[{"month":"01","publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"},{"grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425","name":"Eliminating turbulence in oil pipelines","call_identifier":"H2020"},{"name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","grant_number":"HO 4393/1-2","_id":"25136C54-B435-11E9-9278-68D0E5697425"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7258","file_date_updated":"2021-01-13T23:30:05Z","ec_funded":1,"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","year":"2020","date_updated":"2023-09-15T12:20:08Z","date_created":"2020-01-12T16:07:26Z","author":[{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6228"},{"relation":"part_of_dissertation","status":"public","id":"6486"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"id":"422","relation":"part_of_dissertation","status":"public"}]},"day":"13","article_processing_charge":"No","has_accepted_license":"1","page":"174","citation":{"ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258."},"date_published":"2020-01-13T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.","lang":"eng"}],"title":"New approaches to reduce friction in turbulent pipe flow","status":"public","ddc":["532"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7258","file":[{"file_size":26640830,"content_type":"application/zip","creator":"dscarsel","access_level":"closed","embargo_to":"open_access","file_name":"2020_Scarselli_Thesis.zip","checksum":"4df1ab24e9896635106adde5a54615bf","date_created":"2020-01-12T15:57:14Z","date_updated":"2021-01-13T23:30:05Z","relation":"source_file","file_id":"7259"},{"creator":"dscarsel","content_type":"application/pdf","file_size":8515844,"access_level":"open_access","file_name":"2020_Scarselli_Thesis.pdf","checksum":"48659ab98e3414293c7a721385c2fd1c","date_created":"2020-01-12T15:56:14Z","date_updated":"2021-01-13T23:30:05Z","file_id":"7260","embargo":"2021-01-12","relation":"main_file"}],"oa_version":"None"},{"day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"date_published":"2020-10-13T00:00:00Z","page":"117","citation":{"ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653."},"abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"8666","checksum":"c01d9f59794b4b70528f37637c17ad02","date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_ITomanek_final_201016.docx","file_size":25131884,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"itomanek"},{"content_type":"application/pdf","file_size":15405675,"creator":"itomanek","access_level":"open_access","file_name":"Thesis_ITomanek_final_201016.pdf","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-16T12:14:21Z","relation":"main_file","embargo":"2021-10-19","file_id":"8667"}],"oa_version":"Published Version","status":"public","ddc":["576"],"title":"The evolution of gene expression by copy number and point mutations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8653","month":"10","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8653","oa":1,"file_date_updated":"2021-10-20T22:30:03Z","date_updated":"2023-09-07T13:22:42Z","date_created":"2020-10-13T13:02:33Z","author":[{"full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek"}],"related_material":{"record":[{"id":"7652","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","year":"2020"},{"abstract":[{"lang":"eng","text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"16f7d51fe28f91c21e4896a2028df40b","date_updated":"2020-09-22T09:51:28Z","date_created":"2020-09-22T09:51:28Z","file_id":"8555","relation":"main_file","creator":"dernst","file_size":5360135,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_CurrentBiology_Tan.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7427","ddc":["580"],"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","status":"public","intvolume":" 30","day":"03","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-02-03T00:00:00Z","publication":"Current Biology","citation":{"chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058.","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058","ieee":"S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058"},"article_type":"original","page":"381-395.e8","file_date_updated":"2020-09-22T09:51:28Z","ec_funded":1,"author":[{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","first_name":"Melinda F"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub"},{"first_name":"Pavel","last_name":"Lasák","full_name":"Lasák, Pavel"},{"full_name":"Petřík, Ivan","last_name":"Petřík","first_name":"Ivan"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Pospíšil, Jiří","last_name":"Pospíšil","first_name":"Jiří"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"date_created":"2020-02-02T23:01:00Z","date_updated":"2024-03-28T23:30:38Z","volume":30,"year":"2020","acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","pmid":1,"publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"month":"02","publication_identifier":{"issn":["09609822"]},"doi":"10.1016/j.cub.2019.11.058","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"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"},"oa":1,"external_id":{"pmid":["31956021"],"isi":["000511287900018"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}]},{"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","author":[{"first_name":"E","last_name":"Mazur","full_name":"Mazur, E"},{"last_name":"Kulik","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-02-18T10:03:47Z","date_updated":"2024-03-28T23:30:38Z","volume":226,"file_date_updated":"2020-11-20T09:32:10Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"25239","_id":"2699E3D2-B435-11E9-9278-68D0E5697425","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development"}],"doi":"10.1111/nph.16446","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7500","status":"public","title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","ddc":["580"],"intvolume":" 226","file":[{"relation":"main_file","file_id":"8781","date_created":"2020-11-20T09:32:10Z","date_updated":"2020-11-20T09:32:10Z","checksum":"17de728b0205979feb95ce663ba918c2","success":1,"file_name":"2020_NewPhytologist_Mazur.pdf","access_level":"open_access","file_size":2106888,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts."}],"issue":"5","publication":"New Phytologist","citation":{"ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","apa":"Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446."},"article_type":"original","page":"1375-1383","date_published":"2020-06-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2020-12-01T00:00:00Z","citation":{"chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822"},"page":"249","article_processing_charge":"No","has_accepted_license":"1","day":"01","file":[{"date_updated":"2021-07-16T22:30:03Z","date_created":"2020-12-04T07:27:52Z","checksum":"210a9675af5e4c78b0b56d920ac82866","relation":"source_file","file_id":"8919","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":91279806,"creator":"jhajny","embargo_to":"open_access","file_name":"Jakub Hajný IST Austria final_JH.docx","access_level":"closed"},{"checksum":"1781385b4aa73eba89cc76c6172f71d2","date_updated":"2021-12-08T23:30:03Z","date_created":"2020-12-09T15:04:41Z","embargo":"2021-12-07","file_id":"8933","relation":"main_file","creator":"jhajny","file_size":68707697,"content_type":"application/pdf","access_level":"open_access","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf"}],"oa_version":"Published Version","_id":"8822","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["580"],"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","status":"public","abstract":[{"text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:8822","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7427"},{"id":"6260","relation":"part_of_dissertation","status":"public"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"191"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"author":[{"full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T10:39:33Z","date_created":"2020-12-01T12:38:18Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","file_date_updated":"2021-12-08T23:30:03Z"},{"month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:8350","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-09-11T22:30:05Z","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","year":"2020","publication_status":"published","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"661","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6508"},{"relation":"part_of_dissertation","status":"public","id":"7001"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"date_created":"2020-09-09T11:12:10Z","date_updated":"2023-09-27T14:16:45Z","day":"09","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350."},"page":"107","date_published":"2020-09-09T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8350","status":"public","ddc":["570"],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","file":[{"date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:27Z","checksum":"6e47871c74f85008b9876112eb3fcfa1","file_id":"8351","relation":"source_file","creator":"sshamip","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":65194814,"file_name":"Shayan-Thesis-Final.docx","embargo_to":"open_access","access_level":"closed"},{"file_name":"Shayan-Thesis-Final.pdf","access_level":"open_access","content_type":"application/pdf","file_size":23729605,"creator":"sshamip","relation":"main_file","embargo":"2021-09-10","file_id":"8352","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:13Z","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3"}],"oa_version":"None"},{"doi":"10.3389/fcell.2020.574382","language":[{"iso":"eng"}],"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"},"oa":1,"external_id":{"isi":["000577915900001"],"pmid":["33102480"]},"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2296-634X"]},"month":"09","related_material":{"record":[{"id":"9962","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"volume":8,"date_created":"2020-09-26T06:11:07Z","date_updated":"2024-03-28T23:30:41Z","pmid":1,"acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Frontiers","publication_status":"published","ec_funded":1,"file_date_updated":"2020-09-28T13:11:17Z","article_number":"574382","date_published":"2020-09-25T00:00:00Z","citation":{"ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 2020;8(9). doi:10.3389/fcell.2020.574382","apa":"Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” Frontiers in Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.","ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020, doi:10.3389/fcell.2020.574382.","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"25","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5527139,"creator":"dernst","file_name":"2020_Frontiers_Hansen.pdf","access_level":"open_access","date_updated":"2020-09-28T13:11:17Z","date_created":"2020-09-28T13:11:17Z","checksum":"01f731824194c94c81a5da360d997073","success":1,"relation":"main_file","file_id":"8584"}],"_id":"8569","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 8","ddc":["570"],"status":"public","title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","issue":"9","abstract":[{"text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.","lang":"eng"}],"type":"journal_article"},{"file":[{"file_size":1352186,"content_type":"application/pdf","creator":"rbeattie","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","access_level":"open_access","date_created":"2020-05-11T08:28:38Z","date_updated":"2020-07-14T12:48:03Z","checksum":"3154ea7f90b9fb45e084cd1c2770597d","relation":"main_file","file_id":"7816"}],"oa_version":"Published Version","ddc":["570"],"title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7815","issue":"159","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"type":"journal_article","date_published":"2020-05-08T00:00:00Z","article_type":"original","citation":{"ieee":"R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147."},"publication":"Journal of Visual Experiments","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","date_created":"2020-05-11T08:31:20Z","date_updated":"2024-03-28T23:30:42Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"author":[{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"publisher":"MyJove Corporation","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","article_number":"e61147","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.3791/61147","project":[{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"},{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000546406600043"]},"publication_identifier":{"issn":["1940-087X"]},"month":"05"},{"file":[{"relation":"source_file","file_id":"7927","date_created":"2020-06-05T08:18:08Z","date_updated":"2021-06-07T22:30:03Z","checksum":"43c172bf006c95b65992d473c7240d13","embargo_to":"open_access","file_name":"PhDThesis_Contreras.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":53134142,"creator":"xcontreras"},{"access_level":"open_access","file_name":"PhDThesis_Contreras.pdf","creator":"xcontreras","content_type":"application/pdf","file_size":35117191,"embargo":"2021-06-06","file_id":"7928","relation":"main_file","checksum":"addfed9128271be05cae3608e03a6ec0","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Genetic dissection of neural development in health and disease at single cell resolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7902","abstract":[{"text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-06-05T00:00:00Z","page":"214","citation":{"short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902.","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"05","date_created":"2020-05-29T08:27:32Z","date_updated":"2023-10-18T08:45:16Z","related_material":{"record":[{"id":"6830","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"28"},{"id":"7815","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","language":[{"iso":"eng"}],"supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7902","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06"},{"month":"07","publication_identifier":{"eissn":["1540-8140"]},"isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000573631000004"]},"language":[{"iso":"eng"}],"doi":"10.1083/jcb.202007029","article_number":"e202007029","file_date_updated":"2021-02-02T23:30:03Z","publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"year":"2020","date_updated":"2023-10-17T10:04:49Z","date_created":"2020-08-02T22:00:57Z","volume":219,"author":[{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Anna","last_name":"Huttenlocher","full_name":"Huttenlocher, Anna"}],"scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","article_type":"letter_note","publication":"The Journal of Cell Biology","citation":{"ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029","apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029."},"date_published":"2020-07-22T00:00:00Z","type":"journal_article","issue":"8","title":"Zena Werb (1945-2020): Cell biology in context","ddc":["570"],"status":"public","intvolume":" 219","_id":"8190","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"8200","embargo":"2021-02-01","relation":"main_file","checksum":"30016d778d266b8e17d01094917873b8","date_created":"2020-08-04T13:11:52Z","date_updated":"2021-02-02T23:30:03Z","access_level":"open_access","file_name":"2020_JCB_Sixt.pdf","creator":"dernst","file_size":830725,"content_type":"application/pdf"}]},{"file":[{"file_name":"2020_ScienceAdvances_Zhang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":10578145,"file_id":"8994","relation":"main_file","date_updated":"2021-01-07T12:44:33Z","date_created":"2021-01-07T12:44:33Z","success":1,"checksum":"5ac2500b191c08ef6dab5327f40ff663"}],"oa_version":"Published Version","title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","ddc":["580"],"status":"public","intvolume":" 6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8986","abstract":[{"text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.","lang":"eng"}],"issue":"50","type":"journal_article","date_published":"2020-12-11T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020.","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895.","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020)."},"day":"11","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2024-03-28T23:30:44Z","date_created":"2021-01-03T23:01:23Z","volume":6,"author":[{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"publication_status":"published","publisher":"AAAS","department":[{"_id":"JiFr"}],"year":"2020","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","pmid":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-01-07T12:44:33Z","ec_funded":1,"article_number":"eabc8895","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abc8895","quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"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","grant_number":"25351"}],"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"month":"12","publication_identifier":{"eissn":["2375-2548"]}},{"language":[{"iso":"eng"}],"doi":"10.3390/ijms21165727","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"08","volume":21,"date_updated":"2024-03-28T23:30:44Z","date_created":"2020-08-24T06:24:03Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"author":[{"full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Lai, Linyi","last_name":"Lai","first_name":"Linyi"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"first_name":"Liping","last_name":"Liu","full_name":"Liu, Liping"},{"first_name":"Bello Hassan","last_name":"Jakada","full_name":"Jakada, Bello Hassan"},{"first_name":"Youmei","last_name":"Huang","full_name":"Huang, Youmei"},{"full_name":"He, Qing","first_name":"Qing","last_name":"He"},{"full_name":"Chai, Mengnan","first_name":"Mengnan","last_name":"Chai"},{"last_name":"Niu","first_name":"Xiaoping","full_name":"Niu, Xiaoping"},{"first_name":"Yuan","last_name":"Qin","full_name":"Qin, Yuan"}],"publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","year":"2020","file_date_updated":"2020-08-25T09:53:50Z","article_number":"5272","date_published":"2020-08-10T00:00:00Z","article_type":"original","citation":{"short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727.","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272."},"publication":"International Journal of Molecular Sciences","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2020_IntMolecSciences_Chen.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":5718755,"file_id":"8292","relation":"main_file","date_updated":"2020-08-25T09:53:50Z","date_created":"2020-08-25T09:53:50Z","success":1,"checksum":"03b039244e6ae80580385fd9f577e2b2"}],"intvolume":" 21","status":"public","ddc":["570"],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8283","issue":"16","abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"type":"journal_article"},{"issue":"15","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2021-08-07","file_id":"8815","checksum":"2d11f79a0b4e0a380fb002b933da331a","date_updated":"2021-08-08T22:30:03Z","date_created":"2020-11-26T17:12:51Z","access_level":"open_access","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","content_type":"application/pdf","file_size":15150403,"creator":"ajohnson"}],"_id":"8139","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 133","ddc":["575"],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2020-08-06T00:00:00Z","citation":{"short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062."},"publication":"Journal of Cell Science","article_type":"original","ec_funded":1,"file_date_updated":"2021-08-08T22:30:03Z","article_number":"jcs248062","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"author":[{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha"},{"first_name":"G","last_name":"Vert","full_name":"Vert, G"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"volume":133,"date_created":"2020-07-21T08:58:19Z","date_updated":"2023-12-01T13:51:07Z","pmid":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"08","doi":"10.1242/jcs.248062","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"11","article_type":"original","citation":{"ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020)."},"publication":"Plant Communications","date_published":"2020-05-11T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development."}],"intvolume":" 1","title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","ddc":["580"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9160","oa_version":"Published Version","file":[{"checksum":"785b266d82a94b007cf40dbbe7c4847e","success":1,"date_created":"2021-02-18T10:23:59Z","date_updated":"2021-02-18T10:23:59Z","relation":"main_file","file_id":"9161","file_size":840289,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_PlantComm_Semeradova.pdf"}],"publication_identifier":{"issn":["2590-3462"]},"month":"05","project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2020.100048","article_number":"100048","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-02-18T10:23:59Z","publisher":"Elsevier","department":[{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","volume":1,"date_created":"2021-02-18T10:18:43Z","date_updated":"2024-03-28T23:30:47Z","related_material":{"record":[{"id":"10135","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Montesinos López, Juan C","first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}]},{"date_published":"2019-10-22T00:00:00Z","publication":"BMC Biology","citation":{"chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2.","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","apa":"Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019.","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2"},"article_type":"original","day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["cell biology"],"file":[{"checksum":"31d8bae55a376d30925f53f7e1a02396","success":1,"date_created":"2021-11-26T11:37:54Z","date_updated":"2021-11-26T11:37:54Z","relation":"main_file","file_id":"10356","file_size":1648926,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2019_BMCBio_Harker_Kirschneck.pdf"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10354","status":"public","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","ddc":["570"],"intvolume":" 17","abstract":[{"text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems.","lang":"eng"}],"issue":"1","type":"journal_article","doi":"10.1186/s12915-019-0700-2","language":[{"iso":"eng"}],"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"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"oa":1,"external_id":{"pmid":["31640700"]},"quality_controlled":"1","month":"10","publication_identifier":{"issn":["1741-7007"]},"author":[{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"date_updated":"2021-11-26T11:54:29Z","date_created":"2021-11-26T11:25:03Z","volume":17,"year":"2019","acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","pmid":1,"publication_status":"published","publisher":"Springer Nature","file_date_updated":"2021-11-26T11:37:54Z","extern":"1","article_number":"82"},{"abstract":[{"lang":"eng","text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments."}],"type":"journal_article","oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10355","title":"Minimal coarse-grained models for molecular self-organisation in biology","status":"public","intvolume":" 58","day":"18","article_processing_charge":"No","scopus_import":"1","keyword":["molecular biology","structural biology"],"date_published":"2019-06-18T00:00:00Z","publication":"Current Opinion in Structural Biology","citation":{"mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018.","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","apa":"Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019."},"article_type":"original","page":"43-52","extern":"1","author":[{"last_name":"Hafner","first_name":"Anne E","full_name":"Hafner, Anne E"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"date_updated":"2021-11-26T11:54:25Z","date_created":"2021-11-26T11:33:21Z","volume":58,"acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","month":"06","publication_identifier":{"issn":["0959-440X"]},"doi":"10.1016/j.sbi.2019.05.018","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1906.09349","open_access":"1"}],"external_id":{"pmid":["31226513"]},"oa":1,"quality_controlled":"1"},{"extern":"1","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"last_name":"Yankowitz","first_name":"Matthew","full_name":"Yankowitz, Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Zhang, Yuxuan","first_name":"Yuxuan","last_name":"Zhang"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."}],"date_created":"2022-01-13T15:00:58Z","date_updated":"2022-01-20T09:33:38Z","volume":15,"year":"2019","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","publication_status":"published","publisher":"Springer Nature","month":"08","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-019-0596-3","language":[{"iso":"eng"}],"external_id":{"arxiv":["1902.00763"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.00763"}],"oa":1,"quality_controlled":"1","abstract":[{"text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","_id":"10621","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","status":"public","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","intvolume":" 15","day":"05","article_processing_charge":"No","scopus_import":"1","keyword":["general physics and astronomy"],"date_published":"2019-08-05T00:00:00Z","publication":"Nature Physics","citation":{"ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3","ieee":"H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3","ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3.","chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3."},"article_type":"original","page":"1011-1016"},{"extern":"1","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"volume":19,"date_created":"2022-01-13T15:11:14Z","date_updated":"2022-01-13T15:41:24Z","pmid":1,"acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","year":"2019","publisher":"American Chemical Society","publication_status":"published","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"month":"06","doi":"10.1021/acs.nanolett.9b01983","language":[{"iso":"eng"}],"external_id":{"arxiv":["1905.06303"],"pmid":["31246034"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06303"}],"oa":1,"quality_controlled":"1","issue":"8","abstract":[{"text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"10622","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","intvolume":" 19","status":"public","title":"Manipulating multivortex states in superconducting structures","article_processing_charge":"No","day":"27","scopus_import":"1","keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"date_published":"2019-06-27T00:00:00Z","citation":{"chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983.","short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983"},"publication":"Nano Letters","page":"5476-5482","article_type":"original"},{"oa_version":"Preprint","status":"public","title":"Tuning superconductivity in twisted bilayer graphene","intvolume":" 363","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10625","abstract":[{"text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures.","lang":"eng"}],"issue":"6431","type":"journal_article","date_published":"2019-01-24T00:00:00Z","article_type":"original","page":"1059-1064","publication":"Science","citation":{"mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910.","short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.","chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science. American Association for the Advancement of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910.","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910","ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910","ieee":"M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,” Science, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019."},"day":"24","article_processing_charge":"No","keyword":["multidisciplinary"],"scopus_import":"1","date_updated":"2022-01-14T13:48:32Z","date_created":"2022-01-14T12:14:58Z","volume":363,"author":[{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"last_name":"Zhang","first_name":"Yuxuan","full_name":"Zhang, Yuxuan"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"last_name":"Graf","first_name":"David","full_name":"Graf, David"},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."},{"first_name":"Cory R.","last_name":"Dean","full_name":"Dean, Cory R."}],"publication_status":"published","publisher":"American Association for the Advancement of Science (AAAS)","year":"2019","acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","pmid":1,"extern":"1","language":[{"iso":"eng"}],"doi":"10.1126/science.aav1910","quality_controlled":"1","external_id":{"pmid":["30679385 "],"arxiv":["1808.07865"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07865"}],"oa":1,"month":"01","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]}},{"language":[{"iso":"eng"}],"doi":"10.36471/jccm_february_2019_03","date_published":"2019-02-28T00:00:00Z","article_type":"original","quality_controlled":"1","citation":{"chicago":"Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside, 2019. https://doi.org/10.36471/jccm_february_2019_03.","short":"M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019).","mla":"Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:10.36471/jccm_february_2019_03.","ieee":"M. Yankowitz et al., “New correlated phenomena in magic-angle twisted bilayer graphene/s,” Journal Club for Condensed Matter Physics, vol. 03. Simons Foundation ; University of California, Riverside, 2019.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside. https://doi.org/10.36471/jccm_february_2019_03","ista":"Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03.","ama":"Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 2019;03. doi:10.36471/jccm_february_2019_03"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.condmatjclub.org/?p=3541"}],"publication":"Journal Club for Condensed Matter Physics","article_processing_charge":"No","month":"02","day":"28","oa_version":"Published Version","volume":"03","date_created":"2022-01-25T15:09:58Z","date_updated":"2022-01-25T15:56:39Z","author":[{"full_name":"Yankowitz, Mathew","first_name":"Mathew","last_name":"Yankowitz"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"full_name":"Graf, David","last_name":"Graf","first_name":"David"},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."},{"full_name":"Sharpe, Aaron L.","last_name":"Sharpe","first_name":"Aaron L."},{"full_name":"Fox, E.J.","last_name":"Fox","first_name":"E.J."},{"last_name":"Barnard","first_name":"A.W.","full_name":"Barnard, A.W."},{"last_name":"Finney","first_name":"Joe","full_name":"Finney, Joe"}],"intvolume":" 3","publisher":"Simons Foundation ; University of California, Riverside","publication_status":"published","title":"New correlated phenomena in magic-angle twisted bilayer graphene/s","status":"public","_id":"10664","year":"2019","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points."}],"type":"journal_article"}]