publication_identifier":{"issn":["2397-334X"]},"article_processing_charge":"No","volume":4,"external_id":{"pmid":["32152532"],"isi":["000519008300005"]},"issue":"4","quality_controlled":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"title":"Gene amplification as a form of population-level gene expression regulation","doi":"10.1038/s41559-020-1132-7","author":[{"first_name":"Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","full_name":"Tomanek, Isabella"},{"first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah"},{"full_name":"Lagator, M.","last_name":"Lagator","first_name":"M."},{"full_name":"Andersson, A. M. C.","last_name":"Andersson","first_name":"A. M. C."},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"has_accepted_license":"1","file":[{"file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1,"content_type":"application/pdf","file_id":"8640","date_created":"2020-10-09T09:56:01Z","relation":"main_file","creator":"dernst","checksum":"ef3bbf42023e30b2c24a6278025d2040","access_level":"open_access","file_size":745242,"date_updated":"2020-10-09T09:56:01Z"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publication_status":"published","article_type":"original","type":"journal_article","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"isi":1,"pmid":1,"month":"04","date_updated":"2026-07-23T22:30:51Z","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","ddc":["570"],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/"}],"record":[{"status":"public","id":"7016","relation":"research_data"},{"id":"7383","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"8155"},{"id":"8653","status":"public","relation":"used_in_publication"}]},"date_created":"2020-04-08T15:20:53Z","publication":"Nature Ecology & Evolution","status":"public"},{"corr_author":"1","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","abstract":[{"text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.","lang":"eng"}],"doi":"10.15479/AT:ISTA:8822","has_accepted_license":"1","author":[{"full_name":"Hajny, Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","orcid":"0000-0003-2140-7195"}],"file_date_updated":"2021-12-08T23:30:03Z","oa_version":"Published Version","page":"249","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"_id":"8822","date_published":"2020-12-01T00:00:00Z","citation":{"apa":"Hajny, J. (2020). <i>Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>.","mla":"Hajny, Jakub. <i>Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>."},"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"449","status":"public"},{"status":"public","id":"7500","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7427","status":"public"},{"relation":"part_of_dissertation","id":"191","status":"public"},{"status":"public","id":"6260","relation":"part_of_dissertation"}]},"ddc":["580"],"date_created":"2020-12-01T12:38:18Z","status":"public","file":[{"relation":"source_file","creator":"jhajny","checksum":"210a9675af5e4c78b0b56d920ac82866","embargo_to":"open_access","date_updated":"2021-07-16T22:30:03Z","file_size":91279806,"access_level":"closed","file_name":"Jakub Hajný IST Austria final_JH.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8919","date_created":"2020-12-04T07:27:52Z"},{"date_created":"2020-12-09T15:04:41Z","content_type":"application/pdf","file_id":"8933","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","access_level":"open_access","file_size":68707697,"date_updated":"2021-12-08T23:30:03Z","embargo":"2021-12-07","checksum":"1781385b4aa73eba89cc76c6172f71d2","creator":"jhajny","relation":"main_file"}],"OA_place":"publisher","year":"2020","day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","publication_status":"published","department":[{"_id":"JiFr"}],"date_updated":"2026-06-18T19:02:05Z","language":[{"iso":"eng"}],"month":"12","oa":1},{"corr_author":"1","has_accepted_license":"1","author":[{"orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella"}],"doi":"10.15479/AT:ISTA:8653","title":"The evolution of gene expression by copy number and point mutations","abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously.  Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments.  ","lang":"eng"}],"keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"supervisor":[{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"page":"117","oa_version":"Published Version","file_date_updated":"2021-10-20T22:30:03Z","degree_awarded":"PhD","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8653\">10.15479/AT:ISTA:8653</a>","apa":"Tomanek, I. (2020). <i>The evolution of gene expression by copy number and point mutations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8653\">https://doi.org/10.15479/AT:ISTA:8653</a>","mla":"Tomanek, Isabella. <i>The Evolution of Gene Expression by Copy Number and Point Mutations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8653\">10.15479/AT:ISTA:8653</a>.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8653\">https://doi.org/10.15479/AT:ISTA:8653</a>."},"publication_identifier":{"issn":["2663-337X"]},"date_published":"2020-10-13T00:00:00Z","_id":"8653","status":"public","date_created":"2020-10-13T13:02:33Z","ddc":["576"],"related_material":{"record":[{"id":"7652","status":"public","relation":"research_data"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"13","OA_place":"publisher","file":[{"file_name":"Thesis_ITomanek_final_201016.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8666","date_created":"2020-10-16T12:14:21Z","relation":"source_file","creator":"itomanek","checksum":"c01d9f59794b4b70528f37637c17ad02","embargo_to":"open_access","access_level":"closed","file_size":25131884,"date_updated":"2021-10-20T22:30:03Z"},{"relation":"main_file","creator":"itomanek","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","embargo":"2021-10-19","date_updated":"2021-10-20T22:30:03Z","access_level":"open_access","file_size":15405675,"file_name":"Thesis_ITomanek_final_201016.pdf","content_type":"application/pdf","file_id":"8667","date_created":"2020-10-16T12:14:21Z"}],"language":[{"iso":"eng"}],"oa":1,"month":"10","date_updated":"2026-04-08T07:29:19Z","department":[{"_id":"CaGu"}]},{"page":"141","supervisor":[{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353"}],"oa_version":"Published Version","file_date_updated":"2021-12-31T23:30:04Z","degree_awarded":"PhD","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"citation":{"short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>.","mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>"},"publication_identifier":{"issn":["2663-337X"]},"date_published":"2020-12-30T00:00:00Z","_id":"8983","corr_author":"1","has_accepted_license":"1","author":[{"full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","last_name":"Emtenani","orcid":"0000-0001-6981-6938","first_name":"Shamsi"}],"doi":"10.15479/AT:ISTA:8983","title":"Metabolic regulation of Drosophila macrophage tissue invasion","abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}],"publication_status":"published","type":"dissertation","year":"2020","day":"30","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","file":[{"file_size":10848175,"access_level":"open_access","date_updated":"2021-12-31T23:30:04Z","creator":"semtenan","relation":"main_file","checksum":"ec2797ab7a6f253b35df0572b36d1b43","embargo":"2021-12-30","date_created":"2020-12-30T15:34:01Z","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","content_type":"application/pdf","file_id":"8984"},{"relation":"source_file","creator":"semtenan","checksum":"cc30e6608a9815414024cf548dff3b3a","embargo_to":"open_access","access_level":"closed","file_size":10073648,"date_updated":"2021-12-31T23:30:04Z","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","content_type":"application/pdf","file_id":"8985","date_created":"2020-12-30T15:37:36Z"}],"acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","month":"12","language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-04-08T07:28:54Z","department":[{"_id":"DaSi"}],"status":"public","date_created":"2020-12-30T15:41:26Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"8557","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6187"}]},"alternative_title":["ISTA Thesis"],"ddc":["570"]},{"publication_status":"draft","project":[{"call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","call_identifier":"FP7"},{"grant_number":"24800","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"type":"preprint","year":"2020","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}],"date_updated":"2026-07-23T22:30:52Z","month":"09","acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2020-09-18T00:00:00Z","citation":{"ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. ."},"department":[{"_id":"DaSi"},{"_id":"JoCs"}],"_id":"8557","publication":"bioRxiv","corr_author":"1","status":"public","date_created":"2020-09-23T09:36:47Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10614"},{"id":"8983","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera"},{"full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","first_name":"Stephanie"},{"first_name":"Igor","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn"},{"last_name":"Linder","full_name":"Linder, Markus","first_name":"Markus"},{"orcid":"0000-0001-6981-6938","first_name":"Shamsi","full_name":"Emtenani, Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","full_name":"György, Attila","first_name":"Attila","orcid":"0000-0002-1819-198X"},{"first_name":"Maria","full_name":"Sibilia, Maria","last_name":"Sibilia"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"doi":"10.1101/2020.09.18.301481","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.","lang":"eng"}],"ec_funded":1}]