[{"publication_status":"published","date_published":"2018-10-30T00:00:00Z","doi":"10.15479/AT:ISTA:th1059","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"ddc":["576","579"],"year":"2018","degree_awarded":"PhD","oa":1,"status":"public","date_updated":"2026-04-08T14:15:35Z","author":[{"full_name":"Steinrück, Magdalena","last_name":"Steinrück","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719"}],"month":"10","title":"The influence of sequence context on the evolution of bacterial gene expression","file_date_updated":"2021-02-11T11:17:14Z","OA_place":"publisher","page":"109","date_created":"2018-12-11T11:44:14Z","citation":{"ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>"},"corr_author":"1","type":"dissertation","article_processing_charge":"No","department":[{"_id":"CaGu"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"704","status":"public"}]},"supervisor":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"language":[{"iso":"eng"}],"publist_id":"8029","_id":"26","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"30","pubrep_id":"1059","file":[{"checksum":"413cbce1cd1debeae3abe2a25dbc70d1","file_id":"5941","file_size":9190845,"date_created":"2019-02-08T10:51:22Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:45:43Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Steinrueck_final.docx","relation":"source_file","creator":"dernst"},{"date_updated":"2021-02-11T11:17:14Z","embargo":"2019-11-02","file_name":"Thesis_Steinrueck_final.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"3def8b7854c8b42d643597ce0215efac","date_created":"2019-02-08T10:51:22Z","content_type":"application/pdf","file_id":"5942","file_size":7521973}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:th1059"},{"_id":"28","day":"01","quality_controlled":"1","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1093/brain/awy218","external_id":{"isi":["000446548100012"]},"citation":{"chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>.","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544."},"date_created":"2018-12-11T11:44:14Z","volume":141,"page":"2542 - 2544","department":[{"_id":"SiHi"}],"article_processing_charge":"No","type":"journal_article","related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"publication":"Brain a journal of neurology","year":"2018","isi":1,"abstract":[{"lang":"eng","text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. "}],"oa_version":"None","date_updated":"2026-09-16T22:30:22Z","status":"public","title":"Incorrect trafficking route leads to autism","scopus_import":"1","month":"09","issue":"9","author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"intvolume":"       141","publication_status":"published","date_published":"2018-09-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Oxford University Press","doi":"10.1093/brain/awy218"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"department":[{"_id":"MiSi"},{"_id":"Bio"}],"type":"journal_article","article_processing_charge":"No","ec_funded":1,"acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","acknowledged_ssus":[{"_id":"SSU"}],"citation":{"apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. 2018;19(6):606-616. doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>.","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","ieee":"M. Hons <i>et al.</i>, “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” <i>Nature Immunology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616."},"date_created":"2018-12-11T11:44:10Z","page":"606 - 616","volume":19,"fulldoi":"https://doi.org/10.1038/s41590-018-0109-z","pmid":1,"external_id":{"isi":["000433041500026"],"pmid":["29777221"]},"day":"18","_id":"15","publist_id":"8040","quality_controlled":"1","language":[{"iso":"eng"}],"project":[{"name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"name":"Molecular and system level view of immune cell migration","_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41590-018-0109-z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"date_published":"2018-05-18T00:00:00Z","intvolume":"        19","publication_status":"published","scopus_import":"1","month":"05","title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","issue":"6","author":[{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","full_name":"Hons, Miroslav","last_name":"Hons"},{"last_name":"Kopf","full_name":"Kopf, Aglaja","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F","last_name":"Leithner"},{"first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","orcid":"0000-0003-2856-3369"},{"first_name":"Jens","full_name":"Stein, Jens","last_name":"Stein"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"date_updated":"2026-09-16T22:30:25Z","oa":1,"status":"public","isi":1,"publication":"Nature Immunology","year":"2018","ddc":["570"],"abstract":[{"text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux.","lang":"eng"}],"oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:46:25Z","date_updated":"2026-09-16T22:30:29Z","status":"public","oa":1,"month":"01","scopus_import":"1","title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","author":[{"last_name":"Kühnen","full_name":"Kühnen, Jakob","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179"},{"full_name":"Scarselli, Davide","last_name":"Scarselli","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"last_name":"Schaner","full_name":"Schaner, Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","publication":"Flow Turbulence and Combustion","year":"2018","isi":1,"abstract":[{"lang":"eng","text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle."}],"oa_version":"Published Version","ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589"}],"publisher":"Springer","doi":"10.1007/s10494-018-9896-4","intvolume":"       100","publication_status":"published","date_published":"2018-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/s10494-018-9896-4","file":[{"date_updated":"2020-07-14T12:46:25Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","checksum":"d7c0bade150faabca150b0a9986e60ca","file_size":2210020,"file_id":"5717","content_type":"application/pdf","date_created":"2018-12-17T15:52:37Z"}],"external_id":{"isi":["000433113900004"]},"_id":"422","has_accepted_license":"1","day":"01","publist_id":"7401","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"article_processing_charge":"Yes (via OA deal)","type":"journal_article","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7258"}]},"ec_funded":1,"citation":{"mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>.","apa":"Kühnen, J., Scarselli, D., Schaner, M., &#38; Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. Springer. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. 2018;100(4):919-942. doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4. Springer, pp. 919–942, 2018.","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942."},"date_created":"2018-12-11T11:46:23Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","volume":100,"page":"919 - 942"},{"external_id":{"arxiv":["1711.06543"],"isi":["000429434100020"]},"fulldoi":"https://doi.org/10.1038/s41567-017-0018-3","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"7360","_id":"461","day":"08","acknowledgement":"We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data.","ec_funded":1,"article_processing_charge":"No","type":"journal_article","department":[{"_id":"BjHo"}],"related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"14530"},{"relation":"dissertation_contains","id":"7258","status":"public"}]},"volume":14,"page":"386-390","date_created":"2018-12-11T11:46:36Z","citation":{"ama":"Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. <i>Nature Physics</i>. 2018;14:386-390. doi:<a href=\"https://doi.org/10.1038/s41567-017-0018-3\">10.1038/s41567-017-0018-3</a>","apa":"Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41567-017-0018-3\">https://doi.org/10.1038/s41567-017-0018-3</a>","chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” <i>Nature Physics</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41567-017-0018-3\">https://doi.org/10.1038/s41567-017-0018-3</a>.","mla":"Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” <i>Nature Physics</i>, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:<a href=\"https://doi.org/10.1038/s41567-017-0018-3\">10.1038/s41567-017-0018-3</a>.","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","ieee":"J. Kühnen <i>et al.</i>, “Destabilizing turbulence in pipe flow,” <i>Nature Physics</i>, vol. 14. Nature Publishing Group, pp. 386–390, 2018.","ista":"Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390."},"corr_author":"1","oa":1,"status":"public","date_updated":"2026-09-16T22:30:29Z","author":[{"last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","full_name":"Scarselli, Davide"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"},{"first_name":"Ashley","last_name":"Willis","full_name":"Willis, Ashley"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof"}],"title":"Destabilizing turbulence in pipe flow","scopus_import":"1","month":"01","oa_version":"Preprint","abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism                      measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"year":"2018","publication":"Nature Physics","isi":1,"doi":"10.1038/s41567-017-0018-3","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","project":[{"name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"737549","name":"Eliminating turbulence in oil pipelines"}],"publication_status":"published","intvolume":"        14","date_published":"2018-01-08T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.06543"}]},{"publisher":"Genetics Society of America","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1534/genetics.117.300513","date_published":"2018-01-01T00:00:00Z","intvolume":"       208","publication_status":"published","file_date_updated":"2020-07-14T12:46:50Z","issue":"1","author":[{"full_name":"Kelemen, Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"scopus_import":"1","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","month":"01","status":"public","oa":1,"date_updated":"2026-09-16T22:30:30Z","isi":1,"year":"2018","publication":"Genetics","article_type":"original","ddc":["576"],"oa_version":"Published Version","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5571"},{"relation":"popular_science","id":"5572","status":"public"},{"relation":"dissertation_contains","id":"17119","status":"public"}]},"type":"journal_article","article_processing_charge":"No","department":[{"_id":"BeVi"}],"ec_funded":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","date_created":"2018-12-11T11:47:04Z","citation":{"short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>.","apa":"Kelemen, R. K., &#38; Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. 2018;208(1):365-375. doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>."},"page":"365 - 375","volume":208,"fulldoi":"https://doi.org/10.1534/genetics.117.300513","external_id":{"isi":["000419356300024"]},"file":[{"date_updated":"2020-07-14T12:46:50Z","access_level":"open_access","relation":"main_file","creator":"system","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","checksum":"2123845e7031a0cf043905be160f9e69","file_size":1311661,"file_id":"5132","content_type":"application/pdf","date_created":"2018-12-12T10:15:14Z"}],"has_accepted_license":"1","pubrep_id":"1058","day":"01","_id":"542","language":[{"iso":"eng"}],"publist_id":"7274","quality_controlled":"1"},{"isi":1,"publication":"The Plant Cell","year":"2018","article_type":"original","ddc":["580"],"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-05-23T09:12:38Z","month":"04","scopus_import":"1","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek"},{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml"}],"issue":"3","date_updated":"2026-09-16T22:30:40Z","oa":1,"status":"public","date_published":"2018-04-09T00:00:00Z","intvolume":"        30","publication_status":"published","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publisher":"American Society of Plant Biologists","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1105/tpc.17.00785","has_accepted_license":"1","day":"09","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"_id":"412","quality_controlled":"1","publist_id":"7417","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1105/tpc.17.00785","external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"file":[{"date_updated":"2022-05-23T09:12:38Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2018_PlantCell_Adamowski.pdf","success":1,"checksum":"4e165e653b67d3f0684697f21aace5a1","file_size":4407538,"file_id":"11406","date_created":"2022-05-23T09:12:38Z","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” <i>The Plant Cell</i>, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2018. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., &#38; Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. 2018;30(3):700-716. doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>"},"date_created":"2018-12-11T11:46:20Z","page":"700 - 716","volume":30,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6269"}]},"department":[{"_id":"JiFr"}],"article_processing_charge":"No","type":"journal_article","ec_funded":1,"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417."},{"file_date_updated":"2021-02-11T23:30:22Z","month":"08","title":"Reactivation content is important for consolidation of spatial memory","author":[{"orcid":"0000-0002-1807-1929","first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor","last_name":"Gridchyn"}],"date_updated":"2026-04-08T14:13:15Z","status":"public","oa":1,"degree_awarded":"PhD","year":"2018","ddc":["573"],"abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_1042","date_published":"2018-08-27T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.15479/AT:ISTA:th_1042","file":[{"date_updated":"2021-02-11T23:30:22Z","access_level":"closed","creator":"dernst","relation":"source_file","file_name":"2018_Thesis_Gridchyn_source.docx","embargo_to":"open_access","checksum":"7db4415e435590fa33542c7b0a0321d7","file_size":7666687,"file_id":"6236","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-08T13:36:01Z"},{"access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2018_Thesis_Gridchyn.pdf","embargo":"2019-08-29","date_updated":"2021-02-11T11:17:18Z","file_size":6034153,"file_id":"6237","content_type":"application/pdf","date_created":"2019-04-08T13:36:01Z","checksum":"f96f3fe8979f7b1e6db6acaca962b10c"}],"day":"27","has_accepted_license":"1","pubrep_id":"1042","publication_identifier":{"issn":["2663-337X"]},"_id":"48","publist_id":"8006","supervisor":[{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"article_processing_charge":"No","type":"dissertation","corr_author":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>","apa":"Gridchyn, I. (2018). <i>Reactivation content is important for consolidation of spatial memory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>","chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>.","mla":"Gridchyn, Igor. <i>Reactivation Content Is Important for Consolidation of Spatial Memory</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>.","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018."},"date_created":"2018-12-11T11:44:21Z","page":"104","OA_place":"publisher"},{"author":[{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7777-546X"},{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"issue":"10","scopus_import":"1","title":"Evolutionary potential of transcription factors for gene regulatory rewiring","month":"09","status":"public","oa":1,"date_updated":"2026-09-16T22:30:43Z","file_date_updated":"2020-07-14T12:47:37Z","article_type":"original","ddc":["570"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}],"isi":1,"year":"2018","publication":"Nature Ecology and Evolution","doi":"10.1038/s41559-018-0651-y","publisher":"Nature Publishing Group","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"},{"name":"Design principles underlying genetic switch architecture","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-09-10T00:00:00Z","publication_status":"published","intvolume":"         2","external_id":{"isi":["000447947600021"]},"file":[{"date_updated":"2020-07-14T12:47:37Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2018_NatureEcology_Igler.pdf","checksum":"383a2e2c944a856e2e821ec8e7bf71b6","file_size":1135973,"file_id":"7830","date_created":"2020-05-14T11:28:52Z","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.1038/s41559-018-0651-y","language":[{"iso":"eng"}],"publist_id":"7987","quality_controlled":"1","has_accepted_license":"1","day":"10","_id":"67","ec_funded":1,"related_material":{"record":[{"status":"public","id":"5585","relation":"popular_science"},{"status":"public","id":"6371","relation":"dissertation_contains"}]},"type":"journal_article","article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"page":"1633 - 1643","volume":2,"date_created":"2018-12-11T11:44:27Z","citation":{"mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. 2018;2(10):1633-1643. doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643."}},{"related_material":{"record":[{"relation":"research_paper","id":"67","status":"public"},{"status":"public","relation":"research_paper","id":"6371"}]},"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"},{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"doi":"10.15479/AT:ISTA:108","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"citation":{"ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>."},"date_created":"2018-12-12T12:31:40Z","date_published":"2018-07-20T00:00:00Z","datarep_id":"108","fulldoi":"https://doi.org/10.15479/AT:ISTA:108","file_date_updated":"2020-07-14T12:47:07Z","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","month":"07","author":[{"last_name":"Igler","full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7777-546X"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"file":[{"date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","relation":"main_file","creator":"system","file_name":"IST-2018-108-v1+1_data_figures.xlsx","checksum":"1435781526c77413802adee0d4583cce","file_size":16507,"file_id":"5611","date_created":"2018-12-12T13:02:45Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"}],"date_updated":"2026-09-16T22:30:43Z","oa":1,"status":"public","has_accepted_license":"1","day":"20","year":"2018","_id":"5585","ddc":["576"],"abstract":[{"text":"Mean repression values and standard error of the mean are given for all operator mutant libraries.","lang":"eng"}],"oa_version":"Published Version"},{"article_number":"4605","doi":"10.1038/s41467-018-06899-3","publisher":"Nature Publishing Group","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-11-02T00:00:00Z","publication_status":"published","intvolume":"         9","author":[{"last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia ","orcid":"0000-0003-4710-2082"},{"last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","orcid":"0000-0003-0256-6529","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"}],"issue":"1","month":"11","scopus_import":"1","title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","oa":1,"status":"public","date_updated":"2026-09-16T22:30:44Z","file_date_updated":"2020-07-14T12:45:28Z","ddc":["570"],"article_type":"original","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations"}],"isi":1,"year":"2018","publication":"Nature Communications","ec_funded":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","related_material":{"record":[{"id":"6363","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","description":"News on IST Homepage","relation":"press_release"}]},"type":"journal_article","article_processing_charge":"No","department":[{"_id":"PeJo"}],"volume":9,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2018-12-11T11:44:12Z","citation":{"mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>.","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., &#38; Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>","chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>.","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605."},"external_id":{"isi":["000449069700009"]},"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2018_NatureComm_Espinoza.pdf","date_updated":"2020-07-14T12:45:28Z","file_size":4651930,"file_id":"5715","content_type":"application/pdf","date_created":"2018-12-17T15:41:57Z","checksum":"9fe2a63bd95a5067d896c087d07998f3"}],"fulldoi":"https://doi.org/10.1038/s41467-018-06899-3","language":[{"iso":"eng"}],"publist_id":"8034","quality_controlled":"1","has_accepted_license":"1","day":"02","_id":"21"},{"oa_version":"Published Version","abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"ddc":["570","591","596"],"year":"2018","degree_awarded":"PhD","oa":1,"status":"public","date_updated":"2026-04-16T10:07:33Z","author":[{"last_name":"Capek","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940"}],"title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","month":"06","file_date_updated":"2021-02-11T23:30:21Z","publication_status":"published","date_published":"2018-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1031","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publist_id":"8004","_id":"50","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"22","pubrep_id":"1031","file":[{"date_updated":"2021-02-11T11:17:17Z","embargo":"2019-06-25","creator":"dernst","relation":"main_file","file_name":"2018_Thesis_Capek.pdf","access_level":"open_access","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","content_type":"application/pdf","date_created":"2019-04-08T13:42:26Z","file_size":31576521,"file_id":"6238"},{"date_created":"2019-04-08T13:42:27Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":38992956,"file_id":"6239","checksum":"876deb14067e638aba65d209668bd821","creator":"dernst","relation":"source_file","file_name":"2018_Thesis_Capek_source.docx","embargo_to":"open_access","access_level":"closed","date_updated":"2021-02-11T23:30:21Z"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:TH_1031","OA_place":"publisher","page":"95","date_created":"2018-12-11T11:44:21Z","citation":{"ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. <i>Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>.","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>.","apa":"Capek, D. (2018). <i>Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>"},"corr_author":"1","article_processing_charge":"No","type":"dissertation","department":[{"_id":"CaHe"}],"related_material":{"record":[{"status":"public","id":"661","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1100"},{"id":"676","relation":"part_of_dissertation","status":"public"}]}},{"language":[{"iso":"eng"}],"quality_controlled":"1","day":"01","_id":"5816","publication_identifier":{"issn":["0034-6748"]},"external_id":{"arxiv":["1804.09522"],"isi":["000451735700054"]},"fulldoi":"https://doi.org/10.1063/1.5038258","volume":89,"date_created":"2019-01-10T14:22:23Z","citation":{"ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. <i>Review of Scientific Instruments</i>. 2018;89(11). doi:<a href=\"https://doi.org/10.1063/1.5038258\">10.1063/1.5038258</a>","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., &#38; Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. <i>Review of Scientific Instruments</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5038258\">https://doi.org/10.1063/1.5038258</a>","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” <i>Review of Scientific Instruments</i>. AIP Publishing, 2018. <a href=\"https://doi.org/10.1063/1.5038258\">https://doi.org/10.1063/1.5038258</a>.","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” <i>Review of Scientific Instruments</i>, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:<a href=\"https://doi.org/10.1063/1.5038258\">10.1063/1.5038258</a>.","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” <i>Review of Scientific Instruments</i>, vol. 89, no. 11. AIP Publishing, 2018.","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701."},"related_material":{"record":[{"id":"10058","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","type":"journal_article","department":[{"_id":"GeKa"}],"oa_version":"Preprint","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"isi":1,"year":"2018","publication":"Review of Scientific Instruments","issue":"11","author":[{"first_name":"Arne","full_name":"Hollmann, Arne","last_name":"Hollmann"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","full_name":"Jirovec, Daniel"},{"full_name":"Kucharski, Maciej","last_name":"Kucharski","first_name":"Maciej"},{"first_name":"Dietmar","full_name":"Kissinger, Dietmar","last_name":"Kissinger"},{"full_name":"Fischer, Gunter","last_name":"Fischer","first_name":"Gunter"},{"first_name":"Lars R.","last_name":"Schreiber","full_name":"Schreiber, Lars R."}],"scopus_import":"1","title":"30 GHz-voltage controlled oscillator operating at 4 K","month":"11","status":"public","oa":1,"date_updated":"2026-09-16T22:30:46Z","date_published":"2018-11-01T00:00:00Z","publication_status":"published","intvolume":"        89","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"arxiv":1,"article_number":"114701","doi":"10.1063/1.5038258","publisher":"AIP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2026-09-16T22:30:48Z","oa":1,"status":"public","month":"01","title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","issue":"1","author":[{"full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"}],"file_date_updated":"2020-07-14T12:46:29Z","abstract":[{"text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.","lang":"eng"}],"oa_version":"Published Version","ddc":["576","581"],"article_type":"original","publication":"Bio-protocol","year":"2018","doi":"10.21769/BioProtoc.2685","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publisher":"Bio-protocol","publication_status":"published","intvolume":"         8","date_published":"2018-01-05T00:00:00Z","file":[{"date_updated":"2020-07-14T12:46:29Z","access_level":"open_access","creator":"system","relation":"main_file","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","checksum":"6644ba698206eda32b0abf09128e63e3","file_size":11352389,"file_id":"5299","date_created":"2018-12-12T10:17:43Z","content_type":"application/pdf"}],"fulldoi":"https://doi.org/10.21769/BioProtoc.2685","quality_controlled":"1","publist_id":"7381","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2331-8325"]},"_id":"442","has_accepted_license":"1","day":"05","pubrep_id":"970","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","ec_funded":1,"department":[{"_id":"JiFr"},{"_id":"Bio"}],"article_processing_charge":"No","type":"journal_article","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"volume":8,"citation":{"mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>, vol. 8, no. 1, Bio-protocol, 2018, doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>.","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>. Bio-protocol, 2018. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>.","apa":"Li, L., Krens, G., Fendrych, M., &#38; Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-Protocol</i>. Bio-protocol. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-protocol</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” <i>Bio-protocol</i>, vol. 8, no. 1. Bio-protocol, 2018.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018)."},"date_created":"2018-12-11T11:46:30Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1"},{"issue":"48","author":[{"last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Schmid, Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"scopus_import":"1","title":"Indirect reciprocity with private, noisy, and incomplete information","month":"11","oa":1,"status":"public","date_updated":"2026-09-16T22:30:50Z","oa_version":"Submitted Version","abstract":[{"text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems.","lang":"eng"}],"isi":1,"year":"2018","publication":"PNAS","doi":"10.1073/pnas.1810565115","publisher":"National Academy of Sciences","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-11-27T00:00:00Z","intvolume":"       115","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320"}],"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"pmid":1,"fulldoi":"https://doi.org/10.1073/pnas.1810565115","language":[{"iso":"eng"}],"quality_controlled":"1","day":"27","_id":"2","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10293"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/"}]},"type":"journal_article","article_processing_charge":"No","department":[{"_id":"KrCh"}],"page":"12241-12246","volume":115,"date_created":"2018-12-11T11:44:05Z","citation":{"mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>.","ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. 2018;115(48):12241-12246. doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>.","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” <i>PNAS</i>, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246."}},{"page":"88","OA_place":"publisher","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>.","apa":"Tarlungeanu, D.-C. (2018). <i>The branched chain amino acids in autism spectrum disorders </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>","mla":"Tarlungeanu, Dora-Clara. <i>The Branched Chain Amino Acids in Autism Spectrum Disorders </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria."},"date_created":"2018-12-11T11:46:14Z","related_material":{"record":[{"id":"1183","relation":"part_of_dissertation","status":"public"}]},"department":[{"_id":"GaNo"}],"type":"dissertation","article_processing_charge":"No","publist_id":"7434","supervisor":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"}],"language":[{"iso":"eng"}],"day":"01","has_accepted_license":"1","pubrep_id":"992","publication_identifier":{"issn":["2663-337X"]},"_id":"395","file":[{"file_size":43684035,"file_id":"6217","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T09:19:17Z","checksum":"9f5231c96e0ad945040841a8630232da","access_level":"closed","creator":"dernst","relation":"source_file","file_name":"2018_Thesis_Tarlungeanu_source.docx","embargo_to":"open_access","date_updated":"2021-02-11T23:30:15Z"},{"access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2018_Thesis_Tarlungeanu.pdf","embargo":"2018-03-15","date_updated":"2021-02-11T11:17:16Z","file_size":30511532,"file_id":"6218","date_created":"2019-04-05T09:19:17Z","content_type":"application/pdf","checksum":"0c33c370aa2010df5c552db57a6d01e9"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:th_992","date_published":"2018-03-01T00:00:00Z","publication_status":"published","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_992","project":[{"name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F03523"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570","616"],"abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"oa_version":"Published Version","degree_awarded":"PhD","year":"2018","title":"The branched chain amino acids in autism spectrum disorders ","month":"03","author":[{"full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-08T14:15:20Z","oa":1,"status":"public","file_date_updated":"2021-02-11T23:30:15Z"},{"language":[{"iso":"eng"}],"publist_id":"8007","quality_controlled":"1","day":"01","_id":"47","external_id":{"isi":["000453657800006"]},"fulldoi":"https://doi.org/10.1016/bs.abr.2018.09.007","page":"115 - 138","volume":87,"date_created":"2018-12-11T11:44:20Z","citation":{"ieee":"R. Abualia, E. Benková, and B. Lacombe, “Transporters and mechanisms of hormone transport in arabidopsis,” <i>Advances in Botanical Research</i>, vol. 87. Elsevier, pp. 115–138, 2018.","short":"R. Abualia, E. Benková, B. Lacombe, Advances in Botanical Research 87 (2018) 115–138.","ista":"Abualia R, Benková E, Lacombe B. 2018. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 87, 115–138.","mla":"Abualia, Rashed, et al. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” <i>Advances in Botanical Research</i>, vol. 87, Elsevier, 2018, pp. 115–38, doi:<a href=\"https://doi.org/10.1016/bs.abr.2018.09.007\">10.1016/bs.abr.2018.09.007</a>.","ama":"Abualia R, Benková E, Lacombe B. Transporters and mechanisms of hormone transport in arabidopsis. <i>Advances in Botanical Research</i>. 2018;87:115-138. doi:<a href=\"https://doi.org/10.1016/bs.abr.2018.09.007\">10.1016/bs.abr.2018.09.007</a>","chicago":"Abualia, Rashed, Eva Benková, and Benoît Lacombe. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” <i>Advances in Botanical Research</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/bs.abr.2018.09.007\">https://doi.org/10.1016/bs.abr.2018.09.007</a>.","apa":"Abualia, R., Benková, E., &#38; Lacombe, B. (2018). Transporters and mechanisms of hormone transport in arabidopsis. <i>Advances in Botanical Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/bs.abr.2018.09.007\">https://doi.org/10.1016/bs.abr.2018.09.007</a>"},"related_material":{"record":[{"status":"public","id":"10303","relation":"dissertation_contains"}]},"article_processing_charge":"No","type":"journal_article","department":[{"_id":"EvBe"}],"oa_version":"None","abstract":[{"text":"Plant hormones as signalling molecules play an essential role in the control of plant growth and development. Typically, sites of hormonal action are usually distant from the site of biosynthesis thus relying on efficient transport mechanisms. Over the last decades, molecular identification of proteins and protein complexes involved in hormonal transport has started. Advanced screens for genes involved in hormonal transport in combination with transport assays using heterologous systems such as yeast, insect, or tobacco BY2 cells or Xenopus oocytes provided important insights into mechanisms underlying distribution of hormones in plant body and led to identification of principal transporters for each hormone. This review gives a short overview of the mechanisms of hormonal transport and transporters identified in Arabidopsis thaliana.","lang":"eng"}],"isi":1,"year":"2018","publication":"Advances in Botanical Research","author":[{"full_name":"Abualia, Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed"},{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Lacombe","full_name":"Lacombe, Benoît","first_name":"Benoît"}],"scopus_import":"1","title":"Transporters and mechanisms of hormone transport in arabidopsis","month":"01","status":"public","date_updated":"2026-09-16T22:30:53Z","date_published":"2018-01-01T00:00:00Z","intvolume":"        87","publication_status":"published","doi":"10.1016/bs.abr.2018.09.007","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa":1,"status":"public","date_updated":"2025-09-22T08:27:34Z","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner"}],"title":"Branched actin networks in dendritic cell biology","month":"04","file_date_updated":"2021-02-11T23:30:17Z","oa_version":"Published Version","abstract":[{"text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. ","lang":"eng"}],"ddc":["571","599","610"],"year":"2018","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_998","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","publication_status":"published","date_published":"2018-04-12T00:00:00Z","file":[{"date_updated":"2021-02-11T23:30:17Z","creator":"dernst","relation":"source_file","embargo_to":"open_access","file_name":"PhD_thesis_AlexLeithner_final_version.docx","access_level":"closed","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T09:23:11Z","file_size":29027671,"file_id":"6219"},{"content_type":"application/pdf","date_created":"2019-04-05T09:23:11Z","file_size":66045341,"file_id":"6220","checksum":"071f7476db29e41146824ebd0697cb10","relation":"main_file","creator":"dernst","file_name":"PhD_thesis_AlexLeithner.pdf","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-04-15"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:th_998","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"publist_id":"7542","_id":"323","publication_identifier":{"issn":["2663-337X"]},"day":"12","pubrep_id":"998","has_accepted_license":"1","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe  best  boss  one  can  imagine.  I  would  also  like  to  thank  all  current  and  past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m  proud  that  I  could  be  part  of  it.  Furthermore,  I  would  like  to  say  ‘thank  you’  to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to  Federica  Benvenuti  for  being  part  of  my  committee.  I  am  also  grateful  to  Jack \r\nMerrin  in  the  nanofabrication  facility  and  all  the  people  working  in  the  bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","article_processing_charge":"No","type":"dissertation","department":[{"_id":"MiSi"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1321"}]},"page":"99","date_created":"2018-12-11T11:45:49Z","citation":{"apa":"Leithner, A. F. (2018). <i>Branched actin networks in dendritic cell biology</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>","chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>.","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>","mla":"Leithner, Alexander F. <i>Branched Actin Networks in Dendritic Cell Biology</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1"},{"file_date_updated":"2020-07-14T12:46:30Z","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","month":"01","scopus_import":"1","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Prat, Tomas","last_name":"Prat"},{"full_name":"Hajny, Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","full_name":"Vasileva, Mina K","last_name":"Vasileva"},{"first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"full_name":"Schmid, Markus","last_name":"Schmid","first_name":"Markus"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"issue":"1","date_updated":"2026-09-16T22:30:58Z","oa":1,"status":"public","isi":1,"publication":"PLoS Genetics","year":"2018","ddc":["581"],"abstract":[{"text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.","lang":"eng"}],"oa_version":"Published Version","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"publisher":"Public Library of Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1371/journal.pgen.1007177","date_published":"2018-01-29T00:00:00Z","intvolume":"        14","publication_status":"published","fulldoi":"https://doi.org/10.1371/journal.pgen.1007177","external_id":{"isi":["000423718600034"]},"file":[{"date_updated":"2020-07-14T12:46:30Z","access_level":"open_access","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","relation":"main_file","creator":"system","checksum":"0276d66788ec076f4924164a39e6a712","file_id":"4843","file_size":24709062,"content_type":"application/pdf","date_created":"2018-12-12T10:10:52Z"}],"pubrep_id":"967","day":"29","has_accepted_license":"1","_id":"449","quality_controlled":"1","publist_id":"7373","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7172"},{"status":"public","relation":"dissertation_contains","id":"1127"},{"relation":"dissertation_contains","id":"8822","status":"public"}]},"department":[{"_id":"JiFr"}],"article_processing_charge":"Yes","type":"journal_article","ec_funded":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","citation":{"mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>, vol. 14, no. 1, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>.","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>.","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. 2018;14(1). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>","ieee":"T. Prat <i>et al.</i>, “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” <i>PLoS Genetics</i>, vol. 14, no. 1. Public Library of Science, 2018.","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1)."},"date_created":"2018-12-11T11:46:32Z","volume":14},{"date_published":"2018-07-06T00:00:00Z","intvolume":"         8","publication_status":"published","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"10279","doi":"10.1038/s41598-018-28188-1","isi":1,"publication":"Scientific Reports","year":"2018","ddc":["581"],"abstract":[{"lang":"eng","text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:20Z","month":"07","scopus_import":"1","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"first_name":"Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abas, Melinda F","last_name":"Abas"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny"},{"last_name":"Jones","full_name":"Jones, Angharad","first_name":"Angharad"},{"last_name":"Waidmann","full_name":"Waidmann, Sascha","first_name":"Sascha"},{"first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"issue":"1","date_updated":"2026-09-16T22:30:58Z","oa":1,"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., &#38; Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. Springer. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>. Springer, 2018. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>.","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>, vol. 8, no. 1, 10279, Springer, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","ieee":"P. Grones <i>et al.</i>, “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” <i>Scientific Reports</i>, vol. 8, no. 1. Springer, 2018.","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279."},"date_created":"2018-12-11T11:45:06Z","volume":8,"related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"type":"journal_article","article_processing_charge":"No","ec_funded":1,"day":"06","has_accepted_license":"1","_id":"191","publist_id":"7729","quality_controlled":"1","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41598-018-28188-1","external_id":{"isi":["000437673200053"]},"file":[{"checksum":"266b03f4fb8198e83141617aaa99dcab","file_id":"5714","file_size":2413876,"date_created":"2018-12-17T15:38:56Z","content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","access_level":"open_access","file_name":"2018_ScientificReports_Grones.pdf","creator":"dernst","relation":"main_file"}]}]