[{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-05-24T22:01:00Z","external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"_id":"7883","month":"04","scopus_import":"1","citation":{"ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021)."},"type":"journal_article","abstract":[{"text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.","lang":"eng"}],"pmid":1,"quality_controlled":"1","OA_type":"hybrid","department":[{"_id":"AnKi"}],"corr_author":"1","publisher":"Wiley","oa_version":"Published Version","author":[{"id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna"}],"title":"Regulation of size and scale in vertebrate spinal cord development","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14323"}]},"date_updated":"2026-05-14T22:31:12Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2020-11-24T13:11:39Z","oa":1,"file":[{"file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","success":1,"date_created":"2020-11-24T13:11:39Z","creator":"dernst","file_size":2527276,"access_level":"open_access","date_updated":"2020-11-24T13:11:39Z","file_id":"8800","content_type":"application/pdf","checksum":"f0a7745d48afa09ea7025e876a0145a8","relation":"main_file"}],"doi":"10.1002/wdev.383","day":"15","date_published":"2021-04-15T00:00:00Z","article_number":"e383","article_type":"original","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","publication_identifier":{"issn":["1759-7684"],"eissn":["1759-7692"]},"year":"2021","ec_funded":1,"isi":1,"publication":"Wiley Interdisciplinary Reviews: Developmental Biology","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"}],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"OA_place":"publisher"},{"department":[{"_id":"AnKi"},{"_id":"EdHa"}],"volume":18,"publisher":"IOP Publishing","quality_controlled":"1","citation":{"ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>.","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021)."},"type":"journal_article","pmid":1,"abstract":[{"text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.","lang":"eng"}],"_id":"9349","issue":"4","scopus_import":"1","month":"04","date_created":"2021-04-25T22:01:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"isi":1,"publication":"Physical biology","ddc":["570"],"project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-04-14T00:00:00Z","intvolume":"        18","oa":1,"file":[{"date_created":"2021-04-27T08:38:35Z","success":1,"file_name":"2021_PhysBio_Lenne.pdf","creator":"cziletti","file_size":6296324,"access_level":"open_access","date_updated":"2021-04-27T08:38:35Z","file_id":"9355","content_type":"application/pdf","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","relation":"main_file"}],"doi":"10.1088/1478-3975/abd0db","day":"14","publication_identifier":{"eissn":["1478-3975"]},"article_type":"original","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","year":"2021","ec_funded":1,"article_number":"041501","date_updated":"2026-05-14T22:31:14Z","related_material":{"record":[{"id":"13081","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Pierre François","last_name":"Lenne","full_name":"Lenne, Pierre François"},{"full_name":"Munro, Edwin","last_name":"Munro","first_name":"Edwin"},{"full_name":"Heemskerk, Idse","last_name":"Heemskerk","first_name":"Idse"},{"last_name":"Warmflash","full_name":"Warmflash, Aryeh","first_name":"Aryeh"},{"last_name":"Bocanegra","full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795"},{"first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva"},{"first_name":"Yuchen","full_name":"Long, Yuchen","last_name":"Long"},{"first_name":"Antoine","last_name":"Fruleux","full_name":"Fruleux, Antoine"},{"last_name":"Boudaoud","full_name":"Boudaoud, Arezki","first_name":"Arezki"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"first_name":"Paolo","full_name":"Caldarelli, Paolo","last_name":"Caldarelli"},{"full_name":"Michaut, Arthur","last_name":"Michaut","first_name":"Arthur"},{"first_name":"Jerome","full_name":"Gros, Jerome","last_name":"Gros"},{"first_name":"Yonit","last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit"},{"last_name":"Keren","full_name":"Keren, Kinneret","first_name":"Kinneret"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"full_name":"Gartner, Zev J.","last_name":"Gartner","first_name":"Zev J."},{"last_name":"Stormo","full_name":"Stormo, Benjamin","first_name":"Benjamin"},{"full_name":"Gladfelter, Amy","last_name":"Gladfelter","first_name":"Amy"},{"last_name":"Rodrigues","full_name":"Rodrigues, Alan","first_name":"Alan"},{"last_name":"Shyer","full_name":"Shyer, Amy","first_name":"Amy"},{"full_name":"Minc, Nicolas","last_name":"Minc","first_name":"Nicolas"},{"full_name":"Maître, Jean Léon","last_name":"Maître","first_name":"Jean Léon"},{"first_name":"Stefano","full_name":"Di Talia, Stefano","last_name":"Di Talia"},{"full_name":"Khamaisi, Bassma","last_name":"Khamaisi","first_name":"Bassma"},{"last_name":"Sprinzak","full_name":"Sprinzak, David","first_name":"David"},{"last_name":"Tlili","full_name":"Tlili, Sham","first_name":"Sham"}],"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-04-27T08:38:35Z","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version"},{"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-12-23T23:30:04Z","language":[{"iso":"eng"}],"status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6490"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"id":"66","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6378"},{"id":"311","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6175"},{"status":"public","id":"6340","relation":"part_of_dissertation"},{"id":"7014","relation":"part_of_dissertation","status":"public"},{"id":"6009","relation":"part_of_dissertation","status":"public"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"id":"8728","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8089","status":"public"},{"relation":"part_of_dissertation","id":"6380","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"639"},{"id":"1386","relation":"part_of_dissertation","status":"public"},{"id":"6918","relation":"part_of_dissertation","status":"public"},{"id":"7810","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"949","relation":"part_of_dissertation"}]},"date_updated":"2026-04-16T10:07:18Z","page":"278","title":"Parameterized and algebro-geometric advances in static program analysis","author":[{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","publication_identifier":{"issn":["2663-337X"]},"year":"2021","degree_awarded":"PhD","date_published":"2021-01-01T00:00:00Z","file":[{"access_level":"open_access","creator":"akafshda","embargo":"2021-12-22","file_size":5251507,"file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","content_type":"application/pdf","checksum":"d1b9db3725aed34dadd81274aeb9426c","relation":"main_file","date_updated":"2021-12-23T23:30:04Z","file_id":"8969"},{"content_type":"application/zip","checksum":"1661df7b393e6866d2460eba3c905130","relation":"source_file","date_updated":"2021-03-04T23:30:04Z","file_id":"8970","access_level":"closed","embargo_to":"open_access","creator":"akafshda","file_size":10636756,"date_created":"2020-12-22T20:08:50Z","file_name":"source.zip"}],"oa":1,"day":"01","doi":"10.15479/AT:ISTA:8934","OA_place":"publisher","ddc":["005"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"alternative_title":["ISTA Thesis"],"date_created":"2020-12-10T12:17:07Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publication_status":"published","month":"01","_id":"8934","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021."},"abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","department":[{"_id":"KrCh"},{"_id":"GradSch"}]},{"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2021-02-04T07:49:25Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","author":[{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"full_name":"Zhang, Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous"},{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"first_name":"Zlata","last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata"},{"first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","last_name":"Hajny"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","date_updated":"2026-05-14T22:31:21Z","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"110750","ec_funded":1,"publication_identifier":{"issn":["0168-9452"]},"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","year":"2021","article_type":"original","doi":"10.1016/j.plantsci.2020.110750","day":"01","oa":1,"file":[{"file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z","success":1,"file_size":12563728,"creator":"dernst","access_level":"open_access","file_id":"9083","date_updated":"2021-02-04T07:49:25Z","relation":"main_file","checksum":"a7f2562bdca62d67dfa88e271b62a629","content_type":"application/pdf"}],"intvolume":"       303","date_published":"2021-02-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"ddc":["580"],"publication":"Plant Science","isi":1,"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2020-12-09T14:48:28Z","month":"02","scopus_import":"1","_id":"8931","pmid":1,"abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"type":"journal_article","citation":{"mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021)."},"quality_controlled":"1","publisher":"Elsevier","corr_author":"1","volume":303,"department":[{"_id":"JiFr"},{"_id":"Bio"}]},{"project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["580"],"publication":"Plant Physiology","isi":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1,"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","year":"2021","article_type":"original","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"doi":"10.1093/plphys/kiab134","day":"01","oa":1,"file":[{"file_id":"10273","date_updated":"2021-11-11T15:07:51Z","relation":"main_file","checksum":"532bb9469d3b665907f06df8c383eade","content_type":"application/pdf","success":1,"file_name":"2021_PlantPhysio_Narasimhan.pdf","date_created":"2021-11-11T15:07:51Z","file_size":2289127,"creator":"cziletti","access_level":"open_access"}],"intvolume":"       186","date_published":"2021-06-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2021-11-11T15:07:51Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","author":[{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671"},{"first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Himschoot, E","last_name":"Himschoot","first_name":"E"},{"full_name":"Wang, R","last_name":"Wang","first_name":"R"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"full_name":"Sánchez-Simarro, J","last_name":"Sánchez-Simarro","first_name":"J"},{"first_name":"F","last_name":"Aniento","full_name":"Aniento, F"},{"orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_updated":"2026-05-14T22:31:21Z","related_material":{"link":[{"url":"https://doi.org/10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"page":"1122–1142","oa_version":"Published Version","publisher":"Oxford University Press","corr_author":"1","volume":186,"department":[{"_id":"JiFr"}],"type":"journal_article","pmid":1,"abstract":[{"text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. ","lang":"eng"}],"citation":{"apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142."},"quality_controlled":"1","month":"06","scopus_import":"1","issue":"2","_id":"9287","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-03-26T12:08:38Z"},{"abstract":[{"text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. ","lang":"eng"}],"type":"dissertation","citation":{"short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>."},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","date_created":"2021-10-04T13:33:10Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"alternative_title":["ISTA Thesis"],"_id":"10083","month":"10","date_published":"2021-10-06T00:00:00Z","doi":"10.15479/at:ista:10083","day":"06","file":[{"file_id":"10138","date_updated":"2022-12-20T23:30:03Z","relation":"main_file","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","content_type":"application/pdf","date_created":"2021-10-14T08:00:07Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","file_size":8616142,"creator":"cchlebak","embargo":"2022-10-14","access_level":"open_access"},{"embargo_to":"open_access","access_level":"closed","date_created":"2021-10-14T08:00:13Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","file_size":15058499,"creator":"cchlebak","relation":"source_file","checksum":"f23ed258ca894f6aabf58b0c128bf242","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10139","date_updated":"2022-12-20T23:30:03Z"}],"oa":1,"degree_awarded":"PhD","ec_funded":1,"year":"2021","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"}],"OA_place":"publisher","ddc":["575"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"442","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6627","status":"public"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8986"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"status":"public","id":"8283","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9287","status":"public"},{"relation":"part_of_dissertation","id":"10015","status":"public"}]},"date_updated":"2026-04-16T12:20:41Z","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","file_date_updated":"2022-12-20T23:30:03Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"publication":"Cells","isi":1,"ddc":["575"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"intvolume":"        10","date_published":"2021-07-02T00:00:00Z","day":"02","doi":"10.3390/cells10071665","file":[{"relation":"main_file","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","content_type":"application/pdf","file_id":"10021","date_updated":"2021-09-16T09:07:06Z","access_level":"open_access","success":1,"date_created":"2021-09-16T09:07:06Z","file_name":"2021_Cells_Nikonorova.pdf","file_size":2667848,"creator":"cchlebak"}],"oa":1,"ec_funded":1,"acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","publication_identifier":{"issn":["2073-4409"]},"article_type":"original","year":"2021","article_number":"1665 ","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"}]},"date_updated":"2026-05-14T22:31:22Z","author":[{"first_name":"N","last_name":"Nikonorova","full_name":"Nikonorova, N"},{"first_name":"E","full_name":"Murphy, E","last_name":"Murphy"},{"first_name":"CF","full_name":"Fonseca de Lima, CF","last_name":"Fonseca de Lima"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"last_name":"van de Cotte","full_name":"van de Cotte, B","first_name":"B"},{"last_name":"Vu","full_name":"Vu, LD","first_name":"LD"},{"first_name":"D","last_name":"Balcerowicz","full_name":"Balcerowicz, D"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"first_name":"X","full_name":"Kong, X","last_name":"Kong"},{"first_name":"G","last_name":"De Rop","full_name":"De Rop, G"},{"full_name":"Beeckman, T","last_name":"Beeckman","first_name":"T"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Vissenberg, K","last_name":"Vissenberg","first_name":"K"},{"first_name":"PC","last_name":"Morris","full_name":"Morris, PC"},{"full_name":"Ding, Z","last_name":"Ding","first_name":"Z"},{"last_name":"De Smet","full_name":"De Smet, I","first_name":"I"}],"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","file_date_updated":"2021-09-16T09:07:06Z","has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"department":[{"_id":"JiFr"}],"volume":10,"publisher":"MDPI","quality_controlled":"1","type":"journal_article","abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"pmid":1,"citation":{"mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>, vol. 10, 1665, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>.","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>.","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. 2021;10. doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>","ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021)."},"_id":"10015","scopus_import":"1","month":"07","date_created":"2021-09-14T11:36:20Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"draft","date_created":"2021-10-06T08:56:22Z","_id":"10095","month":"09","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.)."},"abstract":[{"text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.","lang":"eng"}],"type":"preprint","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"corr_author":"1","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"oa_version":"Preprint","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"first_name":"Lesia","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"first_name":"Lana","full_name":"Shabala, Lana","last_name":"Shabala"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"last_name":"Ren","full_name":"Ren, Hong","first_name":"Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Sergey","full_name":"Shabala, Sergey","last_name":"Shabala"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"date_updated":"2026-05-14T22:31:21Z","related_material":{"record":[{"status":"public","id":"10223","relation":"later_version"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa":1,"doi":"10.21203/rs.3.rs-266395/v3","day":"09","date_published":"2021-09-09T00:00:00Z","article_number":"266395","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"year":"2021","publication_identifier":{"issn":["2693-5015"]},"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","ec_funded":1,"publication":"Research Square","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}]},{"citation":{"ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58."},"abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"pmid":1,"type":"journal_article","quality_controlled":"1","publisher":"Oxford University Press ","corr_author":"1","volume":138,"department":[{"_id":"BeVi"}],"external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-10-21T07:49:12Z","month":"06","scopus_import":"1","issue":"12","_id":"10167","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"year":"2021","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","file":[{"access_level":"open_access","success":1,"date_created":"2022-05-06T09:47:18Z","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","creator":"dernst","file_size":1008594,"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","content_type":"application/pdf","relation":"main_file","date_updated":"2022-05-06T09:47:18Z","file_id":"11352"}],"oa":1,"doi":"10.1093/molbev/msab178","day":"19","date_published":"2021-06-19T00:00:00Z","intvolume":"       138","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["610"],"isi":1,"publication":"Molecular Biology and Evolution","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2022-05-06T09:47:18Z","author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A.","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0"},{"first_name":"Marion A L","last_name":"Picard","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","related_material":{"record":[{"id":"19386","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-05-14T22:31:23Z","page":"5345-58"},{"scopus_import":"1","month":"09","_id":"11501","external_id":{"arxiv":["2007.01878"]},"date_created":"2022-07-06T09:38:16Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.01878"}],"publisher":"EDP Sciences","volume":641,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We investigated the ultraviolet (UV) spectral properties of faint Lyman-α emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to prepare future observations of the faint Universe. We used data from the MUSE Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint (median MUV of −18 and down to MUV of −16), low stellar mass (median value of 108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength, UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation rate) properties. We searched for UV spectral features other than Lyα, such as higher ionization nebular emission lines and absorption features. We successfully observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551 doublet either in emission or P-Cygni. We compared the observed spectral properties of the different mean spectra and find the emission lines to vary with the observational and physical properties of the LAEs. In particular, the mean spectra of LAEs with larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes, and lower stellar masses show the strongest nebular emission. The line ratios of these lines are similar to those measured in the spectra of local metal-poor galaxies, while their equivalent widths are weaker compared to the handful of extreme values detected in individual spectra of z >  2 galaxies. This suggests that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs. We publicly released the stacked spectra, as they can serve as empirical templates for the design of future observations, such as those with the James Webb Space Telescope and the Extremely Large Telescope."}],"extern":"1","type":"journal_article","citation":{"short":"A. Feltre, M.V. Maseda, R. Bacon, J. Pradeep, F. Leclercq, H. Kusakabe, L. Wisotzki, T. Hashimoto, K.B. Schmidt, J. Blaizot, J. Brinchmann, L. Boogaard, S. Cantalupo, D. Carton, H. Inami, W. Kollatschny, R.A. Marino, J.J. Matthee, T. Nanayakkara, J. Richard, J. Schaye, L. Tresse, T. Urrutia, A. Verhamme, P.M. Weilbacher, Astronomy &#38; Astrophysics 641 (2020).","apa":"Feltre, A., Maseda, M. V., Bacon, R., Pradeep, J., Leclercq, F., Kusakabe, H., … Weilbacher, P. M. (2020). The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z &#62; 3. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202038133\">https://doi.org/10.1051/0004-6361/202038133</a>","ieee":"A. Feltre <i>et al.</i>, “The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z &#62; 3,” <i>Astronomy &#38; Astrophysics</i>, vol. 641. EDP Sciences, 2020.","ama":"Feltre A, Maseda MV, Bacon R, et al. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z &#62; 3. <i>Astronomy &#38; Astrophysics</i>. 2020;641. doi:<a href=\"https://doi.org/10.1051/0004-6361/202038133\">10.1051/0004-6361/202038133</a>","mla":"Feltre, Anna, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z &#62; 3.” <i>Astronomy &#38; Astrophysics</i>, vol. 641, A118, EDP Sciences, 2020, doi:<a href=\"https://doi.org/10.1051/0004-6361/202038133\">10.1051/0004-6361/202038133</a>.","ista":"Feltre A, Maseda MV, Bacon R, Pradeep J, Leclercq F, Kusakabe H, Wisotzki L, Hashimoto T, Schmidt KB, Blaizot J, Brinchmann J, Boogaard L, Cantalupo S, Carton D, Inami H, Kollatschny W, Marino RA, Matthee JJ, Nanayakkara T, Richard J, Schaye J, Tresse L, Urrutia T, Verhamme A, Weilbacher PM. 2020. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z &#62; 3. Astronomy &#38; Astrophysics. 641, A118.","chicago":"Feltre, Anna, Michael V. Maseda, Roland Bacon, Jayadev Pradeep, Floriane Leclercq, Haruka Kusakabe, Lutz Wisotzki, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z &#62; 3.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2020. <a href=\"https://doi.org/10.1051/0004-6361/202038133\">https://doi.org/10.1051/0004-6361/202038133</a>."},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2022-07-19T09:35:43Z","author":[{"first_name":"Anna","full_name":"Feltre, Anna","last_name":"Feltre"},{"full_name":"Maseda, Michael V.","last_name":"Maseda","first_name":"Michael V."},{"full_name":"Bacon, Roland","last_name":"Bacon","first_name":"Roland"},{"full_name":"Pradeep, Jayadev","last_name":"Pradeep","first_name":"Jayadev"},{"first_name":"Floriane","full_name":"Leclercq, Floriane","last_name":"Leclercq"},{"first_name":"Haruka","last_name":"Kusakabe","full_name":"Kusakabe, Haruka"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"},{"full_name":"Hashimoto, Takuya","last_name":"Hashimoto","first_name":"Takuya"},{"first_name":"Kasper B.","last_name":"Schmidt","full_name":"Schmidt, Kasper B."},{"last_name":"Blaizot","full_name":"Blaizot, Jeremy","first_name":"Jeremy"},{"first_name":"Jarle","full_name":"Brinchmann, Jarle","last_name":"Brinchmann"},{"first_name":"Leindert","full_name":"Boogaard, Leindert","last_name":"Boogaard"},{"first_name":"Sebastiano","full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo"},{"first_name":"David","last_name":"Carton","full_name":"Carton, David"},{"first_name":"Hanae","full_name":"Inami, Hanae","last_name":"Inami"},{"first_name":"Wolfram","last_name":"Kollatschny","full_name":"Kollatschny, Wolfram"},{"full_name":"Marino, Raffaella A.","last_name":"Marino","first_name":"Raffaella A."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya","first_name":"Themiya"},{"first_name":"Johan","last_name":"Richard","full_name":"Richard, Johan"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"first_name":"Laurence","full_name":"Tresse, Laurence","last_name":"Tresse"},{"last_name":"Urrutia","full_name":"Urrutia, Tanya","first_name":"Tanya"},{"first_name":"Anne","last_name":"Verhamme","full_name":"Verhamme, Anne"},{"first_name":"Peter M.","last_name":"Weilbacher","full_name":"Weilbacher, Peter M."}],"title":"The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet: ISM / ultraviolet: galaxies"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"Astronomy & Astrophysics","year":"2020","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_type":"original","acknowledgement":"We thank Margherita Talia, Stéphane Charlot, Adele Plat and Alba Vidal-García for helpful discussions. This work is supported by the ERC advanced grant 339659-MUSICOS (R. Bacon). AF acknowledges the support from grant PRIN MIUR 2017 20173ML3WW. MVM and JP would like to thank the Leiden/ESA Astrophysics Program for Summer Students (LEAPS) for funding at the outset of this project. FL, HK, and AV acknowledge support from the ERC starting grant ERC-757258-TRIPLE. TH was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan. JB acknowledges support by FCT/MCTES through national funds by the grant UID/FIS/04434/2019, UIDB/04434/2020 and UIDP/04434/2020 and through the Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. HI acknowledges support from JSPS KAKENHI Grant Number JP19K23462. We would also like to thank the organizers and participants of the Leiden Lorentz Center workshop: Revolutionary Spectroscopy of Today as a Springboard to Webb. This work made use of several open source python packages: NUMPY (van der Walt et al. 2011), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration 2013) and MPDAF (MUSE Python Data Analysis Framework, Piqueras et al. 2019).","article_number":"A118","intvolume":"       641","date_published":"2020-09-18T00:00:00Z","day":"18","doi":"10.1051/0004-6361/202038133","oa":1},{"author":[{"first_name":"Haruka","full_name":"Kusakabe, Haruka","last_name":"Kusakabe"},{"first_name":"Jérémy","full_name":"Blaizot, Jérémy","last_name":"Blaizot"},{"last_name":"Garel","full_name":"Garel, Thibault","first_name":"Thibault"},{"last_name":"Verhamme","full_name":"Verhamme, Anne","first_name":"Anne"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"full_name":"Richard, Johan","last_name":"Richard","first_name":"Johan"},{"last_name":"Hashimoto","full_name":"Hashimoto, Takuya","first_name":"Takuya"},{"first_name":"Hanae","last_name":"Inami","full_name":"Inami, Hanae"},{"full_name":"Conseil, Simon","last_name":"Conseil","first_name":"Simon"},{"last_name":"Guiderdoni","full_name":"Guiderdoni, Bruno","first_name":"Bruno"},{"full_name":"Drake, Alyssa B.","last_name":"Drake","first_name":"Alyssa B."},{"first_name":"Edmund","last_name":"Christian Herenz","full_name":"Christian Herenz, Edmund"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"first_name":"Pascal","full_name":"Oesch, Pascal","last_name":"Oesch"},{"first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"first_name":"Raffaella","full_name":"Anna Marino, Raffaella","last_name":"Anna Marino"},{"last_name":"Borello Schmidt","full_name":"Borello Schmidt, Kasper","first_name":"Kasper"},{"full_name":"Pelló, Roser","last_name":"Pelló","first_name":"Roser"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"full_name":"Leclercq, Floriane","last_name":"Leclercq","first_name":"Floriane"},{"first_name":"Josephine","full_name":"Kerutt, Josephine","last_name":"Kerutt"},{"first_name":"Guillaume","last_name":"Mahler","full_name":"Mahler, Guillaume"}],"title":"The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6","date_updated":"2022-07-19T09:35:20Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics","dark ages / reionization / first stars / early Universe / cosmology: observations / galaxies: evolution / galaxies: high-redshift / intergalactic medium"],"publication":"Astronomy & Astrophysics","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"03","doi":"10.1051/0004-6361/201937340","oa":1,"intvolume":"       638","date_published":"2020-06-03T00:00:00Z","article_number":"A12","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"year":"2020","article_type":"original","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Stephane De Barros and Pablo Arrabal Haro for kindly providing their data plotted in Figs. 1, 2, and 8. We are grateful to Kazuhiro Shimasaku, Masami Ouchi, Rieko Momose, Daniel Schaerer, Hidenobu Yajima, Taku Okamura, Makoto Ando, and Hinako Goto for giving insightful comments and suggestions. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy (http://www.astropy.org), which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), MARZ, MPDAF, and matplotlib (Hunter 2007). H.K. acknowledges support from Japan Society for the Promotion of Science (JSPS) through the JSPS Research Fellowship for Young Scientists and Overseas Challenge Program for Young Researchers. AV acknowledges support from the ERC starting grant 757258-TRIPLE and the SNF Professorship 176808-TRIPLE. This work was supported by the project FOGHAR (Agence Nationale de la Recherche, ANR-13-BS05-0010-02). JB acknowledges support from the ORAGE project from the Agence Nationale de la Recherche under grant ANR-14-CE33-0016-03. JR acknowledges support from the ERC starting grant 336736-CALENDS. T. H. acknowledges supports by the Grant-inAid for Scientic Research 19J01620.","_id":"11503","month":"06","scopus_import":"1","publication_status":"published","date_created":"2022-07-06T09:50:48Z","external_id":{"arxiv":["2003.12083"]},"volume":638,"publisher":"EDP Sciences","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.12083"}],"abstract":[{"lang":"eng","text":"Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful probe of the evolution of the intergalactic neutral hydrogen gas fraction. However, uncertainties in the measurement of XLAE are still under debate.\r\nAims. Thanks to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes of M1500 ≈ −17.75). This is a significantly fainter range than in former studies (M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift star-forming galaxies.\r\nMethods. We constructed a UV-complete photometric-redshift sample following UV luminosity functions and measured the Lyα emission with MUSE using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey.\r\nResults. We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z − 0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values are consistent with those in the literature within 1σ at z ≲ 5, but our median values are systematically lower than reported values over the whole redshift range. In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα) ≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly arise from selection biases for Lyman Break Galaxies (LBGs) in the literature: UV-faint LBGs are more easily selected if they have strong Lyα emission, hence XLAE is biased towards higher values when those samples are used.\r\nConclusions. Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of a late or patchy reionization process. We compared our results with predictions from a cosmological galaxy evolution model. We find that a model with a bursty star formation (SF) can reproduce our observed LAE fractions much better than models where SF is a smooth function of time."}],"type":"journal_article","extern":"1","citation":{"short":"H. Kusakabe, J. Blaizot, T. Garel, A. Verhamme, R. Bacon, J. Richard, T. Hashimoto, H. Inami, S. Conseil, B. Guiderdoni, A.B. Drake, E. Christian Herenz, J. Schaye, P. Oesch, J.J. Matthee, R. Anna Marino, K. Borello Schmidt, R. Pelló, M. Maseda, F. Leclercq, J. Kerutt, G. Mahler, Astronomy &#38; Astrophysics 638 (2020).","apa":"Kusakabe, H., Blaizot, J., Garel, T., Verhamme, A., Bacon, R., Richard, J., … Mahler, G. (2020). The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201937340\">https://doi.org/10.1051/0004-6361/201937340</a>","ama":"Kusakabe H, Blaizot J, Garel T, et al. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. <i>Astronomy &#38; Astrophysics</i>. 2020;638. doi:<a href=\"https://doi.org/10.1051/0004-6361/201937340\">10.1051/0004-6361/201937340</a>","ieee":"H. Kusakabe <i>et al.</i>, “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6,” <i>Astronomy &#38; Astrophysics</i>, vol. 638. EDP Sciences, 2020.","mla":"Kusakabe, Haruka, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” <i>Astronomy &#38; Astrophysics</i>, vol. 638, A12, EDP Sciences, 2020, doi:<a href=\"https://doi.org/10.1051/0004-6361/201937340\">10.1051/0004-6361/201937340</a>.","ista":"Kusakabe H, Blaizot J, Garel T, Verhamme A, Bacon R, Richard J, Hashimoto T, Inami H, Conseil S, Guiderdoni B, Drake AB, Christian Herenz E, Schaye J, Oesch P, Matthee JJ, Anna Marino R, Borello Schmidt K, Pelló R, Maseda M, Leclercq F, Kerutt J, Mahler G. 2020. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy &#38; Astrophysics. 638, A12.","chicago":"Kusakabe, Haruka, Jérémy Blaizot, Thibault Garel, Anne Verhamme, Roland Bacon, Johan Richard, Takuya Hashimoto, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2020. <a href=\"https://doi.org/10.1051/0004-6361/201937340\">https://doi.org/10.1051/0004-6361/201937340</a>."},"quality_controlled":"1"},{"date_updated":"2022-07-19T09:36:58Z","title":"The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3","author":[{"last_name":"Leclercq","full_name":"Leclercq, Floriane","first_name":"Floriane"},{"first_name":"Roland","full_name":"Bacon, Roland","last_name":"Bacon"},{"last_name":"Verhamme","full_name":"Verhamme, Anne","first_name":"Anne"},{"first_name":"Thibault","last_name":"Garel","full_name":"Garel, Thibault"},{"last_name":"Blaizot","full_name":"Blaizot, Jérémy","first_name":"Jérémy"},{"first_name":"Jarle","last_name":"Brinchmann","full_name":"Brinchmann, Jarle"},{"first_name":"Sebastiano","last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano"},{"full_name":"Claeyssens, Adélaïde","last_name":"Claeyssens","first_name":"Adélaïde"},{"first_name":"Simon","full_name":"Conseil, Simon","last_name":"Conseil"},{"last_name":"Contini","full_name":"Contini, Thierry","first_name":"Thierry"},{"first_name":"Takuya","full_name":"Hashimoto, Takuya","last_name":"Hashimoto"},{"last_name":"Herenz","full_name":"Herenz, Edmund Christian","first_name":"Edmund Christian"},{"last_name":"Kusakabe","full_name":"Kusakabe, Haruka","first_name":"Haruka"},{"first_name":"Raffaella Anna","full_name":"Marino, Raffaella Anna","last_name":"Marino"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"first_name":"Peter","last_name":"Mitchell","full_name":"Mitchell, Peter"},{"last_name":"Pezzulli","full_name":"Pezzulli, Gabriele","first_name":"Gabriele"},{"last_name":"Richard","full_name":"Richard, Johan","first_name":"Johan"},{"first_name":"Kasper Borello","last_name":"Schmidt","full_name":"Schmidt, Kasper Borello"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"publication":"Astronomy & Astrophysics","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-03-11T00:00:00Z","intvolume":"       635","oa":1,"doi":"10.1051/0004-6361/201937339","day":"11","article_type":"original","acknowledgement":"F.L., R.B., and S.C. acknowledge support from the ERC advanced grant 339659-MUSICOS. F.L., T.G., H.K., and A.V. acknowledge support from the ERC starting grant ERC-757258-TRIPLE. A.C. and J.R. acknowledge support from the ERC starting grant 336736-CALENDS. J.B. acknowledges support by FCT/MCTES through national funds (PID-DAC) by grant UID/FIS/04434/2019 and through Investigador FCT Contract No.IF/01654/2014/CP1215/CT0003. T.H. was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan.","year":"2020","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_number":"A82","_id":"11504","scopus_import":"1","month":"03","date_created":"2022-07-06T09:56:20Z","publication_status":"published","external_id":{"arxiv":["2002.05731"]},"volume":635,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.05731"}],"publisher":"EDP Sciences","quality_controlled":"1","citation":{"ieee":"F. Leclercq <i>et al.</i>, “The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z &#62; 3,” <i>Astronomy &#38; Astrophysics</i>, vol. 635. EDP Sciences, 2020.","apa":"Leclercq, F., Bacon, R., Verhamme, A., Garel, T., Blaizot, J., Brinchmann, J., … Wisotzki, L. (2020). The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z &#62; 3. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201937339\">https://doi.org/10.1051/0004-6361/201937339</a>","ama":"Leclercq F, Bacon R, Verhamme A, et al. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z &#62; 3. <i>Astronomy &#38; Astrophysics</i>. 2020;635. doi:<a href=\"https://doi.org/10.1051/0004-6361/201937339\">10.1051/0004-6361/201937339</a>","mla":"Leclercq, Floriane, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z &#62; 3.” <i>Astronomy &#38; Astrophysics</i>, vol. 635, A82, EDP Sciences, 2020, doi:<a href=\"https://doi.org/10.1051/0004-6361/201937339\">10.1051/0004-6361/201937339</a>.","chicago":"Leclercq, Floriane, Roland Bacon, Anne Verhamme, Thibault Garel, Jérémy Blaizot, Jarle Brinchmann, Sebastiano Cantalupo, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z &#62; 3.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2020. <a href=\"https://doi.org/10.1051/0004-6361/201937339\">https://doi.org/10.1051/0004-6361/201937339</a>.","ista":"Leclercq F, Bacon R, Verhamme A, Garel T, Blaizot J, Brinchmann J, Cantalupo S, Claeyssens A, Conseil S, Contini T, Hashimoto T, Herenz EC, Kusakabe H, Marino RA, Maseda M, Matthee JJ, Mitchell P, Pezzulli G, Richard J, Schmidt KB, Wisotzki L. 2020. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z &#62; 3. Astronomy &#38; Astrophysics. 635, A82.","short":"F. Leclercq, R. Bacon, A. Verhamme, T. Garel, J. Blaizot, J. Brinchmann, S. Cantalupo, A. Claeyssens, S. Conseil, T. Contini, T. Hashimoto, E.C. Herenz, H. Kusakabe, R.A. Marino, M. Maseda, J.J. Matthee, P. Mitchell, G. Pezzulli, J. Richard, K.B. Schmidt, L. Wisotzki, Astronomy &#38; Astrophysics 635 (2020)."},"extern":"1","abstract":[{"lang":"eng","text":"We present spatially resolved maps of six individually-detected Lyman α haloes (LAHs) as well as a first statistical analysis of the Lyman α (Lyα) spectral signature in the circum-galactic medium of high-redshift star-forming galaxies (−17.5 >  MUV >  −21.5) using the Multi-Unit Spectroscopic Explorer. Our resolved spectroscopic analysis of the LAHs reveals significant intrahalo variations of the Lyα line profile. Using a three-dimensional two-component model for the Lyα emission, we measured the full width at half maximum (FWHM), the peak velocity shift, and the asymmetry of the Lyα line in the core and in the halo of 19 galaxies. We find that the Lyα line shape is statistically different in the halo compared to the core (in terms of width, peak wavelength, and asymmetry) for ≈40% of our galaxies. Similarly to object-by-object based studies and a recent resolved study using lensing, we find a correlation between the peak velocity shift and the width of the Lyα line both at the interstellar and circum-galactic scales. This trend has been predicted by radiative transfer simulations of galactic winds as a result of resonant scattering in outflows. While there is a lack of correlation between the spectral properties and the spatial scale lengths of our LAHs, we find a correlation between the width of the line in the LAH and the halo flux fraction. Interestingly, UV bright galaxies (MUV <  −20) show broader, more redshifted, and less asymmetric Lyα lines in their haloes. The most significant correlation found is for the FWHM of the line and the UV continuum slope of the galaxy, suggesting that the redder galaxies have broader Lyα lines. The generally broad and red line shapes found in the halo component suggest that the Lyα haloes are powered either by scattering processes through an outflowing medium, fluorescent emission from outflowing cold clumps of gas, or a mix of both. Considering the large diversity of the Lyα line profiles observed in our sample and the lack of strong correlation, the interpretation of our results is still broadly open and underlines the need for realistic spatially resolved models of the LAHs."}],"type":"journal_article"},{"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2022-07-19T09:31:35Z","author":[{"first_name":"Behnam","full_name":"Darvish, Behnam","last_name":"Darvish"},{"first_name":"Nick Z.","full_name":"Scoville, Nick Z.","last_name":"Scoville"},{"full_name":"Martin, Christopher","last_name":"Martin","first_name":"Christopher"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"last_name":"Mobasher","full_name":"Mobasher, Bahram","first_name":"Bahram"},{"first_name":"Alessandro","last_name":"Rettura","full_name":"Rettura, Alessandro"},{"first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"first_name":"Peter","full_name":"Capak, Peter","last_name":"Capak"},{"first_name":"Nima","full_name":"Chartab, Nima","last_name":"Chartab"},{"first_name":"Shoubaneh","full_name":"Hemmati, Shoubaneh","last_name":"Hemmati"},{"first_name":"Daniel","full_name":"Masters, Daniel","last_name":"Masters"},{"last_name":"Nayyeri","full_name":"Nayyeri, Hooshang","first_name":"Hooshang"},{"last_name":"O’Sullivan","full_name":"O’Sullivan, Donal","first_name":"Donal"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"last_name":"Sattari","full_name":"Sattari, Zahra","first_name":"Zahra"},{"first_name":"Abtin","last_name":"Shahidi","full_name":"Shahidi, Abtin"},{"first_name":"Mara","last_name":"Salvato","full_name":"Salvato, Mara"},{"first_name":"Brian C.","full_name":"Lemaux, Brian C.","last_name":"Lemaux"},{"full_name":"Fèvre, Olivier Le","last_name":"Fèvre","first_name":"Olivier Le"},{"last_name":"Cucciati","full_name":"Cucciati, Olga","first_name":"Olga"}],"title":"Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The Astrophysical Journal","arxiv":1,"article_type":"original","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"acknowledgement":"We are thankful to the anonymous referee for useful comments and suggestions that improved the quality of this paper. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. B.D. is thankful to Andreas Faisst, Laura Danly, and Matthew Burlando for their companionship during the observing run. B.D. is grateful to the COSMOS team for their useful comments during the team meeting in New York City 2019 May 14–17. A.R. research was made possible by Friends of W. M. Keck Observatory who philanthropically support the Keck Science Collaborative (KSC) fund. The observations presented herein were obtained at the W. M. Keck Observatory (program C236, PI Scoville), which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors would like to recognize and acknowledge the very prominent cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawaiian community. We are fortunate to have the opportunity to perform observations from this mountain.","year":"2020","article_number":"8","date_published":"2020-03-19T00:00:00Z","intvolume":"       892","oa":1,"doi":"10.3847/1538-4357/ab75c3","day":"19","issue":"1","scopus_import":"1","month":"03","_id":"11513","external_id":{"arxiv":["2002.06207"]},"date_created":"2022-07-06T13:10:51Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.06207"}],"publisher":"IOP Publishing","volume":892,"quality_controlled":"1","citation":{"mla":"Darvish, Behnam, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” <i>The Astrophysical Journal</i>, vol. 892, no. 1, 8, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.3847/1538-4357/ab75c3\">10.3847/1538-4357/ab75c3</a>.","ista":"Darvish B, Scoville NZ, Martin C, Sobral D, Mobasher B, Rettura A, Matthee JJ, Capak P, Chartab N, Hemmati S, Masters D, Nayyeri H, O’Sullivan D, Paulino-Afonso A, Sattari Z, Shahidi A, Salvato M, Lemaux BC, Fèvre OL, Cucciati O. 2020. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. 892(1), 8.","chicago":"Darvish, Behnam, Nick Z. Scoville, Christopher Martin, David Sobral, Bahram Mobasher, Alessandro Rettura, Jorryt J Matthee, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” <i>The Astrophysical Journal</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.3847/1538-4357/ab75c3\">https://doi.org/10.3847/1538-4357/ab75c3</a>.","apa":"Darvish, B., Scoville, N. Z., Martin, C., Sobral, D., Mobasher, B., Rettura, A., … Cucciati, O. (2020). Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ab75c3\">https://doi.org/10.3847/1538-4357/ab75c3</a>","ieee":"B. Darvish <i>et al.</i>, “Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2,” <i>The Astrophysical Journal</i>, vol. 892, no. 1. IOP Publishing, 2020.","ama":"Darvish B, Scoville NZ, Martin C, et al. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. <i>The Astrophysical Journal</i>. 2020;892(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ab75c3\">10.3847/1538-4357/ab75c3</a>","short":"B. Darvish, N.Z. Scoville, C. Martin, D. Sobral, B. Mobasher, A. Rettura, J.J. Matthee, P. Capak, N. Chartab, S. Hemmati, D. Masters, H. Nayyeri, D. O’Sullivan, A. Paulino-Afonso, Z. Sattari, A. Shahidi, M. Salvato, B.C. Lemaux, O.L. Fèvre, O. Cucciati, The Astrophysical Journal 892 (2020)."},"type":"journal_article","abstract":[{"text":"We report the spectroscopic confirmation of a new protocluster in the COSMOS field at z ∼ 2.2, COSMOS Cluster 2.2 (CC2.2), originally identified as an overdensity of narrowband selected Hα emitting candidates. With only two masks of Keck/MOSFIRE near-IR spectroscopy in both H (∼1.47–1.81 μm) and K (∼1.92–2.40 μm) bands (∼1.5 hr each), we confirm 35 unique protocluster members with at least two emission lines detected with S/N > 3. Combined with 12 extra members from the zCOSMOS-deep spectroscopic survey (47 in total), we estimate a mean redshift and a line-of-sight velocity dispersion of zmean = 2.23224 ± 0.00101 and σlos = 645 ± 69 km s−1 for this protocluster, respectively. Assuming virialization and spherical symmetry for the system, we estimate a total mass of Mvir ∼ (1–2) ×1014M⊙ for the structure. We evaluate a number density enhancement of δg ∼ 7 for this system and we argue that the structure is likely not fully virialized at z ∼ 2.2. However, in a spherical collapse model, δg is expected to grow to a linear matter enhancement of ∼1.9 by z = 0, exceeding the collapse threshold of 1.69, and leading to a fully collapsed and virialized Coma-type structure with a total mass of Mdyn(z = 0) ∼ 9.2 × 1014M⊙ by now. This observationally efficient confirmation suggests that large narrowband emission-line galaxy surveys, when combined with ancillary photometric data, can be used to effectively trace the large-scale structure and protoclusters at a time when they are mostly dominated by star-forming galaxies.","lang":"eng"}],"extern":"1"},{"external_id":{"arxiv":["1910.03593"]},"publication_status":"published","date_created":"2022-07-07T10:20:11Z","month":"08","scopus_import":"1","issue":"2","_id":"11528","extern":"1","abstract":[{"lang":"eng","text":"Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ≈10−17 erg cm−2 s−1 (⁠≈1042 erg s−1⁠) and a median star formation rate (SFR) of ≈1.3 M⊙ yr−1 (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, Voffset∝SFR0.16±0.03⁠. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs."}],"type":"journal_article","citation":{"ieee":"S. Muzahid <i>et al.</i>, “MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 496, no. 2. Oxford University Press, pp. 1013–1022, 2020.","ama":"Muzahid S, Schaye J, Marino RA, et al. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;496(2):1013-1022. doi:<a href=\"https://doi.org/10.1093/mnras/staa1347\">10.1093/mnras/staa1347</a>","apa":"Muzahid, S., Schaye, J., Marino, R. A., Cantalupo, S., Brinchmann, J., Contini, T., … Verhamme, A. (2020). MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa1347\">https://doi.org/10.1093/mnras/staa1347</a>","mla":"Muzahid, Sowgat, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 496, no. 2, Oxford University Press, 2020, pp. 1013–22, doi:<a href=\"https://doi.org/10.1093/mnras/staa1347\">10.1093/mnras/staa1347</a>.","ista":"Muzahid S, Schaye J, Marino RA, Cantalupo S, Brinchmann J, Contini T, Wendt M, Wisotzki L, Zabl J, Bouché N, Akhlaghi M, Chen H-W, Claeyssens A, Johnson S, Leclercq F, Maseda M, Matthee JJ, Richard J, Urrutia T, Verhamme A. 2020. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. 496(2), 1013–1022.","chicago":"Muzahid, Sowgat, Joop Schaye, Raffaella Anna Marino, Sebastiano Cantalupo, Jarle Brinchmann, Thierry Contini, Martin Wendt, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa1347\">https://doi.org/10.1093/mnras/staa1347</a>.","short":"S. Muzahid, J. Schaye, R.A. Marino, S. Cantalupo, J. Brinchmann, T. Contini, M. Wendt, L. Wisotzki, J. Zabl, N. Bouché, M. Akhlaghi, H.-W. Chen, A. Claeyssens, S. Johnson, F. Leclercq, M. Maseda, J.J. Matthee, J. Richard, T. Urrutia, A. Verhamme, Monthly Notices of the Royal Astronomical Society 496 (2020) 1013–1022."},"quality_controlled":"1","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.03593"}],"volume":496,"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: haloes","galaxies: high-redshift","quasars: absorption lines"],"oa_version":"Preprint","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"last_name":"Muzahid","full_name":"Muzahid, Sowgat","first_name":"Sowgat"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"},{"full_name":"Marino, Raffaella Anna","last_name":"Marino","first_name":"Raffaella Anna"},{"first_name":"Sebastiano","full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo"},{"full_name":"Brinchmann, Jarle","last_name":"Brinchmann","first_name":"Jarle"},{"first_name":"Thierry","last_name":"Contini","full_name":"Contini, Thierry"},{"first_name":"Martin","last_name":"Wendt","full_name":"Wendt, Martin"},{"first_name":"Lutz","full_name":"Wisotzki, Lutz","last_name":"Wisotzki"},{"first_name":"Johannes","last_name":"Zabl","full_name":"Zabl, Johannes"},{"last_name":"Bouché","full_name":"Bouché, Nicolas","first_name":"Nicolas"},{"first_name":"Mohammad","last_name":"Akhlaghi","full_name":"Akhlaghi, Mohammad"},{"full_name":"Chen, Hsiao-Wen","last_name":"Chen","first_name":"Hsiao-Wen"},{"full_name":"Claeyssens, Adélaîde","last_name":"Claeyssens","first_name":"Adélaîde"},{"last_name":"Johnson","full_name":"Johnson, Sean","first_name":"Sean"},{"last_name":"Leclercq","full_name":"Leclercq, Floriane","first_name":"Floriane"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J"},{"first_name":"Johan","full_name":"Richard, Johan","last_name":"Richard"},{"first_name":"Tanya","full_name":"Urrutia, Tanya","last_name":"Urrutia"},{"last_name":"Verhamme","full_name":"Verhamme, Anne","first_name":"Anne"}],"title":"MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles","date_updated":"2022-08-18T11:00:24Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/mnras/staa2668"}]},"page":"1013-1022","article_type":"original","year":"2020","acknowledgement":"We thank the anonymous referee for useful suggestions. This study is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme(s): 094.A-0131(B), 095.A 0200(A), 096.A0222(A), 097.A-0089(A), and 099.A-0159(A). SM acknowledges support from the Alexander von Humboldt Foundation, Germany. SM thanks Christian Herenz for useful discussion. SC gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. JB acknowledges support by FCT/MCTES through national funds by grant UID/FIS/04434/2019 and through Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. NB and JZ acknowledge support from ANR grant ANR-17-CE31- 0017 (3DGasFlows). AC and JR acknowledge support from the ERC starting grant 336736-CALENDS. MA acknowledges support from European Union’s H2020 Marie Skłodowska-Curie Actions grant 721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P. MA also acknowledges support from the Fundacion BBVA under its 2017 programme of assistance to ´scientific research groups, for the project ‘Using machine-learning techniques to drag galaxies from the noise in deep imaging’. FL and AV acknowledge support from the ERC starting grant ERC757258-TRIPLE.","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"day":"01","doi":"10.1093/mnras/staa1347","oa":1,"intvolume":"       496","date_published":"2020-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"Monthly Notices of the Royal Astronomical Society"},{"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"article_type":"original","year":"2020","doi":"10.1093/mnras/staa2550","day":"01","oa":1,"intvolume":"       498","date_published":"2020-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"Monthly Notices of the Royal Astronomical Society","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"oa_version":"Preprint","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6","author":[{"first_name":"Jorryt J","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"first_name":"Gabriele","full_name":"Pezzulli, Gabriele","last_name":"Pezzulli"},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo","first_name":"Sebastiano"},{"first_name":"Haruka","full_name":"Kusakabe, Haruka","last_name":"Kusakabe"},{"last_name":"Leclercq","full_name":"Leclercq, Floriane","first_name":"Floriane"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"last_name":"Richard","full_name":"Richard, Johan","first_name":"Johan"},{"full_name":"Wisotzki, Lutz","last_name":"Wisotzki","first_name":"Lutz"},{"full_name":"Lilly, Simon","last_name":"Lilly","first_name":"Simon"},{"first_name":"Leindert","last_name":"Boogaard","full_name":"Boogaard, Leindert"},{"first_name":"Raffaella","last_name":"Marino","full_name":"Marino, Raffaella"},{"first_name":"Michael","last_name":"Maseda","full_name":"Maseda, Michael"},{"first_name":"Themiya","last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya"}],"page":"3043-3059","date_updated":"2024-10-14T11:33:21Z","abstract":[{"lang":"eng","text":"CR7 is among the most luminous Ly α emitters (LAEs) known at z = 6.6 and consists of at least three UV components that are surrounded by Ly α emission. Previous studies have suggested that it may host an extreme ionizing source. Here, we present deep integral field spectroscopy of CR7 with VLT/Multi Unit Spectroscopic Explorer (MUSE). We measure extended emission with a similar halo scale length as typical LAEs at z ≈ 5. CR7’s Ly α halo is clearly elongated along the direction connecting the multiple components, likely tracing the underlying gas distribution. The Ly α emission originates almost exclusively from the brightest UV component, but we also identify a faint kinematically distinct Ly α emitting region nearby a fainter component. Combined with new near-infrared data, the MUSE data show that the rest-frame Ly α equivalent width (EW) is ≈100 Å. This is a factor 4 higher than the EW measured in low-redshift analogues with carefully matched Ly α profiles (and thus arguably H I column density), but this EW can plausibly be explained by star formation. Alternative scenarios requiring active galactic nucleus (AGN) powering are also disfavoured by the narrower and steeper Ly α spectrum and much smaller IR to UV ratio compared to obscured AGN in other Ly α blobs. CR7’s Ly α emission, while extremely luminous, resembles the emission in more common LAEs at lower redshifts very well and is likely powered by a young metal-poor starburst."}],"extern":"1","type":"journal_article","citation":{"ama":"Matthee JJ, Pezzulli G, Mackenzie R, et al. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;498(2):3043-3059. doi:<a href=\"https://doi.org/10.1093/mnras/staa2550\">10.1093/mnras/staa2550</a>","ieee":"J. J. Matthee <i>et al.</i>, “The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 498, no. 2. Oxford University Press, pp. 3043–3059, 2020.","apa":"Matthee, J. J., Pezzulli, G., Mackenzie, R., Cantalupo, S., Kusakabe, H., Leclercq, F., … Nanayakkara, T. (2020). The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa2550\">https://doi.org/10.1093/mnras/staa2550</a>","mla":"Matthee, Jorryt J., et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 498, no. 2, Oxford University Press, 2020, pp. 3043–59, doi:<a href=\"https://doi.org/10.1093/mnras/staa2550\">10.1093/mnras/staa2550</a>.","ista":"Matthee JJ, Pezzulli G, Mackenzie R, Cantalupo S, Kusakabe H, Leclercq F, Sobral D, Richard J, Wisotzki L, Lilly S, Boogaard L, Marino R, Maseda M, Nanayakkara T. 2020. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. 498(2), 3043–3059.","chicago":"Matthee, Jorryt J, Gabriele Pezzulli, Ruari Mackenzie, Sebastiano Cantalupo, Haruka Kusakabe, Floriane Leclercq, David Sobral, et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa2550\">https://doi.org/10.1093/mnras/staa2550</a>.","short":"J.J. Matthee, G. Pezzulli, R. Mackenzie, S. Cantalupo, H. Kusakabe, F. Leclercq, D. Sobral, J. Richard, L. Wisotzki, S. Lilly, L. Boogaard, R. Marino, M. Maseda, T. Nanayakkara, Monthly Notices of the Royal Astronomical Society 498 (2020) 3043–3059."},"quality_controlled":"1","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.01731"}],"volume":498,"external_id":{"arxiv":["2008.01731"]},"publication_status":"published","date_created":"2022-07-07T10:36:01Z","month":"10","issue":"2","scopus_import":"1","_id":"11529"},{"page":"1874-1887","date_updated":"2022-08-18T11:17:47Z","title":"Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae","author":[{"first_name":"J S","last_name":"den Brok","full_name":"den Brok, J S"},{"last_name":"Cantalupo","full_name":"Cantalupo, S","first_name":"S"},{"last_name":"Mackenzie","full_name":"Mackenzie, R","first_name":"R"},{"last_name":"Marino","full_name":"Marino, R A","first_name":"R A"},{"last_name":"Pezzulli","full_name":"Pezzulli, G","first_name":"G"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"first_name":"S D","full_name":"Johnson, S D","last_name":"Johnson"},{"first_name":"M","last_name":"Krumpe","full_name":"Krumpe, M"},{"last_name":"Urrutia","full_name":"Urrutia, T","first_name":"T"},{"full_name":"Kollatschny, W","last_name":"Kollatschny","first_name":"W"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high-redshift","intergalactic medium","quasars: emission lines","quasars: general"],"publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       495","date_published":"2020-06-01T00:00:00Z","doi":"10.1093/mnras/staa1269","day":"01","oa":1,"acknowledgement":"SC and GP gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. MK acknowledges support by DLR500R1904.","article_type":"original","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"year":"2020","_id":"11530","issue":"2","scopus_import":"1","month":"06","date_created":"2022-07-07T10:40:17Z","publication_status":"published","external_id":{"arxiv":["2005.01732"]},"volume":495,"main_file_link":[{"url":"https://arxiv.org/abs/2005.01732","open_access":"1"}],"publisher":"Oxford University Press","quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"A prediction of the classic active galactic nucleus (AGN) unification model is the presence of ionization cones with different orientations depending on the AGN type. Confirmations of this model exist for present times, but it is less clear in the early Universe. Here, we use the morphology of giant Ly α nebulae around AGNs at redshift z ∼ 3 to probe AGN emission and therefore the validity of the AGN unification model at this redshift. We compare the spatial morphology of 19 nebulae previously found around type I AGNs with a new sample of four Ly α nebulae detected around type II AGNs. Using two independent techniques, we find that nebulae around type II AGNs are more asymmetric than around type I, at least at radial distances r > 30 physical kpc (pkpc) from the ionizing source. We conclude that the type I and type II AGNs in our sample show evidence of different surrounding ionizing geometries. This suggests that the classical AGN unification model is also valid for high-redshift sources. Finally, we discuss how the lack of asymmetry in the inner parts (r ≲ 30 pkpc) and the associated high values of the He II to Ly α ratios in these regions could indicate additional sources of (hard) ionizing radiation originating within or in proximity of the AGN host galaxies. This work demonstrates that the morphologies of giant Ly α nebulae can be used to understand and study the geometry of high-redshift AGNs on circumnuclear scales and it lays the foundation for future studies using much larger statistical samples."}],"extern":"1","citation":{"chicago":"den Brok, J S, S Cantalupo, R Mackenzie, R A Marino, G Pezzulli, Jorryt J Matthee, S D Johnson, M Krumpe, T Urrutia, and W Kollatschny. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa1269\">https://doi.org/10.1093/mnras/staa1269</a>.","ista":"den Brok JS, Cantalupo S, Mackenzie R, Marino RA, Pezzulli G, Matthee JJ, Johnson SD, Krumpe M, Urrutia T, Kollatschny W. 2020. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. 495(2), 1874–1887.","mla":"den Brok, J. S., et al. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 495, no. 2, Oxford University Press, 2020, pp. 1874–87, doi:<a href=\"https://doi.org/10.1093/mnras/staa1269\">10.1093/mnras/staa1269</a>.","ama":"den Brok JS, Cantalupo S, Mackenzie R, et al. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;495(2):1874-1887. doi:<a href=\"https://doi.org/10.1093/mnras/staa1269\">10.1093/mnras/staa1269</a>","apa":"den Brok, J. S., Cantalupo, S., Mackenzie, R., Marino, R. A., Pezzulli, G., Matthee, J. J., … Kollatschny, W. (2020). Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa1269\">https://doi.org/10.1093/mnras/staa1269</a>","ieee":"J. S. den Brok <i>et al.</i>, “Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 495, no. 2. Oxford University Press, pp. 1874–1887, 2020.","short":"J.S. den Brok, S. Cantalupo, R. Mackenzie, R.A. Marino, G. Pezzulli, J.J. Matthee, S.D. Johnson, M. Krumpe, T. Urrutia, W. Kollatschny, Monthly Notices of the Royal Astronomical Society 495 (2020) 1874–1887."}},{"date_created":"2022-07-07T10:46:41Z","publication_status":"published","external_id":{"arxiv":["2002.11117"]},"_id":"11531","scopus_import":"1","issue":"4","month":"04","quality_controlled":"1","type":"journal_article","abstract":[{"text":"While low-luminosity galaxies dominate number counts at all redshifts, their contribution to cosmic reionization is poorly understood due to a lack of knowledge of their physical properties. We isolate a sample of 35 z ≈ 4–5 continuum-faint Lyman-α emitters from deep VLT/MUSE spectroscopy and directly measure their H α emission using stacked Spitzer/IRAC Ch. 1 photometry. Based on Hubble Space Telescope imaging, we determine that the average UV continuum magnitude is fainter than −16 (≈ 0.01 L⋆), implying a median Lyman-α equivalent width of 259 Å. By combining the H α measurement with the UV magnitude, we determine the ionizing photon production efficiency, ξion, a first for such faint galaxies. The measurement of log10 (ξion [Hz erg−1]) = 26.28 (⁠+0.28−0.40⁠) is in excess of literature measurements of both continuum- and emission line-selected samples, implying a more efficient production of ionizing photons in these lower luminosity, Lyman-α-selected systems. We conclude that this elevated efficiency can be explained by stellar populations with metallicities between 4 × 10−4 and 0.008, with light-weighted ages less than 3 Myr.","lang":"eng"}],"extern":"1","citation":{"short":"M.V. Maseda, R. Bacon, D. Lam, J.J. Matthee, J. Brinchmann, J. Schaye, I. Labbe, K.B. Schmidt, L. Boogaard, R. Bouwens, S. Cantalupo, M. Franx, T. Hashimoto, H. Inami, H. Kusakabe, G. Mahler, T. Nanayakkara, J. Richard, L. Wisotzki, Monthly Notices of the Royal Astronomical Society 493 (2020) 5120–5130.","mla":"Maseda, Michael V., et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 4, Oxford University Press, 2020, pp. 5120–30, doi:<a href=\"https://doi.org/10.1093/mnras/staa622\">10.1093/mnras/staa622</a>.","chicago":"Maseda, Michael V, Roland Bacon, Daniel Lam, Jorryt J Matthee, Jarle Brinchmann, Joop Schaye, Ivo Labbe, et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa622\">https://doi.org/10.1093/mnras/staa622</a>.","ista":"Maseda MV, Bacon R, Lam D, Matthee JJ, Brinchmann J, Schaye J, Labbe I, Schmidt KB, Boogaard L, Bouwens R, Cantalupo S, Franx M, Hashimoto T, Inami H, Kusakabe H, Mahler G, Nanayakkara T, Richard J, Wisotzki L. 2020. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. 493(4), 5120–5130.","ieee":"M. V. Maseda <i>et al.</i>, “Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 4. Oxford University Press, pp. 5120–5130, 2020.","ama":"Maseda MV, Bacon R, Lam D, et al. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;493(4):5120-5130. doi:<a href=\"https://doi.org/10.1093/mnras/staa622\">10.1093/mnras/staa622</a>","apa":"Maseda, M. V., Bacon, R., Lam, D., Matthee, J. J., Brinchmann, J., Schaye, J., … Wisotzki, L. (2020). Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa622\">https://doi.org/10.1093/mnras/staa622</a>"},"volume":493,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/mnras/staa622"}],"publisher":"Oxford University Press","oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics","Galaxies: evolution","Galaxies: high-redshift","Galaxies: ISM"],"date_updated":"2022-08-18T11:23:27Z","page":"5120-5130","title":"Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters","author":[{"last_name":"Maseda","full_name":"Maseda, Michael V","first_name":"Michael V"},{"first_name":"Roland","last_name":"Bacon","full_name":"Bacon, Roland"},{"first_name":"Daniel","last_name":"Lam","full_name":"Lam, Daniel"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"full_name":"Brinchmann, Jarle","last_name":"Brinchmann","first_name":"Jarle"},{"full_name":"Schaye, Joop","last_name":"Schaye","first_name":"Joop"},{"last_name":"Labbe","full_name":"Labbe, Ivo","first_name":"Ivo"},{"full_name":"Schmidt, Kasper B","last_name":"Schmidt","first_name":"Kasper B"},{"last_name":"Boogaard","full_name":"Boogaard, Leindert","first_name":"Leindert"},{"first_name":"Rychard","last_name":"Bouwens","full_name":"Bouwens, Rychard"},{"first_name":"Sebastiano","last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano"},{"first_name":"Marijn","last_name":"Franx","full_name":"Franx, Marijn"},{"first_name":"Takuya","last_name":"Hashimoto","full_name":"Hashimoto, Takuya"},{"last_name":"Inami","full_name":"Inami, Hanae","first_name":"Hanae"},{"first_name":"Haruka","last_name":"Kusakabe","full_name":"Kusakabe, Haruka"},{"full_name":"Mahler, Guillaume","last_name":"Mahler","first_name":"Guillaume"},{"first_name":"Themiya","last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya"},{"last_name":"Richard","full_name":"Richard, Johan","first_name":"Johan"},{"last_name":"Wisotzki","full_name":"Wisotzki, Lutz","first_name":"Lutz"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"intvolume":"       493","date_published":"2020-04-01T00:00:00Z","day":"01","doi":"10.1093/mnras/staa622","oa":1,"acknowledgement":"We would like to thank the anonymous referee for a thoughtful report and suggestions that have improved this manuscript. We are also grateful to everyone involved in the Spitzer Space Telescope mission and everyone at the Spitzer Science Center: we are truly fortunate to have been able to use data from this facility. J. B. acknowledges support by FCT/MCTES through national funds by this grant UID/FIS/04434/2019 and through the Investigador FCT contract no. IF/01654/2014/CP1215/CT0003. S. C. gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. We would also like to thank Mauro Stefanon for his assistance with de-blending the IRAC photometry, Pieter van Dokkum for a number of useful suggestions, and Daniel Schaerer for information regarding the stellar population models. This study is based on observations made with ESO telescopes at the La Silla Paranal Observatory under programs IDs 094.A-2089(B), 095.A0010(A), 096.A-0045(A), and 096.A-0045(B).","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"year":"2020","article_type":"original","publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"We explore deep rest-frame UV to FIR data in the COSMOS field to measure the individual spectral energy distributions (SED) of the ∼4000 SC4K (Sobral et al.) Lyman α (Ly α) emitters (LAEs) at z ∼ 2–6. We find typical stellar masses of 109.3 ± 0.6 M⊙ and star formation rates (SFR) of SFRSED=4.4+10.5−2.4 M⊙ yr−1 and SFRLyα=5.9+6.3−2.6 M⊙ yr−1, combined with very blue UV slopes of β=−2.1+0.5−0.4⁠, but with significant variations within the population. MUV and β are correlated in a similar way to UV-selected sources, but LAEs are consistently bluer. This suggests that LAEs are the youngest and/or most dust-poor subset of the UV-selected population. We also study the Ly α rest-frame equivalent width (EW0) and find 45 ‘extreme’ LAEs with EW0 > 240 Å (3σ), implying a low number density of (7 ± 1) × 10−7 Mpc−3. Overall, we measure little to no evolution of the Ly α EW0 and scale length parameter (w0), which are consistently high (EW0=140+280−70 Å, w0=129+11−11 Å) from z ∼ 6 to z ∼ 2 and below. However, w0 is anticorrelated with MUV and stellar mass. Our results imply that sources selected as LAEs have a high Ly α escape fraction (fesc,Ly α) irrespective of cosmic time, but fesc,Ly α is still higher for UV-fainter and lower mass LAEs. The least massive LAEs (<109.5 M⊙) are typically located above the star formation ‘main sequence’ (MS), but the offset from the MS decreases towards z ∼ 6 and towards 1010 M⊙. Our results imply a lack of evolution in the properties of LAEs across time and reveals the increasing overlap in properties of LAEs and UV-continuum selected galaxies as typical star-forming galaxies at high redshift effectively become LAEs."}],"citation":{"short":"S. Santos, D. Sobral, J.J. Matthee, J. Calhau, E. da Cunha, B. Ribeiro, A. Paulino-Afonso, P. Arrabal Haro, J. Butterworth, Monthly Notices of the Royal Astronomical Society 493 (2020) 141–160.","ieee":"S. Santos <i>et al.</i>, “The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 1. Oxford University Press, pp. 141–160, 2020.","ama":"Santos S, Sobral D, Matthee JJ, et al. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;493(1):141-160. doi:<a href=\"https://doi.org/10.1093/mnras/staa093\">10.1093/mnras/staa093</a>","apa":"Santos, S., Sobral, D., Matthee, J. J., Calhau, J., da Cunha, E., Ribeiro, B., … Butterworth, J. (2020). The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa093\">https://doi.org/10.1093/mnras/staa093</a>","mla":"Santos, S., et al. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 1, Oxford University Press, 2020, pp. 141–60, doi:<a href=\"https://doi.org/10.1093/mnras/staa093\">10.1093/mnras/staa093</a>.","chicago":"Santos, S, D Sobral, Jorryt J Matthee, J Calhau, E da Cunha, B Ribeiro, A Paulino-Afonso, P Arrabal Haro, and J Butterworth. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa093\">https://doi.org/10.1093/mnras/staa093</a>.","ista":"Santos S, Sobral D, Matthee JJ, Calhau J, da Cunha E, Ribeiro B, Paulino-Afonso A, Arrabal Haro P, Butterworth J. 2020. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. 493(1), 141–160."},"volume":493,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.02959"}],"publisher":"Oxford University Press","date_created":"2022-07-07T12:05:23Z","publication_status":"published","external_id":{"arxiv":["1910.02959"]},"_id":"11533","issue":"1","scopus_import":"1","month":"03","intvolume":"       493","date_published":"2020-03-01T00:00:00Z","day":"01","doi":"10.1093/mnras/staa093","oa":1,"article_type":"original","acknowledgement":"We thank the anonymous referee for the valuable feedback that significantly improved the quality and clarity of this paper. SS and JC acknowledge studentships from Lancaster University. APA acknowledges support from Fundação para a Ciência e a Tecnologia through the project PTDC/FISAST/31546/2017. The authors would like to thank Ali Khostovan, Sara Perez Sanchez, Alex Bennett and Tom Rose for contributions and discussions in the early stages of this work. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by CALET and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Finally, the authors acknowledge the unique value of the publicly available analysis software TOPCAT (Taylor 2005) and publicly available programming language Python, including the numpy, pyfits, matplotlib, scipy and astropy (Astropy Collaboration et al. 2013) packages. This work is based on the public SC4K sample of LAEs (Sobral et al. 2018a) and we release the full catalogue with all the photometry and properties derived in this paper, in electronic format, along with the relevant tables.","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"year":"2020","publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: star formation"],"date_updated":"2022-08-18T11:27:43Z","page":"141-160","title":"The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs","author":[{"first_name":"S","last_name":"Santos","full_name":"Santos, S"},{"full_name":"Sobral, D","last_name":"Sobral","first_name":"D"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"full_name":"Calhau, J","last_name":"Calhau","first_name":"J"},{"first_name":"E","full_name":"da Cunha, E","last_name":"da Cunha"},{"full_name":"Ribeiro, B","last_name":"Ribeiro","first_name":"B"},{"last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, A","first_name":"A"},{"first_name":"P","full_name":"Arrabal Haro, P","last_name":"Arrabal Haro"},{"first_name":"J","last_name":"Butterworth","full_name":"Butterworth, J"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"title":"Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ","author":[{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"first_name":"Max","last_name":"Gronke","full_name":"Gronke, Max"},{"first_name":"Gabriele","last_name":"Pezzulli","full_name":"Pezzulli, Gabriele"},{"last_name":"Cantalupo","full_name":"Cantalupo, Sebastiano","first_name":"Sebastiano"},{"last_name":"Röttgering","full_name":"Röttgering, Huub","first_name":"Huub"},{"full_name":"Darvish, Behnam","last_name":"Darvish","first_name":"Behnam"},{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"}],"page":"1778-1790","date_updated":"2024-10-14T11:33:34Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.1093/mnras/stz3554","day":"01","date_published":"2020-02-01T00:00:00Z","intvolume":"       492","article_type":"original","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"year":"2020","acknowledgement":"We thank the referee for their suggestions and constructive comments that helped to improve the presentation of our results. Based on observations obtained with the Very Large Telescope, program 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program #14699. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan) and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. MG acknowledges support from NASA grant NNX17AK58G. GP and SC gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. BD acknowledges financial support from the National Science Foundation, grant number 1716907. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, SCIPY (Jones et al. 2001; Hunter 2007; van der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration 2013) packages, the astronomical imaging tools SEXTRACTOR, SWARP, and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010) and the TOPCAT analysis tool (Taylor 2013).","_id":"11534","month":"02","scopus_import":"1","issue":"2","publication_status":"published","date_created":"2022-07-07T12:21:36Z","external_id":{"arxiv":["1909.06376"]},"volume":492,"publisher":"Oxford University Press","main_file_link":[{"url":"https://arxiv.org/abs/1909.06376","open_access":"1"}],"citation":{"apa":"Matthee, J. J., Sobral, D., Gronke, M., Pezzulli, G., Cantalupo, S., Röttgering, H., … Santos, S. (2020). Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stz3554\">https://doi.org/10.1093/mnras/stz3554</a>","ieee":"J. J. Matthee <i>et al.</i>, “Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 492, no. 2. Oxford University Press, pp. 1778–1790, 2020.","ama":"Matthee JJ, Sobral D, Gronke M, et al. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;492(2):1778-1790. doi:<a href=\"https://doi.org/10.1093/mnras/stz3554\">10.1093/mnras/stz3554</a>","ista":"Matthee JJ, Sobral D, Gronke M, Pezzulli G, Cantalupo S, Röttgering H, Darvish B, Santos S. 2020. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. 492(2), 1778–1790.","chicago":"Matthee, Jorryt J, David Sobral, Max Gronke, Gabriele Pezzulli, Sebastiano Cantalupo, Huub Röttgering, Behnam Darvish, and Sérgio Santos. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/stz3554\">https://doi.org/10.1093/mnras/stz3554</a>.","mla":"Matthee, Jorryt J., et al. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 492, no. 2, Oxford University Press, 2020, pp. 1778–90, doi:<a href=\"https://doi.org/10.1093/mnras/stz3554\">10.1093/mnras/stz3554</a>.","short":"J.J. Matthee, D. Sobral, M. Gronke, G. Pezzulli, S. Cantalupo, H. Röttgering, B. Darvish, S. Santos, Monthly Notices of the Royal Astronomical Society 492 (2020) 1778–1790."},"type":"journal_article","extern":"1","abstract":[{"text":"The observed properties of the Lyman-α (Ly α) emission line are a powerful probe of neutral gas in and around galaxies. We present spatially resolved Ly α spectroscopy with VLT/MUSE targeting VR7, a UV-luminous galaxy at z = 6.532 with moderate Ly α equivalent width (EW0 ≈ 38 Å). These data are combined with deep resolved [CII]158μm spectroscopy obtained with ALMA and UV imaging from HST and we also detect UV continuum with MUSE. Ly α emission is clearly detected with S/N ≈ 40 and FWHM of 374 km s−1. Ly α and [C II] are similarly extended beyond the UV, with effective radius reff = 2.1 ± 0.2 kpc for a single exponential model or reff,Lyα,halo=3.45+1.08−0.87 kpc when measured jointly with the UV continuum. The Ly α profile is broader and redshifted with respect to the [C II] line (by 213 km s−1), but there are spatial variations that are qualitatively similar in both lines and coincide with resolved UV components. This suggests that the emission originates from two components with plausibly different H I column densities. We place VR7 in the context of other galaxies at similar and lower redshift. The Ly α halo scale length is similar at different redshifts and velocity shifts with respect to the systemic are typically smaller. Overall, we find little indications of a more neutral vicinity at higher redshift. This means that the local (∼10 kpc) neutral gas conditions that determine the observed Ly α properties in VR7 resemble the conditions in post-reionization galaxies.","lang":"eng"}],"quality_controlled":"1"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","quasars: supermassive black holes","galaxies: star formation","cosmology: observations","X-rays: galaxies"],"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2022-08-18T11:25:31Z","page":"3341-3362","author":[{"last_name":"Calhau","full_name":"Calhau, João","first_name":"João"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana","first_name":"Ana"},{"full_name":"Stroe, Andra","last_name":"Stroe","first_name":"Andra"},{"last_name":"Simmons","full_name":"Simmons, Brooke","first_name":"Brooke"},{"first_name":"Cassandra","full_name":"Barlow-Hall, Cassandra","last_name":"Barlow-Hall"},{"last_name":"Adams","full_name":"Adams, Benjamin","first_name":"Benjamin"}],"title":"The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population","acknowledgement":"JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013).","article_type":"original","year":"2020","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"intvolume":"       493","date_published":"2020-04-01T00:00:00Z","day":"01","doi":"10.1093/mnras/staa476","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"Monthly Notices of the Royal Astronomical Society","external_id":{"arxiv":["1909.11672"]},"date_created":"2022-07-08T07:34:10Z","publication_status":"published","issue":"3","scopus_import":"1","month":"04","_id":"11539","quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Despite recent progress in understanding Ly α emitters (LAEs), relatively little is known regarding their typical black hole activity across cosmic time. Here, we study the X-ray and radio properties of ∼4000 LAEs at 2.2 < z < 6 from the SC4K survey in the COSMOS field. We detect 254 (⁠6.8per cent±0.4per cent⁠) LAEs individually in the X-rays (S/N > 3) with an average luminosity of 1044.31±0.01ergs−1 and average black hole accretion rate (BHAR) of 0.72±0.01 M⊙ yr−1, consistent with moderate to high accreting active galactic neuclei (AGNs). We detect 120 sources in deep radio data (radio AGN fraction of 3.2per cent±0.3per cent⁠). The global AGN fraction (⁠8.6per cent±0.4per cent⁠) rises with Ly α luminosity and declines with increasing redshift. For X-ray-detected LAEs, Ly α luminosities correlate with the BHARs, suggesting that Ly α luminosity becomes a BHAR indicator. Most LAEs (⁠93.1per cent±0.6per cent⁠) at 2 < z < 6 have no detectable X-ray emission (BHARs < 0.017 M⊙ yr−1). The median star formation rate (SFR) of star-forming LAEs from Ly α and radio luminosities is 7.6+6.6−2.8 M⊙ yr−1. The black hole to galaxy growth ratio (BHAR/SFR) for LAEs is <0.0022, consistent with typical star-forming galaxies and the local BHAR/SFR relation. We conclude that LAEs at 2 < z < 6 include two different populations: an AGN population, where Ly α luminosity traces BHAR, and another with low SFRs which remain undetected in even the deepest X-ray stacks but is detected in the radio stacks."}],"extern":"1","citation":{"chicago":"Calhau, João, David Sobral, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Andra Stroe, Brooke Simmons, Cassandra Barlow-Hall, and Benjamin Adams. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/mnras/staa476\">https://doi.org/10.1093/mnras/staa476</a>.","ista":"Calhau J, Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Stroe A, Simmons B, Barlow-Hall C, Adams B. 2020. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. 493(3), 3341–3362.","mla":"Calhau, João, et al. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 3, Oxford University Press, 2020, pp. 3341–62, doi:<a href=\"https://doi.org/10.1093/mnras/staa476\">10.1093/mnras/staa476</a>.","ama":"Calhau J, Sobral D, Santos S, et al. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. <i>Monthly Notices of the Royal Astronomical Society</i>. 2020;493(3):3341-3362. doi:<a href=\"https://doi.org/10.1093/mnras/staa476\">10.1093/mnras/staa476</a>","ieee":"J. Calhau <i>et al.</i>, “The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 493, no. 3. Oxford University Press, pp. 3341–3362, 2020.","apa":"Calhau, J., Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Stroe, A., … Adams, B. (2020). The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staa476\">https://doi.org/10.1093/mnras/staa476</a>","short":"J. Calhau, D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, A. Stroe, B. Simmons, C. Barlow-Hall, B. Adams, Monthly Notices of the Royal Astronomical Society 493 (2020) 3341–3362."},"main_file_link":[{"url":"https://arxiv.org/abs/1909.11672","open_access":"1"}],"publisher":"Oxford University Press","volume":493}]