[{"title":"Polynomial invariant generation for non-deterministic recursive programs","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.04373"],"isi":["000614622300045"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-06-11T00:00:00Z","doi":"10.1145/3385412.3385969","date_created":"2020-07-05T22:00:45Z","page":"672-687","day":"11","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","isi":1,"year":"2020","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:33Z","status":"public","type":"conference","conference":{"start_date":"2020-06-15","end_date":"2020-06-20","location":"London, United Kingdom","name":"PLDI: Programming Language Design and Implementation"},"_id":"8089","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","month":"06","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.","lang":"eng"}]},{"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"_id":"6918","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["09518320"]},"language":[{"iso":"eng"}],"volume":193,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"abstract":[{"lang":"eng","text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1712.09692","open_access":"1"}],"scopus_import":"1","intvolume":" 193","month":"01","citation":{"mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.","ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665","apa":"Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020.","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1712.09692"],"isi":["000501641400050"]},"author":[{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fatemeh","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi"}],"title":"An efficient algorithm for computing network reliability in small treewidth","article_number":"106665","project":[{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"year":"2020","isi":1,"publication":"Reliability Engineering and System Safety","day":"01","date_created":"2019-09-29T22:00:44Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1016/j.ress.2019.106665","acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"status":"public","type":"journal_article","article_type":"original","_id":"7161","department":[{"_id":"VlKo"}],"file_date_updated":"2021-03-16T23:30:04Z","ddc":["518","510","515"],"date_updated":"2023-09-06T11:27:15Z","intvolume":" 184","month":"03","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.","lang":"eng"}],"ec_funded":1,"volume":184,"language":[{"iso":"eng"}],"file":[{"embargo":"2021-03-15","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","file_id":"8647","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","date_created":"2020-10-12T10:40:27Z","creator":"dernst","file_size":332641,"date_updated":"2021-03-16T23:30:04Z"}],"publication_status":"published","publication_identifier":{"eissn":["1573-2878"],"issn":["0022-3239"]},"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","article_processing_charge":"No","external_id":{"isi":["000511805200009"]},"author":[{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini"},{"first_name":"Aviv","last_name":"Gibali","full_name":"Gibali, Aviv"},{"first_name":"Simone","full_name":"Sagratella, Simone","last_name":"Sagratella"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894.","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.","ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","date_created":"2019-12-09T21:33:44Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1007/s10957-019-01616-6","page":"877–894","publication":"Journal of Optimization Theory and Applications","day":"01","year":"2020","has_accepted_license":"1","isi":1},{"acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Nature Ecology & Evolution","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1038/s41559-020-1132-7","date_published":"2020-04-01T00:00:00Z","date_created":"2020-04-08T15:20:53Z","page":"612-625","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7."},"title":"Gene amplification as a form of population-level gene expression regulation","author":[{"orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"},{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"M.","full_name":"Lagator, M.","last_name":"Lagator"},{"last_name":"Andersson","full_name":"Andersson, A. M. C.","first_name":"A. M. C."},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"article_processing_charge":"No","external_id":{"isi":["000519008300005"]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"month":"04","intvolume":" 4","scopus_import":"1","file":[{"date_updated":"2020-10-09T09:56:01Z","file_size":745242,"creator":"dernst","date_created":"2020-10-09T09:56:01Z","file_name":"2020_NatureEcolEvo_Tomanek.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ef3bbf42023e30b2c24a6278025d2040","file_id":"8640","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2397-334X"]},"publication_status":"published","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage"}],"record":[{"id":"8155","status":"public","relation":"dissertation_contains"},{"id":"7383","status":"public","relation":"research_data"},{"relation":"research_data","id":"7016","status":"public"},{"id":"8653","status":"public","relation":"used_in_publication"}]},"volume":4,"issue":"4","_id":"7652","status":"public","article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2024-03-27T23:30:36Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-10-09T09:56:01Z"},{"_id":"7258","type":"dissertation","status":"public","date_updated":"2023-09-15T12:20:08Z","supervisor":[{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"ddc":["532"],"department":[{"_id":"BjHo"}],"file_date_updated":"2021-01-13T23:30:05Z","abstract":[{"lang":"eng","text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings."}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"01","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_id":"7259","checksum":"4df1ab24e9896635106adde5a54615bf","creator":"dscarsel","file_size":26640830,"date_updated":"2021-01-13T23:30:05Z","file_name":"2020_Scarselli_Thesis.zip","date_created":"2020-01-12T15:57:14Z"},{"file_size":8515844,"date_updated":"2021-01-13T23:30:05Z","creator":"dscarsel","file_name":"2020_Scarselli_Thesis.pdf","date_created":"2020-01-12T15:56:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2021-01-12","file_id":"7260","checksum":"48659ab98e3414293c7a721385c2fd1c"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6228"},{"relation":"part_of_dissertation","id":"6486","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"461"},{"relation":"part_of_dissertation","status":"public","id":"422"}]},"project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Eliminating turbulence in oil pipelines","grant_number":"737549","call_identifier":"H2020","_id":"25104D44-B435-11E9-9278-68D0E5697425"},{"grant_number":"HO 4393/1-2","name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","_id":"25136C54-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide"}],"title":"New approaches to reduce friction in turbulent pipe flow","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"13","page":"174","date_created":"2020-01-12T16:07:26Z","doi":"10.15479/AT:ISTA:7258","date_published":"2020-01-13T00:00:00Z"},{"type":"dissertation","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"status":"public","_id":"8653","file_date_updated":"2021-10-20T22:30:03Z","department":[{"_id":"CaGu"}],"date_updated":"2023-09-07T13:22:42Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"ddc":["576"],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"lang":"eng","text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. "}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7652","relation":"research_data"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"c01d9f59794b4b70528f37637c17ad02","file_id":"8666","file_size":25131884,"date_updated":"2021-10-20T22:30:03Z","creator":"itomanek","file_name":"Thesis_ITomanek_final_201016.docx","date_created":"2020-10-16T12:14:21Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","file_id":"8667","embargo":"2021-10-19","date_updated":"2021-10-20T22:30:03Z","file_size":15405675,"creator":"itomanek","date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.pdf"}],"article_processing_charge":"No","author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"}],"title":"The evolution of gene expression by copy number and point mutations","citation":{"ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"117","date_created":"2020-10-13T13:02:33Z","doi":"10.15479/AT:ISTA:8653","date_published":"2020-10-13T00:00:00Z","year":"2020","has_accepted_license":"1","day":"13"},{"ddc":["580"],"date_updated":"2024-03-27T23:30:37Z","file_date_updated":"2020-09-22T09:51:28Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"7427","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2020-09-22T09:51:28Z","file_size":5360135,"creator":"dernst","date_created":"2020-09-22T09:51:28Z","file_name":"2020_CurrentBiology_Tan.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"16f7d51fe28f91c21e4896a2028df40b","file_id":"8555","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09609822"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"volume":30,"issue":"3","ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"02","intvolume":" 30","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","ieee":"S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058."},"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"first_name":"Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","full_name":"Abas, Melinda F"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"first_name":"Pavel","last_name":"Lasák","full_name":"Lasák, Pavel"},{"full_name":"Petřík, Ivan","last_name":"Petřík","first_name":"Ivan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Pospíšil","full_name":"Pospíšil, Jiří","first_name":"Jiří"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"article_processing_charge":"No","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Long Term Fellowship","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"day":"03","publication":"Current Biology","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-02-03T00:00:00Z","doi":"10.1016/j.cub.2019.11.058","date_created":"2020-02-02T23:01:00Z","page":"381-395.e8","acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","quality_controlled":"1","publisher":"Cell Press","oa":1},{"ddc":["580"],"date_updated":"2024-03-27T23:30:37Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-11-20T09:32:10Z","_id":"7500","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"17de728b0205979feb95ce663ba918c2","file_id":"8781","creator":"dernst","file_size":2106888,"date_updated":"2020-11-20T09:32:10Z","file_name":"2020_NewPhytologist_Mazur.pdf","date_created":"2020-11-20T09:32:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","volume":226,"related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"issue":"5","ec_funded":1,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.","lang":"eng"}],"month":"06","intvolume":" 226","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446","apa":"Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383."},"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","author":[{"first_name":"E","full_name":"Mazur, E","last_name":"Mazur"},{"full_name":"Kulik, Ivan","last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","first_name":"Ivan"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"article_processing_charge":"No","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development"}],"day":"01","publication":"New Phytologist","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1111/nph.16446","date_published":"2020-06-01T00:00:00Z","date_created":"2020-02-18T10:03:47Z","page":"1375-1383","acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","publisher":"Wiley","quality_controlled":"1","oa":1},{"status":"public","type":"dissertation","_id":"8822","department":[{"_id":"JiFr"}],"file_date_updated":"2021-12-08T23:30:03Z","ddc":["580"],"date_updated":"2023-09-19T10:39:33Z","supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization."}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7427","status":"public"},{"id":"6260","status":"public","relation":"part_of_dissertation"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"191","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"210a9675af5e4c78b0b56d920ac82866","file_id":"8919","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Jakub Hajný IST Austria final_JH.docx","date_created":"2020-12-04T07:27:52Z","file_size":91279806,"date_updated":"2021-07-16T22:30:03Z","creator":"jhajny"},{"file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","date_created":"2020-12-09T15:04:41Z","file_size":68707697,"date_updated":"2021-12-08T23:30:03Z","creator":"jhajny","embargo":"2021-12-07","checksum":"1781385b4aa73eba89cc76c6172f71d2","file_id":"8933","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","article_processing_charge":"No","author":[{"last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-12-01T12:38:18Z","doi":"10.15479/AT:ISTA:8822","date_published":"2020-12-01T00:00:00Z","page":"249","day":"01","year":"2020","has_accepted_license":"1"},{"day":"09","has_accepted_license":"1","year":"2020","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8350","date_created":"2020-09-09T11:12:10Z","page":"107","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.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria."},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"}],"article_processing_charge":"No","file":[{"creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","file_size":65194814,"date_created":"2020-09-09T11:06:27Z","file_name":"Shayan-Thesis-Final.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"6e47871c74f85008b9876112eb3fcfa1","file_id":"8351"},{"creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","file_size":23729605,"date_created":"2020-09-09T11:06:13Z","file_name":"Shayan-Thesis-Final.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8352","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","embargo":"2021-09-10"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"661","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6508","relation":"part_of_dissertation"},{"id":"7001","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"735","relation":"part_of_dissertation"}]},"oa_version":"None","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","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."}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"date_updated":"2023-09-27T14:16:45Z","file_date_updated":"2021-09-11T22:30:05Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"_id":"8350","status":"public","type":"dissertation"}]