[{"file":[{"relation":"main_file","file_id":"7660","file_size":1556190,"file_name":"2020_JournRoyalSociety_Larsson.pdf","checksum":"4eb102304402f5c56432516b84df86d6","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T12:31:16Z"}],"doi":"10.1098/rsif.2019.0721","quality_controlled":"1","article_processing_charge":"No","publication":"Journal of the Royal Society Interface","abstract":[{"lang":"eng","text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods."}],"article_type":"original","publisher":"Royal Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","fulldoi":"https://doi.org/10.1098/rsif.2019.0721","volume":17,"article_number":"20190721","oa_version":"Published Version","publication_status":"published","status":"public","year":"2020","citation":{"apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., &#38; Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of the Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of the Royal Society Interface</i>. 2020;17(163). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163, 20190721, Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>.","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 163. Royal Society, 2020.","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of the Royal Society Interface. 17(163), 20190721."},"date_created":"2020-04-08T15:19:17Z","department":[{"_id":"NiBa"}],"month":"02","has_accepted_license":"1","oa":1,"author":[{"last_name":"Larsson","first_name":"J.","full_name":"Larsson, J."},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"S.","last_name":"Bengmark","full_name":"Bengmark, S."},{"full_name":"Lundh, T.","last_name":"Lundh","first_name":"T."},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"intvolume":"        17","file_date_updated":"2020-07-14T12:48:01Z","ddc":["570"],"date_updated":"2026-08-12T14:06:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-02-01T00:00:00Z","title":"A developmentally descriptive method for quantifying shape in gastropod shells","_id":"7651","language":[{"iso":"eng"}],"issue":"163","day":"01"},{"department":[{"_id":"EdHa"}],"year":"2020","citation":{"mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162, 0623, Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>.","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. 2020;17(162). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","apa":"Kolchinsky, A., &#38; Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>.","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162. Royal Society, 2020."},"date_created":"2020-02-02T23:01:03Z","status":"public","author":[{"first_name":"Artemy","last_name":"Kolchinsky","full_name":"Kolchinsky, Artemy"},{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"}],"oa":1,"month":"01","external_id":{"arxiv":["1903.10693"],"isi":["000538369800002"],"pmid":["31964273"]},"date_updated":"2026-08-12T14:08:47Z","date_published":"2020-01-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        17","publication_identifier":{"eissn":["1742-5662"]},"issue":"162","isi":1,"pmid":1,"day":"29","language":[{"iso":"eng"}],"_id":"7431","arxiv":1,"title":"Decomposing information into copying versus transformation","acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","doi":"10.1098/rsif.2019.0623","abstract":[{"text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.","lang":"eng"}],"article_type":"original","publication":"Journal of the Royal Society Interface","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","fulldoi":"https://doi.org/10.1098/rsif.2019.0623","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"publisher":"Royal Society","oa_version":"Preprint","publication_status":"published","volume":17,"article_number":"0623"},{"publisher":"Royal Society","OA_place":"publisher","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","date_published":"2020-10-15T00:00:00Z","date_updated":"2026-08-12T14:08:28Z","type":"research_data_reference","fulldoi":"https://doi.org/10.6084/m9.figshare.5973013.v1","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","_id":"9814","oa_version":"Published Version","day":"15","status":"public","year":"2020","OA_type":"hybrid","doi":"10.6084/m9.figshare.5973013.v1","citation":{"ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>.","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","mla":"Ibsen-Jensen, Rasmus, et al. <i>Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners</i>. Royal Society, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>"},"date_created":"2021-08-06T13:09:57Z","department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"198"}]},"month":"10","article_processing_charge":"No","oa":1,"abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"author":[{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}]},{"department":[{"_id":"BjHo"}],"citation":{"ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” <i>Chaos</i>, vol. 30, no. 3. AIP Publishing, 2020.","chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>.","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","apa":"Yalniz, G., &#38; Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. 2020;30(3). doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>","mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>."},"date_created":"2020-03-04T08:06:25Z","year":"2020","status":"public","author":[{"orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan"},{"first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"}],"oa":1,"month":"03","external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-03-03T00:00:00Z","ddc":["530"],"date_updated":"2026-09-02T08:16:31Z","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"intvolume":"        30","day":"03","isi":1,"issue":"3","language":[{"iso":"eng"}],"_id":"7563","arxiv":1,"title":"Inferring symbolic dynamics of chaotic flows from persistence","related_material":{"record":[{"id":"19684","status":"public","relation":"dissertation_contains"}]},"doi":"10.1063/1.5122969","abstract":[{"lang":"eng","text":"We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings."}],"article_type":"original","publication":"Chaos","article_processing_charge":"No","quality_controlled":"1","fulldoi":"https://doi.org/10.1063/1.5122969","type":"journal_article","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5122969"}],"publisher":"AIP Publishing","publication_status":"published","oa_version":"Published Version","corr_author":"1","article_number":"033109","volume":30},{"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2021-03-29T11:43:20Z","date_created":"2021-03-29T11:43:20Z","relation":"main_file","file_id":"9300","success":1,"file_name":"2020_PhysReviewApplied_Peruzzo.pdf","checksum":"2a634abe75251ae7628cd54c8a4ce2e8","file_size":2607823,"creator":"dernst"}],"acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","related_material":{"record":[{"id":"13070","relation":"research_data","status":"public"},{"id":"9920","relation":"dissertation_contains","status":"public"},{"id":"20371","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"17133"}]},"doi":"10.1103/PhysRevApplied.14.044055","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. ","lang":"eng"}],"article_type":"original","publication":"Physical Review Applied","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"scopus_import":"1","publisher":"American Physical Society","ec_funded":1,"fulldoi":"https://doi.org/10.1103/PhysRevApplied.14.044055","type":"journal_article","acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"044055","volume":14,"publication_status":"published","oa_version":"Published Version","status":"public","department":[{"_id":"JoFi"}],"date_created":"2020-11-15T23:01:17Z","citation":{"mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” <i>Physical Review Applied</i>, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">10.1103/PhysRevApplied.14.044055</a>.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. <i>Physical Review Applied</i>. 2020;14(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">10.1103/PhysRevApplied.14.044055</a>","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., &#38; Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">https://doi.org/10.1103/PhysRevApplied.14.044055</a>","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” <i>Physical Review Applied</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">https://doi.org/10.1103/PhysRevApplied.14.044055</a>.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” <i>Physical Review Applied</i>, vol. 14, no. 4. American Physical Society, 2020."},"year":"2020","month":"10","external_id":{"isi":["000582797300003"],"arxiv":["2007.01644"]},"author":[{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"has_accepted_license":"1","oa":1,"file_date_updated":"2021-03-29T11:43:20Z","publication_identifier":{"eissn":["2331-7019"]},"intvolume":"        14","date_updated":"2026-10-02T11:28:16Z","ddc":["530"],"date_published":"2020-10-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Surpassing the resistance quantum with a geometric superinductor","day":"29","issue":"4","isi":1,"_id":"8755","language":[{"iso":"eng"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["000"],"date_published":"2020-07-14T00:00:00Z","date_updated":"2026-10-16T08:04:15Z","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030532901"]},"intvolume":"     12225","file_date_updated":"2020-08-17T11:32:44Z","isi":1,"day":"14","_id":"8272","language":[{"iso":"eng"}],"arxiv":1,"title":"Stochastic games with lexicographic reachability-safety objectives","department":[{"_id":"KrCh"}],"year":"2020","citation":{"ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in <i>International Conference on Computer Aided Verification</i>, 2020, vol. 12225, pp. 398–420.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 12225:398–420. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., &#38; Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 12225, pp. 398–420). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">https://doi.org/10.1007/978-3-030-53291-8_21</a>","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 12225. Springer Nature; 2020:398-420. doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:<a href=\"https://doi.org/10.1007/978-3-030-53291-8_21\">10.1007/978-3-030-53291-8_21</a>."},"date_created":"2020-08-16T22:00:58Z","status":"public","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Katoen, Joost P","orcid":"0000-0002-6143-1926","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"conference":{"name":"CAV: Computer Aided Verification"},"oa":1,"has_accepted_license":"1","month":"07","external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"type":"conference","ec_funded":1,"fulldoi":"https://doi.org/10.1007/978-3-030-53291-8_21","scopus_import":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","volume":12225,"alternative_title":["LNCS"],"page":"398-420","related_material":{"record":[{"id":"12738","relation":"later_version","status":"public"}]},"doi":"10.1007/978-3-030-53291-8_21","file":[{"file_id":"8276","success":1,"creator":"dernst","file_name":"2020_LNCS_CAV_Chatterjee.pdf","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","file_size":625056,"relation":"main_file","date_updated":"2020-08-17T11:32:44Z","date_created":"2020-08-17T11:32:44Z","access_level":"open_access","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in   NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is   PSPACE -hard and can be solved in   NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies."}],"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"publication":"International Conference on Computer Aided Verification","article_processing_charge":"No","quality_controlled":"1"},{"publication":"Journal of Structural Biology","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"article_type":"original","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.jsb.2020.107633","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14592"},{"relation":"dissertation_contains","status":"public","id":"12491"}]},"file":[{"date_updated":"2020-12-10T14:01:10Z","date_created":"2020-12-10T14:01:10Z","content_type":"application/pdf","access_level":"open_access","checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_name":"2020_JourStrucBiology_Faessler.pdf","creator":"dernst","file_size":7076870,"file_id":"8937","success":1,"relation":"main_file"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","volume":212,"article_number":"107633","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.jsb.2020.107633","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","has_accepted_license":"1","oa":1,"author":[{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"external_id":{"pmid":["32987119"],"isi":["000600997800008"]},"month":"12","year":"2020","citation":{"short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>."},"date_created":"2020-09-29T13:24:06Z","department":[{"_id":"FlSc"}],"status":"public","_id":"8586","language":[{"iso":"eng"}],"issue":"3","pmid":1,"isi":1,"day":"01","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"date_updated":"2026-10-25T23:30:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-12-01T00:00:00Z","ddc":["570"],"publication_identifier":{"issn":["1047-8477"]},"intvolume":"       212","file_date_updated":"2020-12-10T14:01:10Z"},{"date_updated":"2026-10-25T23:30:04Z","date_published":"2020-03-18T00:00:00Z","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-11-20T08:58:53Z","publication_identifier":{"issn":["0896-6273"]},"intvolume":"       105","_id":"7473","language":[{"iso":"eng"}],"day":"18","isi":1,"pmid":1,"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","date_created":"2020-02-10T15:59:45Z","citation":{"mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>, vol. 105, Elsevier, 2020, pp. 992–1006, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. 2020;105:992-1006. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">10.1016/j.neuron.2019.12.022</a>","apa":"Borges Merjane, C., Kim, O., &#38; Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2019.12.022\">https://doi.org/10.1016/j.neuron.2019.12.022</a>.","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” <i>Neuron</i>, vol. 105. Elsevier, pp. 992–1006, 2020."},"year":"2020","department":[{"_id":"PeJo"}],"status":"public","oa":1,"has_accepted_license":"1","author":[{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina"},{"last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"month":"03","fulldoi":"https://doi.org/10.1016/j.neuron.2019.12.022","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Elsevier","scopus_import":"1","corr_author":"1","publication_status":"published","oa_version":"Published Version","page":"992-1006","volume":105,"doi":"10.1016/j.neuron.2019.12.022","acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"11196"}]},"file":[{"file_id":"8778","success":1,"file_name":"2020_Neuron_BorgesMerjane.pdf","creator":"dernst","file_size":9712957,"checksum":"3582664addf26859e86ac5bec3e01416","relation":"main_file","date_updated":"2020-11-20T08:58:53Z","date_created":"2020-11-20T08:58:53Z","access_level":"open_access","content_type":"application/pdf"}],"project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF"}],"publication":"Neuron","article_type":"original","abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No"},{"oa":1,"author":[{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"last_name":"Hernández-Rocamora","first_name":"Víctor M.","full_name":"Hernández-Rocamora, Víctor M."},{"last_name":"Alfonso","first_name":"Carlos","full_name":"Alfonso, Carlos"},{"first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"full_name":"Rivas, Germán","last_name":"Rivas","first_name":"Germán"},{"last_name":"Vollmer","first_name":"Waldemar","full_name":"Vollmer, Waldemar"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"external_id":{"isi":["000508584700007"],"pmid":["31959972"]},"month":"01","date_created":"2020-01-28T16:14:41Z","citation":{"ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020."},"year":"2020","department":[{"_id":"MaLo"}],"status":"public","_id":"7387","language":[{"iso":"eng"}],"day":"20","pmid":1,"isi":1,"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","date_updated":"2026-10-25T23:30:08Z","date_published":"2020-01-20T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2058-5276"]},"intvolume":"         5","publication":"Nature Microbiology","project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.","lang":"eng"}],"article_type":"letter_note","quality_controlled":"1","article_processing_charge":"No","doi":"10.1038/s41564-019-0657-5","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14280"}]},"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","corr_author":"1","publication_status":"published","oa_version":"Submitted Version","page":"407-417","volume":5,"ec_funded":1,"fulldoi":"https://doi.org/10.1038/s41564-019-0657-5","type":"journal_article","publisher":"Springer Nature","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}]},{"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"publication":"eLife","article_type":"original","abstract":[{"text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.7554/elife.55190","related_material":{"record":[{"id":"12891","relation":"dissertation_contains","status":"public"}]},"file":[{"checksum":"f6aad884cf706846ae9357fcd728f8b5","file_name":"2020_eLife_Schauer.pdf","creator":"dernst","file_size":7744848,"file_id":"7890","relation":"main_file","date_created":"2020-05-25T15:15:43Z","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","access_level":"open_access"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","volume":9,"article_number":"e55190","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.55190","ec_funded":1,"publisher":"eLife Sciences Publications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"has_accepted_license":"1","author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra"},{"first_name":"Diana C","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"month":"04","year":"2020","date_created":"2020-05-25T15:01:40Z","citation":{"ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., &#38; Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>, vol. 9, e55190, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>."},"department":[{"_id":"CaHe"},{"_id":"Bio"}],"status":"public","language":[{"iso":"eng"}],"_id":"7888","isi":1,"pmid":1,"day":"06","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","ddc":["570"],"date_updated":"2026-10-25T23:30:12Z","date_published":"2020-04-06T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"         9","publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2020-07-14T12:48:04Z"},{"publication_status":"published","oa_version":"Preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"page":"582–585","volume":582,"ec_funded":1,"fulldoi":"https://doi.org/10.1038/s41586-020-2283-z","type":"journal_article","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/793919","open_access":"1"}],"publisher":"Springer Nature","article_type":"original","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin"},{"grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Nature","article_processing_charge":"No","quality_controlled":"1","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12401"},{"id":"14697","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/","relation":"press_release","description":"News on IST Homepage"}]},"doi":"10.1038/s41586-020-2283-z","day":"25","pmid":1,"isi":1,"_id":"7885","language":[{"iso":"eng"}],"title":"Cellular locomotion using environmental topography","date_published":"2020-06-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-25T23:30:16Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"intvolume":"       582","OA_place":"repository","author":[{"first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"},{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","full_name":"Stopp, Julian A"},{"first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren"},{"orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"first_name":"Andrew","last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew"},{"full_name":"Voituriez, Raphael","last_name":"Voituriez","first_name":"Raphael"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"oa":1,"month":"06","external_id":{"pmid":["32581372"],"isi":["000532688300008"]},"department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"date_created":"2020-05-24T22:01:01Z","citation":{"short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. <i>Nature</i>. 2020;582:582–585. doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>, vol. 582, Springer Nature, 2020, pp. 582–585, doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>.","ieee":"A. Reversat <i>et al.</i>, “Cellular locomotion using environmental topography,” <i>Nature</i>, vol. 582. Springer Nature, pp. 582–585, 2020.","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585."},"OA_type":"green","year":"2020","status":"public"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"article_number":"e61147","publication_status":"published","oa_version":"Published Version","corr_author":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"MyJove Corporation","fulldoi":"https://doi.org/10.3791/61147","ec_funded":1,"type":"journal_article","article_processing_charge":"No","quality_controlled":"1","article_type":"original","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"publication":"Journal of Visual Experiments","project":[{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2020-05-11T08:28:38Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7816","checksum":"3154ea7f90b9fb45e084cd1c2770597d","file_size":1352186,"file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","creator":"rbeattie"}],"related_material":{"record":[{"id":"7902","relation":"part_of_dissertation","status":"public"}]},"doi":"10.3791/61147","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","day":"08","pmid":1,"issue":"159","isi":1,"_id":"7815","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","publication_identifier":{"issn":["1940-087X"]},"ddc":["570"],"date_published":"2020-05-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-25T23:30:20Z","month":"05","external_id":{"isi":["000546406600043"],"pmid":["32449730"]},"author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"SiHi"}],"date_created":"2020-05-11T08:31:20Z","citation":{"mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>, no. 159, e61147, MyJove Corporation, 2020, doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., &#38; Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. 2020;(159). doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>","ieee":"R. J. Beattie <i>et al.</i>, “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” <i>Journal of Visual Experiments</i>, no. 159. MyJove Corporation, 2020.","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>. MyJove Corporation, 2020. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>."},"year":"2020"},{"supervisor":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"doi":"10.15479/AT:ISTA:7902","related_material":{"record":[{"id":"28","relation":"dissertation_contains","status":"public"},{"id":"7815","status":"public","relation":"dissertation_contains"},{"id":"6830","relation":"dissertation_contains","status":"public"}]},"file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2020-06-05T08:18:08Z","date_updated":"2021-06-07T22:30:03Z","relation":"source_file","file_id":"7927","creator":"xcontreras","file_size":53134142,"checksum":"43c172bf006c95b65992d473c7240d13","file_name":"PhDThesis_Contreras.docx"},{"relation":"main_file","file_id":"7928","checksum":"addfed9128271be05cae3608e03a6ec0","file_size":35117191,"file_name":"PhDThesis_Contreras.pdf","creator":"xcontreras","access_level":"open_access","content_type":"application/pdf","embargo":"2021-06-06","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z"}],"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"article_processing_charge":"No","ec_funded":1,"fulldoi":"https://doi.org/10.15479/AT:ISTA:7902","type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","oa_version":"Published Version","page":"214","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"citation":{"chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","mla":"Contreras, Ximena. <i>Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). <i>Genetic dissection of neural development in health and disease at single cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>"},"date_created":"2020-05-29T08:27:32Z","year":"2020","department":[{"_id":"SiHi"}],"status":"public","has_accepted_license":"1","oa":1,"degree_awarded":"PhD","author":[{"full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"}],"month":"06","date_published":"2020-06-05T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-06-18T19:12:39Z","ddc":["570"],"OA_place":"publisher","file_date_updated":"2021-06-07T22:30:03Z","publication_identifier":{"issn":["2663-337X"]},"_id":"7902","language":[{"iso":"eng"}],"day":"05","title":"Genetic dissection of neural development in health and disease at single cell resolution"},{"external_id":{"isi":["000573631000004"],"pmid":["32699885"]},"month":"07","oa":1,"has_accepted_license":"1","author":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Huttenlocher, Anna","first_name":"Anna","last_name":"Huttenlocher"}],"status":"public","year":"2020","date_created":"2020-08-02T22:00:57Z","citation":{"short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029."},"department":[{"_id":"MiSi"}],"title":"Zena Werb (1945-2020): Cell biology in context","language":[{"iso":"eng"}],"_id":"8190","issue":"8","isi":1,"pmid":1,"day":"22","intvolume":"       219","publication_identifier":{"eissn":["1540-8140"]},"file_date_updated":"2021-02-02T23:30:03Z","date_published":"2020-07-22T00:00:00Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-12T07:34:40Z","article_processing_charge":"No","publication":"The Journal of Cell Biology","article_type":"letter_note","file":[{"date_updated":"2021-02-02T23:30:03Z","date_created":"2020-08-04T13:11:52Z","embargo":"2021-02-01","content_type":"application/pdf","access_level":"open_access","file_size":830725,"file_name":"2020_JCB_Sixt.pdf","creator":"dernst","checksum":"30016d778d266b8e17d01094917873b8","file_id":"8200","relation":"main_file"}],"doi":"10.1083/jcb.202007029","volume":219,"article_number":"e202007029","oa_version":"Published Version","publication_status":"published","publisher":"Rockefeller University Press","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"journal_article","fulldoi":"https://doi.org/10.1083/jcb.202007029"},{"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:27Z","relation":"source_file","checksum":"6e47871c74f85008b9876112eb3fcfa1","creator":"sshamip","file_name":"Shayan-Thesis-Final.docx","file_size":65194814,"file_id":"8351"},{"date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:13Z","access_level":"open_access","embargo":"2021-09-10","content_type":"application/pdf","file_id":"8352","file_size":23729605,"checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","file_name":"Shayan-Thesis-Final.pdf","creator":"sshamip","relation":"main_file"}],"supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"doi":"10.15479/AT:ISTA:8350","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","related_material":{"record":[{"id":"7001","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6508"},{"id":"735","status":"public","relation":"part_of_dissertation"},{"id":"661","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","fulldoi":"https://doi.org/10.15479/AT:ISTA:8350","alternative_title":["ISTA Thesis"],"page":"107","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"corr_author":"1","oa_version":"None","publication_status":"published","status":"public","year":"2020","date_created":"2020-09-09T11:12:10Z","citation":{"ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). <i>Bulk actin dynamics drive phase segregation in zebrafish oocytes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8350\">https://doi.org/10.15479/AT:ISTA:8350</a>","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>","mla":"Shamipour, Shayan. <i>Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes </i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8350\">10.15479/AT:ISTA:8350</a>."},"department":[{"_id":"BjHo"},{"_id":"CaHe"}],"month":"09","has_accepted_license":"1","degree_awarded":"PhD","oa":1,"author":[{"full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-09-11T22:30:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-09-11T07:08:52Z","ddc":["570"],"date_published":"2020-09-09T00:00:00Z","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","_id":"8350","language":[{"iso":"eng"}],"day":"09"},{"publication_status":"published","oa_version":"Published Version","article_number":"jcs239020","volume":133,"fulldoi":"https://doi.org/10.1242/jcs.239020","type":"journal_article","publisher":"The Company of Biologists","scopus_import":"1","project":[{"call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"publication":"Journal of Cell Science","abstract":[{"lang":"eng","text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. "}],"article_type":"original","quality_controlled":"1","article_processing_charge":"No","doi":"10.1242/jcs.239020","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","file":[{"date_created":"2020-09-17T14:07:51Z","date_updated":"2020-10-11T22:30:02Z","embargo":"2020-10-10","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":13493302,"file_name":"2020_JournalCellScience_Dimchev.pdf","checksum":"ba917e551acc4ece2884b751434df9ae","file_id":"8435","relation":"main_file"}],"language":[{"iso":"eng"}],"_id":"8434","day":"09","isi":1,"issue":"7","pmid":1,"title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","keyword":["Cell Biology"],"date_updated":"2025-04-15T07:52:13Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"date_published":"2020-04-09T00:00:00Z","file_date_updated":"2020-10-11T22:30:02Z","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"intvolume":"       133","oa":1,"has_accepted_license":"1","author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"last_name":"Humphries","first_name":"Ashley C.","full_name":"Humphries, Ashley C."},{"full_name":"Schaks, Matthias","last_name":"Schaks","first_name":"Matthias"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"last_name":"Stradal","first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B."},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"last_name":"Krause","first_name":"Matthias","full_name":"Krause, Matthias"},{"last_name":"Way","first_name":"Michael","full_name":"Way, Michael"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"month":"04","date_created":"2020-09-17T14:00:33Z","citation":{"mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020.","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>."},"year":"2020","department":[{"_id":"FlSc"}],"status":"public"},{"year":"2020","citation":{"mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>.","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria."},"date_created":"2020-12-30T15:41:26Z","department":[{"_id":"DaSi"}],"status":"public","degree_awarded":"PhD","oa":1,"has_accepted_license":"1","author":[{"first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi"}],"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T07:28:54Z","ddc":["570"],"date_published":"2020-12-30T00:00:00Z","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-12-31T23:30:04Z","_id":"8983","language":[{"iso":"eng"}],"day":"30","title":"Metabolic regulation of Drosophila macrophage tissue invasion","doi":"10.15479/AT:ISTA:8983","supervisor":[{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","related_material":{"record":[{"id":"8557","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6187"}]},"file":[{"file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","checksum":"ec2797ab7a6f253b35df0572b36d1b43","file_size":10848175,"creator":"semtenan","file_id":"8984","relation":"main_file","date_created":"2020-12-30T15:34:01Z","date_updated":"2021-12-31T23:30:04Z","content_type":"application/pdf","embargo":"2021-12-30","access_level":"open_access"},{"access_level":"closed","content_type":"application/pdf","embargo_to":"open_access","date_created":"2020-12-30T15:37:36Z","date_updated":"2021-12-31T23:30:04Z","relation":"source_file","file_id":"8985","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","checksum":"cc30e6608a9815414024cf548dff3b3a","creator":"semtenan","file_size":10073648}],"abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}],"article_processing_charge":"No","type":"dissertation","fulldoi":"https://doi.org/10.15479/AT:ISTA:8983","publisher":"Institute of Science and Technology Austria","corr_author":"1","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"page":"141","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}]},{"main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-18T00:00:00Z","date_updated":"2026-10-25T23:30:25Z","fulldoi":"https://doi.org/10.1101/2020.09.18.301481","ec_funded":1,"type":"preprint","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","acknowledged_ssus":[{"_id":"LifeSc"}],"_id":"8557","corr_author":"1","language":[{"iso":"eng"}],"day":"18","publication_status":"draft","oa_version":"Preprint","status":"public","citation":{"chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. .","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>."},"date_created":"2020-09-23T09:36:47Z","doi":"10.1101/2020.09.18.301481","year":"2020","related_material":{"record":[{"relation":"later_version","status":"public","id":"10614"},{"id":"8983","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"article_processing_charge":"No","month":"09","publication":"bioRxiv","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077"},{"name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.","lang":"eng"}],"author":[{"full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera"},{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","first_name":"Stephanie","full_name":"Wachner, Stephanie"},{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929"},{"full_name":"Linder, Markus","last_name":"Linder","first_name":"Markus"},{"last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","first_name":"Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"}]},{"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"OA_type":"hybrid","year":"2020","date_created":"2020-06-22T13:33:52Z","citation":{"ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences of the United States of America. 117(26), 202003346.","chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2003346117\">https://doi.org/10.1073/pnas.2003346117</a>.","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 26. National Academy of Sciences, 2020.","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(26). doi:<a href=\"https://doi.org/10.1073/pnas.2003346117\">10.1073/pnas.2003346117</a>","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 117 (2020).","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., &#38; Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2003346117\">https://doi.org/10.1073/pnas.2003346117</a>","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 26, 202003346, National Academy of Sciences, 2020, doi:<a href=\"https://doi.org/10.1073/pnas.2003346117\">10.1073/pnas.2003346117</a>."},"status":"public","author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"full_name":"Marhavá, Petra","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko","orcid":"0000-0001-6111-9353","full_name":"Yoshida, Saiko"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"has_accepted_license":"1","oa":1,"month":"06","external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"date_published":"2020-06-30T00:00:00Z","date_updated":"2026-10-25T23:30:26Z","intvolume":"       117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"file_date_updated":"2020-07-14T12:48:07Z","OA_place":"publisher","issue":"26","pmid":1,"isi":1,"day":"30","_id":"8002","language":[{"iso":"eng"}],"title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/","relation":"press_release"}],"record":[{"id":"9992","relation":"dissertation_contains","status":"public"}]},"doi":"10.1073/pnas.2003346117","file":[{"file_name":"2020_PNAS_Hoermayer.pdf","checksum":"908b09437680181de9990915f2113aca","file_size":2407102,"creator":"dernst","file_id":"8009","relation":"main_file","date_updated":"2020-07-14T12:48:07Z","date_created":"2020-06-23T11:30:53Z","content_type":"application/pdf","access_level":"open_access"}],"article_type":"original","abstract":[{"lang":"eng","text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity."}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1073/pnas.2003346117","scopus_import":"1","publisher":"National Academy of Sciences","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version","publication_status":"published","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":117,"article_number":"202003346"},{"month":"12","oa":1,"conference":{"start_date":"2020-12-06","location":"Vancouver, Canada","name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2020-12-12"},"author":[{"full_name":"Confavreux, Basile J","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux"},{"first_name":"Friedemann","last_name":"Zenke","full_name":"Zenke, Friedemann"},{"last_name":"Agnes","first_name":"Everton J.","full_name":"Agnes, Everton J."},{"last_name":"Lillicrap","first_name":"Timothy","full_name":"Lillicrap, Timothy"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"status":"public","citation":{"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.","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.","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.","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.","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.","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."},"date_created":"2021-07-04T22:01:27Z","year":"2020","department":[{"_id":"TiVo"}],"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","_id":"9633","language":[{"iso":"eng"}],"day":"06","das_tickbox":"1","intvolume":"        33","publication_identifier":{"issn":["1049-5258"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_published":"2020-12-06T00:00:00Z","date_updated":"2026-10-25T23:30:28Z","quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"},{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z"}],"publication":"34th Conference on Neural Information Processing Systems","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."}],"related_material":{"link":[{"url":"https://doi.org/10.1101/2020.10.24.353409","relation":"is_continued_by"}],"record":[{"id":"14422","status":"public","relation":"dissertation_contains"}]},"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.","page":"16398-16408","volume":33,"alternative_title":["Advances in Neural Information Processing Systems"],"publication_status":"published","oa_version":"Published Version","publisher":"Neural Information Processing Systems Foundation","main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html"}],"scopus_import":"1","ec_funded":1,"type":"conference"}]