[{"citation":{"apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., &#38; Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 16398–16408). Vancouver, Canada: Neural Information Processing Systems Foundation.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Neural Information Processing Systems Foundation; 2020:16398-16408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. 34th Conference on Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 33, 16398–16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:16398–408. Neural Information Processing Systems Foundation, 2020.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 16398–408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, 34th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2020, pp. 16398–16408."},"abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2020-12-06","end_date":"2020-12-12"},"oa_version":"Published Version","author":[{"full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","last_name":"Confavreux"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"},{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J."},{"full_name":"Lillicrap, Timothy","first_name":"Timothy","last_name":"Lillicrap"},{"orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","related_material":{"record":[{"id":"14422","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"is_continued_by","url":"https://doi.org/10.1101/2020.10.24.353409"}]},"year":"2020","date_updated":"2026-08-11T22:30:27Z","type":"conference","publication_identifier":{"issn":["1049-5258"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":33,"date_published":"2020-12-06T00:00:00Z","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"},{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"month":"12","scopus_import":"1","day":"06","date_created":"2021-07-04T22:01:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"intvolume":"        33","publication_status":"published","status":"public","alternative_title":["Advances in Neural Information Processing Systems"],"publication":"34th Conference on Neural Information Processing Systems","oa":1,"department":[{"_id":"TiVo"}],"page":"16398-16408","publisher":"Neural Information Processing Systems Foundation","acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","article_processing_charge":"No","_id":"9633","quality_controlled":"1","ddc":["570"],"das_tickbox":"1"},{"corr_author":"1","file_date_updated":"2020-09-18T13:02:37Z","has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"ec_funded":1,"volume":11,"date_published":"2020-09-08T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","month":"09","doi":"10.1038/s41467-020-18269-z","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"first_name":"Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"first_name":"Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","orcid":"0000-0001-9868-2166","last_name":"Hease","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","first_name":"Farid"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","article_number":"4460","citation":{"mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>"},"abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"date_updated":"2026-08-11T22:30:32Z","year":"2020","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"research_data","id":"13056"},{"id":"18871","status":"public","relation":"dissertation_contains"}]},"department":[{"_id":"JoFi"}],"publisher":"Springer Nature","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2020-09-18T13:02:37Z","access_level":"open_access","file_id":"8530","relation":"main_file","creator":"dernst","success":1,"checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"date_created":"2020-09-18T13:02:37Z","file_name":"2020_NatureComm_Arnold.pdf"}],"status":"public","publication":"Nature Communications","external_id":{"isi":["000577280200001"],"pmid":["32901014"]},"quality_controlled":"1","ddc":["530"],"isi":1,"article_processing_charge":"No","_id":"8529","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2020-09-18T10:56:20Z","day":"08","pmid":1,"acknowledged_ssus":[{"_id":"NanoFab"}],"publication_status":"published","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"intvolume":"        11"},{"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"research_data","status":"public","id":"13071"},{"status":"public","relation":"dissertation_contains","id":"13175"},{"id":"12900","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18871"}]},"year":"2020","date_updated":"2026-08-11T22:30:33Z","type":"journal_article","publication_identifier":{"issn":["2691-3399"]},"citation":{"ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel HGL, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 1(2), 020315.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald G.L. Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>.","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state,” <i>PRX Quantum</i>, vol. 1, no. 2. American Physical Society, 2020.","mla":"Hease, William J., et al. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>, vol. 1, no. 2, 020315, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H.G.L. Schwefel, J.M. Fink, PRX Quantum 1 (2020).","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H. G. L., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. 2020;1(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>"},"article_number":"020315","abstract":[{"text":"Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion\r\nefficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"},{"first_name":"Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","first_name":"Georg M"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"doi":"10.1103/prxquantum.1.020315","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"volume":1,"date_published":"2020-11-23T00:00:00Z","corr_author":"1","file_date_updated":"2021-02-12T11:16:16Z","has_accepted_license":"1","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","call_identifier":"H2020"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"intvolume":"         1","publication_status":"published","acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2021-02-12T10:41:28Z","day":"23","issue":"2","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors acknowledge the support of T. Menner, A. Arslani, and T. Asenov from the Miba machine shop for machining the microwave cavity, and thank S. Barzanjeh, F. Sedlmeir, and C. Marquardt for fruitful discussions. This work is supported by IST Austria and the European Research Council under Grant No. 758053 (ERC StG QUNNECT). W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411.\r\nG.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71) and the European Union’s Horizon 2020 research and innovation program under Grant No. 899354 (FET Open SuperQuLAN). H.G.L.S. acknowledges support from the Aotearoa/New Zealand’s MBIE Endeavour Smart Ideas Grant No UOOX1805.","isi":1,"article_processing_charge":"No","_id":"9114","external_id":{"isi":["000674680100001"]},"quality_controlled":"1","ddc":["530"],"status":"public","publication":"PRX Quantum","file":[{"creator":"dernst","file_id":"9115","relation":"main_file","content_type":"application/pdf","date_updated":"2021-02-12T11:16:16Z","access_level":"open_access","date_created":"2021-02-12T11:16:16Z","file_size":2146924,"checksum":"b70b12ded6d7660d4c9037eb09bfed0c","file_name":"2020_PRXQuantum_Hease.pdf","success":1}],"oa":1,"department":[{"_id":"JoFi"}],"publisher":"American Physical Society"},{"corr_author":"1","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"has_accepted_license":"1","file_date_updated":"2020-12-02T10:42:31Z","ec_funded":1,"date_published":"2020-12-02T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2012.00322","month":"12","author":[{"full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra","orcid":"0000-0001-9985-9293","last_name":"Aggarwal"},{"full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann"},{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"full_name":"Sammak, Amir","last_name":"Sammak","first_name":"Amir"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"full_name":"Marti-Sanchez, Sara","last_name":"Marti-Sanchez","first_name":"Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Scappucci","first_name":"Giordano","full_name":"Scappucci, Giordano"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","citation":{"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>.","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.","ieee":"K. Aggarwal <i>et al.</i>, “Enhancement of proximity induced superconductivity in planar Germanium,” <i>arXiv</i>. .","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>.","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.).","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>","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>"},"article_number":"2012.00322","abstract":[{"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.","lang":"eng"}],"type":"preprint","arxiv":1,"date_updated":"2026-08-11T22:30:42Z","year":"2020","title":"Enhancement of proximity induced superconductivity in planar Germanium","related_material":{"record":[{"status":"public","relation":"later_version","id":"10559"},{"relation":"research_data","status":"public","id":"8834"},{"id":"10058","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"GeKa"}],"oa":1,"file":[{"file_name":"Superconducting_2D_Ge.pdf","checksum":"22a612e206232fa94b138b2c2f957582","date_created":"2020-12-02T10:42:31Z","file_size":1697939,"relation":"main_file","file_id":"8832","creator":"gkatsaro","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-12-02T10:42:31Z"}],"status":"public","publication":"arXiv","external_id":{"arxiv":["2012.00322"]},"ddc":["530"],"_id":"8831","article_processing_charge":"No","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-12-02T10:42:53Z","day":"02","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_status":"draft"},{"pmid":1,"date_created":"2021-01-03T23:01:23Z","day":"11","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"issue":"50","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"         6","publication_status":"published","publication":"Science Advances","status":"public","file":[{"relation":"main_file","file_id":"8994","creator":"dernst","access_level":"open_access","date_updated":"2021-01-07T12:44:33Z","content_type":"application/pdf","file_name":"2020_ScienceAdvances_Zhang.pdf","checksum":"5ac2500b191c08ef6dab5327f40ff663","date_created":"2021-01-07T12:44:33Z","file_size":10578145,"success":1}],"oa":1,"publisher":"AAAS","department":[{"_id":"JiFr"}],"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. ","article_processing_charge":"No","_id":"8986","isi":1,"ddc":["580"],"quality_controlled":"1","external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"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"}],"article_number":"eabc8895","citation":{"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.","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>.","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>.","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.","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>"},"oa_version":"Published Version","author":[{"orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","year":"2020","date_updated":"2026-08-11T22:30:44Z","publication_identifier":{"eissn":["2375-2548"]},"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","date_published":"2020-12-11T00:00:00Z","volume":6,"ec_funded":1,"has_accepted_license":"1","file_date_updated":"2021-01-07T12:44:33Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"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"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"12","doi":"10.1126/sciadv.abc8895","scopus_import":"1"},{"language":[{"iso":"eng"}],"article_type":"original","volume":21,"date_published":"2020-08-10T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-08-25T09:53:50Z","month":"08","doi":"10.3390/ijms21165727","scopus_import":"1","citation":{"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).","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.","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>.","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>.","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.","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>","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>"},"article_number":"5272","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Lai, Linyi","last_name":"Lai","first_name":"Linyi"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"last_name":"Liu","first_name":"Liping","full_name":"Liu, Liping"},{"full_name":"Jakada, Bello Hassan","first_name":"Bello Hassan","last_name":"Jakada"},{"last_name":"Huang","first_name":"Youmei","full_name":"Huang, Youmei"},{"first_name":"Qing","last_name":"He","full_name":"He, Qing"},{"last_name":"Chai","first_name":"Mengnan","full_name":"Chai, Mengnan"},{"full_name":"Niu, Xiaoping","first_name":"Xiaoping","last_name":"Niu"},{"full_name":"Qin, Yuan","last_name":"Qin","first_name":"Yuan"}],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"year":"2020","date_updated":"2026-08-11T22:30:44Z","type":"journal_article","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"status":"public","publication":"International Journal of Molecular Sciences","file":[{"relation":"main_file","file_id":"8292","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-08-25T09:53:50Z","file_name":"2020_IntMolecSciences_Chen.pdf","checksum":"03b039244e6ae80580385fd9f577e2b2","date_created":"2020-08-25T09:53:50Z","file_size":5718755,"success":1}],"oa":1,"department":[{"_id":"JiFr"}],"publisher":"MDPI","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","isi":1,"article_processing_charge":"No","_id":"8283","external_id":{"isi":["000565090300001"],"pmid":["32785037"]},"quality_controlled":"1","ddc":["570"],"day":"10","date_created":"2020-08-24T06:24:03Z","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        21","publication_status":"published"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.xplc.2020.100048","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","volume":1,"date_published":"2020-05-11T00:00:00Z","file_date_updated":"2021-02-18T10:23:59Z","has_accepted_license":"1","project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","grant_number":"24746","_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"}],"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10135"}]},"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","year":"2020","date_updated":"2026-08-11T22:30:46Z","publication_identifier":{"issn":["2590-3462"]},"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"}],"article_number":"100048","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>","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","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>.","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.","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>.","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."},"oa_version":"Published Version","author":[{"last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semeradova, Hana"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"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.","_id":"9160","OA_type":"gold","article_processing_charge":"No","isi":1,"ddc":["580"],"external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"quality_controlled":"1","publication":"Plant Communications","status":"public","OA_place":"publisher","file":[{"file_name":"2020_PlantComm_Semeradova.pdf","date_created":"2021-02-18T10:23:59Z","file_size":840289,"checksum":"785b266d82a94b007cf40dbbe7c4847e","success":1,"creator":"dernst","relation":"main_file","file_id":"9161","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-02-18T10:23:59Z"}],"oa":1,"publisher":"Elsevier","department":[{"_id":"EvBe"}],"intvolume":"         1","DOAJ_listed":"1","publication_status":"published","pmid":1,"day":"11","date_created":"2021-02-18T10:18:43Z","issue":"3","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0"},{"type":"journal_article","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"date_updated":"2025-04-14T07:49:47Z","year":"2020","title":"Plants with genetically encoded autoluminescence","related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"author":[{"last_name":"Mitiouchkina","first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa"},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"first_name":"Tatiana A.","last_name":"Karataeva","full_name":"Karataeva, Tatiana A."},{"full_name":"Palkina, Kseniia A.","first_name":"Kseniia A.","last_name":"Palkina"},{"last_name":"Shakhova","first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S."},{"last_name":"Fakhranurova","first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I."},{"full_name":"Chekova, Sofia V.","last_name":"Chekova","first_name":"Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S.","last_name":"Tsarkova"},{"first_name":"Yaroslav V.","last_name":"Golubev","full_name":"Golubev, Yaroslav V."},{"full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky","first_name":"Vadim V."},{"first_name":"Sergey A.","last_name":"Dolgushin","full_name":"Dolgushin, Sergey A."},{"full_name":"Shalaev, Pavel V.","last_name":"Shalaev","first_name":"Pavel V."},{"full_name":"Shlykov, Dmitry","last_name":"Shlykov","first_name":"Dmitry"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"last_name":"Shipunova","first_name":"Victoria O.","full_name":"Shipunova, Victoria O."},{"last_name":"Deyev","first_name":"Sergey M.","full_name":"Deyev, Sergey M."},{"full_name":"Bubyrev, Andrey I.","first_name":"Andrey I.","last_name":"Bubyrev"},{"full_name":"Pushin, Alexander S.","first_name":"Alexander S.","last_name":"Pushin"},{"first_name":"Vladimir V.","last_name":"Choob","full_name":"Choob, Vladimir V."},{"full_name":"Dolgov, Sergey V.","last_name":"Dolgov","first_name":"Sergey V."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"oa_version":"Submitted Version","citation":{"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>.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","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>.","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.","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.","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>"},"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"}],"scopus_import":"1","month":"04","doi":"10.1038/s41587-020-0500-9","has_accepted_license":"1","project":[{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020"}],"file_date_updated":"2021-03-02T23:30:03Z","ec_funded":1,"date_published":"2020-04-27T00:00:00Z","volume":38,"article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"27","date_created":"2020-05-25T15:02:00Z","pmid":1,"external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"quality_controlled":"1","ddc":["570"],"isi":1,"_id":"7889","article_processing_charge":"No","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.","page":"944-946","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","file":[{"access_level":"open_access","date_updated":"2021-03-02T23:30:03Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8316","embargo":"2021-03-01","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","file_size":1180086,"date_created":"2020-08-28T08:57:07Z","checksum":"1b30467500ec6277229a875b06e196d0"}],"oa":1,"status":"public","publication":"Nature Biotechnology"},{"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2021-08-08T22:30:03Z","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"has_accepted_license":"1","date_published":"2020-08-06T00:00:00Z","volume":133,"ec_funded":1,"month":"08","doi":"10.1242/jcs.248062","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"}],"article_number":"jcs248062","citation":{"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>","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","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.","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.","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>."},"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vert","first_name":"G","full_name":"Vert, G"},{"full_name":"Bednarek, SY","first_name":"SY","last_name":"Bednarek"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","year":"2020","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"type":"journal_article","date_updated":"2026-08-11T22:30:51Z","publication":"Journal of Cell Science","status":"public","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"file":[{"file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","date_created":"2020-11-26T17:12:51Z","file_size":15150403,"checksum":"2d11f79a0b4e0a380fb002b933da331a","creator":"ajohnson","file_id":"8815","relation":"main_file","embargo":"2021-08-07","access_level":"open_access","date_updated":"2021-08-08T22:30:03Z","content_type":"application/pdf"}],"oa":1,"article_processing_charge":"No","_id":"8139","isi":1,"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. ","ddc":["575"],"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"quality_controlled":"1","issue":"15","pmid":1,"date_created":"2020-07-21T08:58:19Z","day":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","intvolume":"       133","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}]},{"date_published":"2020-09-09T00:00:00Z","ec_funded":1,"file_date_updated":"2021-09-11T22:30:04Z","has_accepted_license":"1","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","language":[{"iso":"eng"}],"month":"09","doi":"10.15479/AT:ISTA:8340","oa_version":"None","author":[{"last_name":"Kampjut","first_name":"Domen","orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen"}],"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."}],"citation":{"short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","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>.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","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>.","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>"},"date_updated":"2026-04-08T07:43:58Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6848"}]},"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","year":"2020","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"file":[{"date_created":"2020-09-08T13:32:06Z","file_size":166146359,"checksum":"dd270baf82121eb4472ad19d77bf227c","file_name":"ThesisFull20200908.docx","embargo_to":"open_access","creator":"dkampjut","relation":"source_file","file_id":"8345","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-09-11T22:30:04Z","access_level":"closed"},{"creator":"dernst","file_id":"8393","relation":"main_file","embargo":"2021-09-10","access_level":"open_access","date_updated":"2021-09-11T22:30:04Z","content_type":"application/pdf","file_name":"2020_Thesis_Kampjut.pdf","file_size":13873769,"date_created":"2020-09-14T15:02:20Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c"}],"oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"LeSa"}],"page":"242","status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","ddc":["572"],"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.","article_processing_charge":"No","_id":"8340","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_created":"2020-09-07T18:42:23Z","day":"09","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_status":"published"},{"related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","year":"2020","date_updated":"2026-08-11T22:30:53Z","publication_identifier":{"issn":["09609822"]},"type":"journal_article","abstract":[{"lang":"eng","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."}],"citation":{"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.","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.","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>.","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>"},"oa_version":"Published Version","author":[{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abas, Melinda F","last_name":"Abas","first_name":"Melinda F"},{"first_name":"Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"full_name":"Lasák, Pavel","first_name":"Pavel","last_name":"Lasák"},{"full_name":"Petřík, Ivan","last_name":"Petřík","first_name":"Ivan"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"last_name":"Pospíšil","first_name":"Jiří","full_name":"Pospíšil, Jiří"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"doi":"10.1016/j.cub.2019.11.058","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","date_published":"2020-02-03T00:00:00Z","volume":30,"ec_funded":1,"file_date_updated":"2020-09-22T09:51:28Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","corr_author":"1","intvolume":"        30","publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"day":"03","date_created":"2020-02-02T23:01:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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). ","article_processing_charge":"No","_id":"7427","isi":1,"ddc":["580"],"quality_controlled":"1","external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"publication":"Current Biology","status":"public","oa":1,"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-09-22T09:51:28Z","creator":"dernst","file_id":"8555","relation":"main_file","success":1,"file_name":"2020_CurrentBiology_Tan.pdf","date_created":"2020-09-22T09:51:28Z","file_size":5360135,"checksum":"16f7d51fe28f91c21e4896a2028df40b"}],"publisher":"Cell Press","page":"381-395.e8","department":[{"_id":"JiFr"},{"_id":"EvBe"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","date_created":"2020-02-18T10:03:47Z","pmid":1,"issue":"5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"       226","publication_status":"published","file":[{"file_name":"2020_NewPhytologist_Mazur.pdf","checksum":"17de728b0205979feb95ce663ba918c2","file_size":2106888,"date_created":"2020-11-20T09:32:10Z","success":1,"relation":"main_file","file_id":"8781","creator":"dernst","access_level":"open_access","date_updated":"2020-11-20T09:32:10Z","content_type":"application/pdf"}],"oa":1,"page":"1375-1383","department":[{"_id":"JiFr"}],"publisher":"Wiley","status":"public","publication":"New Phytologist","external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"quality_controlled":"1","ddc":["580"],"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.","isi":1,"article_processing_charge":"No","_id":"7500","oa_version":"Published Version","author":[{"full_name":"Mazur, E","first_name":"E","last_name":"Mazur"},{"first_name":"Ivan","last_name":"Kulik","full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"citation":{"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>.","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.","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>.","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.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 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>"},"abstract":[{"lang":"eng","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."}],"date_updated":"2026-08-11T22:30:53Z","type":"journal_article","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"year":"2020","ec_funded":1,"date_published":"2020-06-01T00:00:00Z","volume":226,"corr_author":"1","has_accepted_license":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","grant_number":"25239","_id":"2699E3D2-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-11-20T09:32:10Z","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","month":"06","doi":"10.1111/nph.16446"},{"publication_status":"published","intvolume":"         4","issue":"4","day":"01","date_created":"2020-04-08T15:20:53Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"_id":"7652","article_processing_charge":"No","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.","external_id":{"pmid":["32152532"],"isi":["000519008300005"]},"quality_controlled":"1","ddc":["570"],"status":"public","publication":"Nature Ecology & Evolution","page":"612-625","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"Springer Nature","oa":1,"file":[{"file_id":"8640","relation":"main_file","creator":"dernst","date_updated":"2020-10-09T09:56:01Z","content_type":"application/pdf","access_level":"open_access","checksum":"ef3bbf42023e30b2c24a6278025d2040","file_size":745242,"date_created":"2020-10-09T09:56:01Z","file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1}],"year":"2020","title":"Gene amplification as a form of population-level gene expression regulation","related_material":{"record":[{"id":"7016","relation":"research_data","status":"public"},{"id":"7383","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8155"},{"id":"8653","relation":"used_in_publication","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/"}]},"type":"journal_article","publication_identifier":{"issn":["2397-334X"]},"date_updated":"2026-08-11T22:30:53Z","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>","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.","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>.","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>.","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."},"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."}],"author":[{"last_name":"Tomanek","orcid":"0000-0001-6197-363X","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella"},{"full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","last_name":"Grah"},{"full_name":"Lagator, M.","last_name":"Lagator","first_name":"M."},{"full_name":"Andersson, A. M. C.","first_name":"A. M. C.","last_name":"Andersson"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"oa_version":"Submitted Version","doi":"10.1038/s41559-020-1132-7","month":"04","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-10-09T09:56:01Z","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"has_accepted_license":"1","date_published":"2020-04-01T00:00:00Z","volume":4},{"doi":"10.15479/AT:ISTA:8822","month":"12","language":[{"iso":"eng"}],"date_published":"2020-12-01T00:00:00Z","has_accepted_license":"1","file_date_updated":"2021-12-08T23:30:03Z","corr_author":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"449"},{"relation":"part_of_dissertation","status":"public","id":"7500"},{"id":"7427","relation":"part_of_dissertation","status":"public"},{"id":"191","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6260"}]},"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","year":"2020","date_updated":"2026-06-18T19:02:05Z","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","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"}],"citation":{"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.","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>.","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.","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>.","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.","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>","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>"},"oa_version":"Published Version","author":[{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"}],"article_processing_charge":"No","_id":"8822","ddc":["580"],"alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"relation":"source_file","file_id":"8919","creator":"jhajny","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-07-16T22:30:03Z","access_level":"closed","checksum":"210a9675af5e4c78b0b56d920ac82866","date_created":"2020-12-04T07:27:52Z","file_size":91279806,"file_name":"Jakub Hajný IST Austria final_JH.docx","embargo_to":"open_access"},{"embargo":"2021-12-07","creator":"jhajny","relation":"main_file","file_id":"8933","date_updated":"2021-12-08T23:30:03Z","content_type":"application/pdf","access_level":"open_access","date_created":"2020-12-09T15:04:41Z","file_size":68707697,"checksum":"1781385b4aa73eba89cc76c6172f71d2","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf"}],"oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"page":"249","publication_status":"published","date_created":"2020-12-01T12:38:18Z","day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","day":"13","date_created":"2020-10-13T13:02:33Z","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"publication_status":"published","supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-10-20T22:30:03Z","access_level":"closed","file_id":"8666","relation":"source_file","creator":"itomanek","embargo_to":"open_access","checksum":"c01d9f59794b4b70528f37637c17ad02","file_size":25131884,"date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.docx"},{"file_size":15405675,"date_created":"2020-10-16T12:14:21Z","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","file_name":"Thesis_ITomanek_final_201016.pdf","content_type":"application/pdf","date_updated":"2021-10-20T22:30:03Z","access_level":"open_access","embargo":"2021-10-19","creator":"itomanek","relation":"main_file","file_id":"8667"}],"oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"page":"117","status":"public","alternative_title":["ISTA Thesis"],"OA_place":"publisher","ddc":["576"],"_id":"8653","article_processing_charge":"No","oa_version":"Published Version","author":[{"orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek","full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","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.  "}],"citation":{"short":"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>.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","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>.","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>"},"date_updated":"2026-04-08T07:29:19Z","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","related_material":{"record":[{"relation":"research_data","status":"public","id":"7652"}]},"title":"The evolution of gene expression by copy number and point mutations","year":"2020","date_published":"2020-10-13T00:00:00Z","file_date_updated":"2021-10-20T22:30:03Z","has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8653","month":"10"},{"abstract":[{"text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in   O((n+m)⋅t2)  time, given a tree decomposition of the MC with width t. Our results also imply a bound of   O(κ⋅(n+m)⋅t2)  for each objective on MDPs, where   κ  is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.","lang":"eng"}],"citation":{"short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270.","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” <i>Automated Technology for Verification and Analysis</i>, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">10.1007/978-3-030-59152-6_14</a>.","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in <i>Automated Technology for Verification and Analysis</i>, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In <i>Automated Technology for Verification and Analysis</i>, 12302:253–70. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">https://doi.org/10.1007/978-3-030-59152-6_14</a>.","ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.","ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: <i>Automated Technology for Verification and Analysis</i>. Vol 12302. Springer Nature; 2020:253-270. doi:<a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">10.1007/978-3-030-59152-6_14</a>","apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., &#38; Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In <i>Automated Technology for Verification and Analysis</i> (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">https://doi.org/10.1007/978-3-030-59152-6_14</a>"},"oa_version":"Submitted Version","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Hanoi, Vietnam","start_date":"2020-10-19","end_date":"2020-10-23"},"author":[{"last_name":"Asadi","first_name":"Ali","full_name":"Asadi, Ali"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"full_name":"Mohammadi, Kiarash","first_name":"Kiarash","last_name":"Mohammadi"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","year":"2020","date_updated":"2026-08-11T22:30:56Z","publication_identifier":{"eisbn":["9783030591526"],"isbn":["9783030591519"],"eissn":["1611-3349"],"issn":["0302-9743"]},"type":"conference","language":[{"iso":"eng"}],"date_published":"2020-10-12T00:00:00Z","volume":12302,"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","file_date_updated":"2020-11-06T07:41:03Z","doi":"10.1007/978-3-030-59152-6_14","month":"10","scopus_import":"1","date_created":"2020-11-06T07:30:05Z","day":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     12302","publication_status":"published","publication":"Automated Technology for Verification and Analysis","alternative_title":["LNCS"],"status":"public","oa":1,"file":[{"success":1,"file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","date_created":"2020-11-06T07:41:03Z","file_size":726648,"checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","access_level":"open_access","date_updated":"2020-11-06T07:41:03Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8729"}],"publisher":"Springer Nature","page":"253-270","department":[{"_id":"KrCh"}],"article_processing_charge":"No","_id":"8728","isi":1,"ddc":["000"],"quality_controlled":"1","external_id":{"isi":["000723555700014"]}},{"oa":1,"page":"672-687","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","status":"public","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","external_id":{"arxiv":["1902.04373"],"isi":["000614622300045"]},"quality_controlled":"1","isi":1,"article_processing_charge":"No","_id":"8089","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"day":"11","date_created":"2020-07-05T22:00:45Z","publication_status":"published","date_published":"2020-06-11T00:00:00Z","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","doi":"10.1145/3385412.3385969","oa_version":"Preprint","conference":{"location":"London, United Kingdom","start_date":"2020-06-15","end_date":"2020-06-20","name":"PLDI: Programming Language Design and Implementation"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"}],"citation":{"ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: <i>Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2020:672-687. doi:<a href=\"https://doi.org/10.1145/3385412.3385969\">10.1145/3385412.3385969</a>","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In <i>Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation</i> (pp. 672–687). London, United Kingdom: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3385412.3385969\">https://doi.org/10.1145/3385412.3385969</a>","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In <i>Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, 672–87. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3385412.3385969\">https://doi.org/10.1145/3385412.3385969</a>.","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in <i>Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, London, United Kingdom, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” <i>Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2020, pp. 672–87, doi:<a href=\"https://doi.org/10.1145/3385412.3385969\">10.1145/3385412.3385969</a>."},"abstract":[{"text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.","lang":"eng"}],"date_updated":"2026-08-11T22:30:56Z","type":"conference","arxiv":1,"publication_identifier":{"isbn":["9781450376136"]},"title":"Polynomial invariant generation for non-deterministic recursive programs","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"year":"2020"},{"abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” <i>European Symposium on Programming</i>, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in <i>European Symposium on Programming</i>, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In <i>European Symposium on Programming</i>, 12075:112–40. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In <i>European Symposium on Programming</i> (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: <i>European Symposium on Programming</i>. Vol 12075. Springer Nature; 2020:112-140. doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>"},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"conference":{"start_date":"2020-04-25","location":"Dublin, Ireland","end_date":"2020-04-30","name":"ESOP: Programming Languages and Systems"},"oa_version":"Published Version","year":"2020","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","publication_identifier":{"isbn":["9783030449131"],"eissn":["1611-3349"],"issn":["0302-9743"]},"type":"conference","date_updated":"2026-08-11T22:30:56Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","has_accepted_license":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"corr_author":"1","date_published":"2020-04-18T00:00:00Z","volume":12075,"doi":"10.1007/978-3-030-44914-8_5","month":"04","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"18","date_created":"2020-05-10T22:00:50Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","intvolume":"     12075","publication":"European Symposium on Programming","alternative_title":["LNCS"],"status":"public","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"page":"112-140","file":[{"checksum":"8618b80f4cf7b39a60e61a6445ad9807","date_created":"2020-05-26T13:34:48Z","file_size":651250,"file_name":"2020_LNCS_Chatterjee.pdf","relation":"main_file","file_id":"7895","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access"}],"oa":1,"_id":"7810","article_processing_charge":"No","isi":1,"ddc":["000"],"quality_controlled":"1","external_id":{"isi":["000681656800005"]}},{"abstract":[{"text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem.","lang":"eng"}],"citation":{"short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering and System Safety</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.ress.2019.106665\">https://doi.org/10.1016/j.ress.2019.106665</a>.","mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering and System Safety</i>, vol. 193, 106665, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.ress.2019.106665\">10.1016/j.ress.2019.106665</a>.","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” <i>Reliability Engineering and System Safety</i>, vol. 193. Elsevier, 2020.","ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. <i>Reliability Engineering and System Safety</i>. 2020;193. doi:<a href=\"https://doi.org/10.1016/j.ress.2019.106665\">10.1016/j.ress.2019.106665</a>","apa":"Goharshady, A. K., &#38; Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. <i>Reliability Engineering and System Safety</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ress.2019.106665\">https://doi.org/10.1016/j.ress.2019.106665</a>"},"article_number":"106665","oa_version":"Preprint","author":[{"last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"title":"An efficient algorithm for computing network reliability in small treewidth","year":"2020","date_updated":"2026-08-11T22:30:56Z","publication_identifier":{"issn":["0951-8320"]},"arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","volume":193,"date_published":"2020-01-01T00:00:00Z","project":[{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.ress.2019.106665","month":"01","scopus_import":"1","day":"01","date_created":"2019-09-29T22:00:44Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"url":"https://arxiv.org/abs/1712.09692","open_access":"1"}],"intvolume":"       193","publication_status":"published","publication":"Reliability Engineering and System Safety","status":"public","oa":1,"publisher":"Elsevier","department":[{"_id":"KrCh"}],"acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","_id":"6918","article_processing_charge":"No","isi":1,"external_id":{"arxiv":["1712.09692"],"isi":["000501641400050"]},"quality_controlled":"1"},{"doi":"10.15479/AT:ISTA:7525","month":"02","corr_author":"1","has_accepted_license":"1","file_date_updated":"2021-03-01T23:30:04Z","date_published":"2020-02-28T00:00:00Z","language":[{"iso":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-08T07:27:27Z","year":"2020","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","author":[{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481"}],"oa_version":"Published Version","citation":{"ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>","apa":"Bhandari, P. (2020). <i>Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>.","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. <i>Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>."},"abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"ddc":["570"],"_id":"7525","article_processing_charge":"No","page":"79","department":[{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"open_access","date_updated":"2021-03-01T23:30:04Z","content_type":"application/pdf","file_id":"7538","relation":"main_file","creator":"pbhandari","embargo":"2021-02-28","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_name":"Pradeep Bhandari Thesis.pdf","checksum":"4589234fdb12b4ad72273b311723a7b4","file_size":9646346,"date_created":"2020-02-28T08:37:53Z"},{"access_level":"closed","date_updated":"2021-03-01T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_id":"7539","creator":"pbhandari","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","embargo_to":"open_access","file_name":"Pradeep Bhandari Thesis.docx","checksum":"aa79490553ca0a5c9b6fbcd152e93928","date_created":"2020-02-28T08:47:14Z","file_size":35252164}],"oa":1,"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"OA_place":"publisher","status":"public","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"publication_status":"published","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2020-02-26T10:56:37Z","day":"28"}]