[{"publisher":"Springer Nature","editor":[{"first_name":"Elison B","full_name":"Blancaflor, Elison B","last_name":"Blancaflor"}],"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","doi":"10.1007/978-1-0716-1677-2_2","series_title":"MIMB","type":"book_chapter","_id":"10267","date_updated":"2022-08-26T09:13:00Z","page":"43-51","quality_controlled":"1","external_id":{"pmid":["34647246"]},"year":"2021","publication":"Plant Gravitropism","status":"public","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"The Ceratopteris richardii spores were obtained from the lab of Jo Ann Banks at Purdue University. This work was supported by funding from the European Union’s Horizon 2020 research and innovation program (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program and DOC Fellowship of the Austrian Academy of Sciences.","date_published":"2021-10-14T00:00:00Z","ec_funded":1,"pmid":1,"oa_version":"None","title":"Evaluation of gravitropism in non-seed plants","day":"14","scopus_import":"1","author":[{"orcid":"0000-0003-2627-6956","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_created":"2021-11-11T09:26:10Z","volume":2368,"intvolume":"      2368","abstract":[{"text":"Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species.","lang":"eng"}],"publication_identifier":{"eisbn":["978-1-0716-1677-2"],"isbn":["978-1-0716-1676-5"]},"publication_status":"published","month":"10","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Zhang, Y., Li, L., &#38; Friml, J. (2021). Evaluation of gravitropism in non-seed plants. In E. B. Blancaflor (Ed.), <i>Plant Gravitropism</i> (Vol. 2368, pp. 43–51). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>","mla":"Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021, pp. 43–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>.","chicago":"Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in Non-Seed Plants.” In <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, 2368:43–51. MIMB. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>.","ista":"Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants. In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.","ieee":"Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,” in <i>Plant Gravitropism</i>, vol. 2368, E. B. Blancaflor, Ed. Springer Nature, 2021, pp. 43–51.","short":"Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism, Springer Nature, 2021, pp. 43–51.","ama":"Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In: Blancaflor EB, ed. <i>Plant Gravitropism</i>. Vol 2368. MIMB. Springer Nature; 2021:43-51. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>"}},{"oa_version":"None","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","author":[{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous"}],"scopus_import":"1","day":"28","date_created":"2021-11-11T10:03:30Z","volume":2382,"intvolume":"      2382","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication_status":"published","publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-0716-1743-4"],"eissn":["1940-6029"],"eisbn":["978-1-0716-1744-1"]},"month":"10","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>.","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>","ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114."},"publisher":"Humana Press","doi":"10.1007/978-1-0716-1744-1_6","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","type":"book_chapter","series_title":"MIMB","date_updated":"2022-06-03T06:47:06Z","_id":"10268","page":"105-114","quality_controlled":"1","external_id":{"pmid":["34705235"]},"year":"2021","publication":"Plant Cell Division","status":"public","date_published":"2021-10-28T00:00:00Z","acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","pmid":1},{"type":"journal_article","_id":"10270","date_updated":"2023-08-14T11:49:23Z","publisher":"eLife Sciences Publications","article_processing_charge":"Yes","doi":"10.7554/elife.72132","quality_controlled":"1","ddc":["570"],"external_id":{"pmid":["34723798"],"isi":["000734671200001"]},"isi":1,"year":"2021","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","date_published":"2021-11-01T00:00:00Z","pmid":1,"status":"public","publication":"eLife","date_created":"2021-11-11T10:05:18Z","article_type":"original","volume":10,"oa_version":"Published Version","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","day":"01","scopus_import":"1","author":[{"first_name":"Marco","full_name":"Marconi, Marco","last_name":"Marconi"},{"last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","first_name":"Marçal","orcid":"0000-0003-4675-6893"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Wabnik, Krzysztof","last_name":"Wabnik","first_name":"Krzysztof"}],"file_date_updated":"2022-05-13T09:00:29Z","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","intvolume":"        10","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"has_accepted_license":"1","article_number":"72132","file":[{"date_created":"2022-05-13T09:00:29Z","file_size":14137503,"date_updated":"2022-05-13T09:00:29Z","creator":"dernst","file_id":"11372","success":1,"file_name":"2021_eLife_Marconi.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"fad13c509b53bb7a2bef9c946a7ca60a"}],"department":[{"_id":"EvBe"}],"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>.","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>, vol. 10, 72132, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>.","apa":"Marconi, M., Gallemi, M., Benková, E., &#38; Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"language":[{"iso":"eng"}],"oa":1},{"quality_controlled":"1","ddc":["530"],"date_updated":"2023-08-14T11:48:37Z","_id":"10280","type":"journal_article","doi":"10.1038/s41467-021-26699-6","article_processing_charge":"Yes","publisher":"Springer Nature","pmid":1,"acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","date_published":"2021-11-04T00:00:00Z","status":"public","publication":"Nature Communications","isi":1,"year":"2021","external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2021-11-15T13:25:52Z","has_accepted_license":"1","intvolume":"        12","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials."}],"volume":12,"article_type":"original","date_created":"2021-11-14T23:01:23Z","author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin","first_name":"Quentin","orcid":"0000-0002-2916-6632"},{"last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","orcid":"0000-0002-7253-9465"}],"scopus_import":"1","day":"04","oa_version":"Published Version","title":"Metamachines of pluripotent colloids","issue":"1","citation":{"short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>.","apa":"Aubret, A., Martinet, Q., &#38; Palacci, J. A. (2021). Metamachines of pluripotent colloids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"JePa"}],"article_number":"6398","file":[{"date_created":"2021-11-15T13:25:52Z","file_size":6282703,"creator":"cchlebak","date_updated":"2021-11-15T13:25:52Z","file_id":"10292","file_name":"2021_NatComm_Aubret.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1c392b12b9b7b615d422d9fabe19cdb9"}],"month":"11"},{"month":"10","article_number":"1746","file":[{"file_size":1335308,"date_created":"2022-05-16T07:02:27Z","date_updated":"2022-05-16T07:02:27Z","creator":"dernst","file_id":"11380","success":1,"file_name":"2021_Genes_Vasic.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"256cb832a9c3051c7dc741f6423b8cbd"}],"department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","citation":{"ama":"Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. <i>Genes</i>. 2021;12(11). doi:<a href=\"https://doi.org/10.3390/genes12111746\">10.3390/genes12111746</a>","ieee":"V. Vasic <i>et al.</i>, “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” <i>Genes</i>, vol. 12, no. 11. MDPI, 2021.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","chicago":"Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12111746\">https://doi.org/10.3390/genes12111746</a>.","ista":"Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.","apa":"Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., &#38; Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12111746\">https://doi.org/10.3390/genes12111746</a>","mla":"Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” <i>Genes</i>, vol. 12, no. 11, 1746, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12111746\">10.3390/genes12111746</a>."},"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","oa_version":"Published Version","author":[{"full_name":"Vasic, Verica","last_name":"Vasic","first_name":"Verica"},{"first_name":"Mattson S.O.","full_name":"Jones, Mattson S.O.","last_name":"Jones"},{"id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","full_name":"Haslinger, Denise","last_name":"Haslinger","first_name":"Denise"},{"last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","first_name":"Lisa"},{"first_name":"Michael J.","full_name":"Schmeisser, Michael J.","last_name":"Schmeisser"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Andreas G.","full_name":"Chiocchetti, Andreas G.","last_name":"Chiocchetti"}],"scopus_import":"1","day":"30","article_type":"original","date_created":"2021-11-14T23:01:24Z","volume":12,"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems"}],"intvolume":"        12","has_accepted_license":"1","publication_identifier":{"eissn":["2073-4425"]},"publication_status":"published","file_date_updated":"2022-05-16T07:02:27Z","external_id":{"isi":["000834044200002"]},"isi":1,"year":"2021","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"}],"status":"public","publication":"Genes","acknowledgement":"This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.","date_published":"2021-10-30T00:00:00Z","ec_funded":1,"publisher":"MDPI","doi":"10.3390/genes12111746","article_processing_charge":"No","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"type":"journal_article","date_updated":"2023-08-14T11:46:12Z","_id":"10281","ddc":["570"],"quality_controlled":"1"},{"doi":"10.1111/nph.17792","article_processing_charge":"No","publisher":"Wiley","date_updated":"2023-08-14T11:46:43Z","_id":"10282","type":"journal_article","page":"329-343","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"quality_controlled":"1","year":"2021","isi":1,"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"status":"public","publication":"New Phytologist","pmid":1,"acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","date_published":"2021-11-05T00:00:00Z","author":[{"first_name":"Ivan","full_name":"Kashkan, Ivan","last_name":"Kashkan"},{"first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katarzyna","full_name":"Retzer, Katarzyna","last_name":"Retzer"},{"last_name":"Humpolíčková","full_name":"Humpolíčková, Jana","first_name":"Jana"},{"full_name":"Jayasree, Aswathy","last_name":"Jayasree","first_name":"Aswathy"},{"first_name":"Roberta","full_name":"Filepová, Roberta","last_name":"Filepová"},{"first_name":"Zuzana","last_name":"Vondráková","full_name":"Vondráková, Zuzana"},{"orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"last_name":"Rombaut","full_name":"Rombaut, Debbie","first_name":"Debbie"},{"last_name":"Jacobs","full_name":"Jacobs, Thomas B.","first_name":"Thomas B."},{"first_name":"Mikko J.","last_name":"Frilander","full_name":"Frilander, Mikko J."},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"first_name":"Kamil","full_name":"Růžička, Kamil","last_name":"Růžička"}],"scopus_import":"1","day":"05","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","oa_version":"Preprint","volume":233,"article_type":"original","date_created":"2021-11-14T23:01:24Z","abstract":[{"text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.","lang":"eng"}],"intvolume":"       233","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"publication_status":"published","month":"11","department":[{"_id":"JiFr"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 233, Wiley, 2021, pp. 329–43, doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343.","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","ieee":"I. Kashkan <i>et al.</i>, “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 233. Wiley, pp. 329–343, 2021.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;233:329-343. doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"quality_controlled":"1","ddc":["570"],"_id":"10283","date_updated":"2023-08-14T11:47:35Z","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","doi":"10.15252/embr.202153824","publisher":"EMBO Press","acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","date_published":"2021-11-04T00:00:00Z","publication":"EMBO Reports","status":"public","isi":1,"year":"2021","external_id":{"isi":["000714350000001"]},"file_date_updated":"2022-05-16T07:07:41Z","publication_status":"published","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","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)"},"intvolume":"        22","abstract":[{"lang":"eng","text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research."}],"volume":22,"date_created":"2021-11-14T23:01:24Z","article_type":"original","day":"04","scopus_import":"1","author":[{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"first_name":"Michael","last_name":"Tsoory","full_name":"Tsoory, Michael"},{"first_name":"Lior","full_name":"Bikovski, Lior","last_name":"Bikovski"},{"first_name":"Sylvia","full_name":"Badurek, Sylvia","last_name":"Badurek"},{"first_name":"Claudia","last_name":"Pitzer","full_name":"Pitzer, Claudia"},{"full_name":"Kos-Braun, Isabelle C.","last_name":"Kos-Braun","first_name":"Isabelle C."},{"first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont"},{"last_name":"Ward","full_name":"Ward, Jonathan","first_name":"Jonathan"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","full_name":"Schunn, Michael","last_name":"Schunn","orcid":"0000-0003-4326-5300","first_name":"Michael"},{"first_name":"Lucas P.J.J.","last_name":"Noldus","full_name":"Noldus, Lucas P.J.J."},{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"}],"title":"Towards best practices in research: Role of academic core facilities","oa_version":"Published Version","citation":{"mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>, vol. 22, e53824, EMBO Press, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>. EMBO Press, 2021. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","ieee":"L. Restivo <i>et al.</i>, “Towards best practices in research: Role of academic core facilities,” <i>EMBO Reports</i>, vol. 22. EMBO Press, 2021.","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. 2021;22. doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"PreCl"}],"article_number":"e53824","file":[{"relation":"main_file","checksum":"74743baa6ef431ef60c3de3bc4da045a","success":1,"file_name":"2021_EmboReports_Restivo.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"11381","file_size":488583,"date_created":"2022-05-16T07:07:41Z","date_updated":"2022-05-16T07:07:41Z","creator":"dernst"}],"month":"11"},{"author":[{"full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","last_name":"Dubach","orcid":"0000-0001-6892-8137","first_name":"Guillaume"}],"scopus_import":"1","day":"28","oa_version":"Published Version","title":"On eigenvector statistics in the spherical and truncated unitary ensembles","volume":26,"article_type":"original","date_created":"2021-11-14T23:01:25Z","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        26","abstract":[{"lang":"eng","text":"We study the overlaps between right and left eigenvectors for random matrices of the spherical ensemble, as well as truncated unitary ensembles in the regime where half of the matrix at least is truncated. These two integrable models exhibit a form of duality, and the essential steps of our investigation can therefore be performed in parallel. In every case, conditionally on all eigenvalues, diagonal overlaps are shown to be distributed as a product of independent random variables with explicit distributions. This enables us to prove that the scaled diagonal overlaps, conditionally on one eigenvalue, converge in distribution to a heavy-tail limit, namely, the inverse of a γ2 distribution. We also provide formulae for the conditional expectation of diagonal and off-diagonal overlaps, either with respect to one eigenvalue, or with respect to the whole spectrum. These results, analogous to what is known for the complex Ginibre ensemble, can be obtained in these cases thanks to integration techniques inspired from a previous work by Forrester & Krishnapur."}],"publication_identifier":{"eissn":["1083-6489"]},"publication_status":"published","file_date_updated":"2021-11-15T10:10:17Z","month":"09","department":[{"_id":"LaEr"}],"article_number":"124","file":[{"relation":"main_file","checksum":"1c975afb31460277ce4d22b93538e5f9","success":1,"file_name":"2021_ElecJournalProb_Dubach.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"10288","date_created":"2021-11-15T10:10:17Z","file_size":735940,"creator":"cchlebak","date_updated":"2021-11-15T10:10:17Z"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>, vol. 26, 124, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>.","apa":"Dubach, G. (2021). On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>","chicago":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>.","ista":"Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary ensembles. Electronic Journal of Probability. 26, 124.","short":"G. Dubach, Electronic Journal of Probability 26 (2021).","ieee":"G. Dubach, “On eigenvector statistics in the spherical and truncated unitary ensembles,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ama":"Dubach G. On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1214/21-EJP686","article_processing_charge":"No","publisher":"Institute of Mathematical Statistics","date_updated":"2021-11-15T10:48:46Z","_id":"10285","type":"journal_article","ddc":["519"],"quality_controlled":"1","year":"2021","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Electronic Journal of Probability","ec_funded":1,"date_published":"2021-09-28T00:00:00Z","acknowledgement":"We acknowledge partial support from the grants NSF DMS-1812114 of P. Bourgade (PI) and NSF CAREER DMS-1653602 of L.-P. Arguin (PI). This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We would like to thank Paul Bourgade and László Erdős for many helpful comments."},{"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"intvolume":"       213","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["1047-8477"]},"file_date_updated":"2021-11-15T13:11:27Z","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","oa_version":"Published Version","author":[{"orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur"}],"day":"03","scopus_import":"1","article_type":"original","date_created":"2021-11-15T12:21:42Z","volume":213,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","citation":{"short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808."},"month":"11","file":[{"file_id":"10291","date_updated":"2021-11-15T13:11:27Z","creator":"cchlebak","file_size":16818304,"date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_JournalStructBiol_Dimchev.pdf","success":1}],"article_number":"107808","department":[{"_id":"FlSc"}],"ddc":["572"],"quality_controlled":"1","publisher":"Elsevier ","doi":"10.1016/j.jsb.2021.107808","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-11-21T08:36:02Z","_id":"10290","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"publication":"Journal of Structural Biology","status":"public","date_published":"2021-11-03T00:00:00Z","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","external_id":{"isi":["000720259500002"]},"related_material":{"record":[{"relation":"software","status":"public","id":"14502"}]},"year":"2021","isi":1,"keyword":["Structural Biology"]},{"year":"2021","related_material":{"record":[{"id":"9997","status":"public","relation":"part_of_dissertation"},{"id":"2","status":"public","relation":"part_of_dissertation"},{"id":"9402","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","status":"public","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"ec_funded":1,"date_published":"2021-11-17T00:00:00Z","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","doi":"10.15479/at:ista:10293","publisher":"Institute of Science and Technology Austria","_id":"10293","date_updated":"2025-07-14T09:10:09Z","type":"dissertation","page":"171","ddc":["519","576"],"supervisor":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"}],"month":"11","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"file":[{"access_level":"closed","content_type":"application/zip","file_name":"submission_new.zip","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","relation":"source_file","date_updated":"2022-12-20T23:30:08Z","creator":"lschmid","file_size":29703124,"date_created":"2021-11-18T12:41:46Z","embargo_to":"open_access","file_id":"10305"},{"relation":"main_file","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_name":"thesis_new_upload.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"10306","file_size":8320985,"date_created":"2021-11-18T12:59:15Z","embargo":"2022-10-18","date_updated":"2022-12-20T23:30:08Z","creator":"lschmid"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Schmid, L. (2021). <i>Evolution of cooperation via (in)direct reciprocity under imperfect information</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>","mla":"Schmid, Laura. <i>Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10293\">https://doi.org/10.15479/at:ista:10293</a>.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10293\">10.15479/at:ista:10293</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"17","author":[{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329"}],"oa_version":"Published Version","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","date_created":"2021-11-15T17:12:57Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"file_date_updated":"2022-12-20T23:30:08Z","publication_status":"published","publication_identifier":{"issn":["2663-337X"]}},{"department":[{"_id":"BjHo"}],"article_number":"e2102350118","arxiv":1,"month":"11","issue":"45","citation":{"short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"volume":118,"article_type":"original","date_created":"2021-11-17T13:24:24Z","author":[{"first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","first_name":"Jose M"},{"first_name":"Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sankar, Sarath","last_name":"Sankar","first_name":"Sarath"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"day":"03","scopus_import":"1","title":"Experimental observation of the origin and structure of elastoinertial turbulence","oa_version":"Preprint","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number."}],"intvolume":"       118","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"year":"2021","isi":1,"external_id":{"isi":["000720926900019"],"arxiv":["2103.00023"],"pmid":[" 34732570"]},"pmid":1,"date_published":"2021-11-03T00:00:00Z","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","project":[{"call_identifier":"FWF","grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","publication":"Proceedings of the National Academy of Sciences","date_updated":"2023-08-14T11:50:10Z","_id":"10299","type":"journal_article","doi":"10.1073/pnas.2102350118","article_processing_charge":"No","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"quality_controlled":"1"},{"status":"public","publication":"eLife","date_published":"2021-11-17T00:00:00Z","acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","external_id":{"isi":["000720945900001"]},"year":"2021","isi":1,"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"ddc":["570"],"quality_controlled":"1","publisher":"eLife Sciences Publications","article_processing_charge":"No","doi":"10.7554/elife.71575","type":"journal_article","_id":"10301","date_updated":"2023-08-14T11:50:50Z","language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","ieee":"M. J. Conde-Dusman <i>et al.</i>, “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>, vol. 10, e71575, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>."},"month":"11","article_number":"e71575","file":[{"success":1,"file_name":"elife-71575-v1.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"59318e9e41507cec83c2f4070e6ad540","date_created":"2021-11-18T07:02:02Z","file_size":2477302,"creator":"lgarciar","date_updated":"2021-11-18T07:02:02Z","file_id":"10302"}],"department":[{"_id":"GaNo"}],"abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        10","has_accepted_license":"1","file_date_updated":"2021-11-18T07:02:02Z","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","oa_version":"Published Version","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","day":"17","author":[{"first_name":"María J","last_name":"Conde-Dusman","full_name":"Conde-Dusman, María J"},{"last_name":"Dey","full_name":"Dey, Partha N","first_name":"Partha N"},{"full_name":"Elía-Zudaire, Óscar","last_name":"Elía-Zudaire","first_name":"Óscar"},{"first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","last_name":"García-Lira","full_name":"García-Lira, Carmen"},{"full_name":"Grand, Teddy","last_name":"Grand","first_name":"Teddy"},{"first_name":"Victor","last_name":"Briz","full_name":"Briz, Victor"},{"full_name":"Velasco, Eric R","last_name":"Velasco","first_name":"Eric R"},{"full_name":"Andero Galí, Raül","last_name":"Andero Galí","first_name":"Raül"},{"last_name":"Niñerola","full_name":"Niñerola, Sergio","first_name":"Sergio"},{"first_name":"Angel","last_name":"Barco","full_name":"Barco, Angel"},{"first_name":"Pierre","last_name":"Paoletti","full_name":"Paoletti, Pierre"},{"full_name":"Wesseling, John F","last_name":"Wesseling","first_name":"John F"},{"last_name":"Gardoni","full_name":"Gardoni, Fabrizio","first_name":"Fabrizio"},{"full_name":"Tavalin, Steven J","last_name":"Tavalin","first_name":"Steven J"},{"full_name":"Perez-Otaño, Isabel","last_name":"Perez-Otaño","first_name":"Isabel"}],"date_created":"2021-11-18T06:59:45Z","article_type":"original","volume":10},{"abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2022-12-20T23:30:06Z","title":"Role of hormones in nitrate regulated growth","oa_version":"Published Version","author":[{"first_name":"Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed"}],"day":"22","date_created":"2021-11-18T11:20:59Z","language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>."},"month":"11","supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"file":[{"file_id":"10331","embargo":"2022-11-23","creator":"rabualia","date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:21Z","file_size":28005730,"checksum":"dea38b98aa4da1cea03dcd0f10862818","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf"},{"file_id":"10332","embargo_to":"open_access","file_size":62841883,"date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z","creator":"rabualia","relation":"source_file","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_name":"AbualiaPhDthesisfinalv3.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"ddc":["580","581"],"page":"139","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:10303","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"type":"dissertation","date_updated":"2023-09-19T14:42:45Z","_id":"10303","status":"public","degree_awarded":"PhD","date_published":"2021-11-22T00:00:00Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9010"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"id":"47","status":"public","relation":"part_of_dissertation"}]},"year":"2021"},{"month":"11","supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","first_name":"Michael K"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"}],"file":[{"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","embargo":"2022-11-18","date_created":"2021-11-18T15:07:31Z","file_size":13266088,"file_id":"10308","access_level":"open_access","content_type":"application/pdf","file_name":"ThesisTomasekKathrin.pdf","checksum":"b39c9e0ef18d0484d537a67551effd02","relation":"main_file"},{"relation":"source_file","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_name":"ThesisTomasekKathrin.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"10309","embargo_to":"open_access","file_size":7539509,"date_created":"2021-11-18T15:07:46Z","date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek"}],"department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>"},"title":"Pathogenic Escherichia coli hijack the host immune response","oa_version":"Published Version","author":[{"orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"}],"day":"18","date_created":"2021-11-18T15:05:06Z","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2022-12-20T23:30:05Z","related_material":{"record":[{"id":"10316","status":"public","relation":"part_of_dissertation"}]},"year":"2021","status":"public","degree_awarded":"PhD","date_published":"2021-11-18T00:00:00Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:10307","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","type":"dissertation","date_updated":"2023-09-07T13:34:38Z","_id":"10307","ddc":["570"],"page":"73"},{"file_date_updated":"2021-11-19T15:09:18Z","publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","has_accepted_license":"1","intvolume":"         4","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700."}],"volume":4,"date_created":"2021-11-19T11:37:29Z","article_type":"original","day":"08","scopus_import":"1","author":[{"full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun"},{"first_name":"Anna","last_name":"Frank","full_name":"Frank, Anna"},{"first_name":"Hideaki","full_name":"Tanaka, Hideaki","last_name":"Tanaka"},{"last_name":"Kawamoto","full_name":"Kawamoto, Akihiro","first_name":"Akihiro"},{"full_name":"El-Mohsnawy, Eithar","last_name":"El-Mohsnawy","first_name":"Eithar"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"},{"first_name":"Keiichi","full_name":"Namba, Keiichi","last_name":"Namba"},{"first_name":"Christoph","full_name":"Gerle, Christoph","last_name":"Gerle"},{"last_name":"Nowaczyk","full_name":"Nowaczyk, Marc M.","first_name":"Marc M."},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"}],"oa_version":"Published Version","title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","citation":{"ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>","ieee":"M. O. Çoruh <i>et al.</i>, “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” <i>Communications Biology</i>, vol. 4, no. 1. Springer , 2021.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>. Springer , 2021. <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. Springer . <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>, vol. 4, no. 1, 304, Springer , 2021, doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>."},"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"file":[{"file_id":"10318","date_updated":"2021-11-19T15:09:18Z","creator":"cchlebak","date_created":"2021-11-19T15:09:18Z","file_size":6030261,"checksum":"8ffd39f2bba7152a2441802ff313bf0b","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_CommBio_Çoruh.pdf","success":1}],"article_number":"304","month":"03","quality_controlled":"1","ddc":["570"],"_id":"10310","date_updated":"2023-08-14T11:51:19Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s42003-021-01808-9","publisher":"Springer ","pmid":1,"acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","date_published":"2021-03-08T00:00:00Z","status":"public","publication":"Communications Biology","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"isi":1,"year":"2021","external_id":{"isi":["000627440700001"],"pmid":["33686186"]}},{"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","date_published":"2021-10-18T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ec_funded":1,"citation":{"ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, <a href=\"https://doi.org/10.1101/2021.10.18.464770\">10.1101/2021.10.18.464770</a>.","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.10.18.464770\">https://doi.org/10.1101/2021.10.18.464770</a>."},"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911","call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425"}],"publication":"bioRxiv","language":[{"iso":"eng"}],"status":"public","oa":1,"department":[{"_id":"CaGu"},{"_id":"MiSi"}],"related_material":{"record":[{"id":"11843","status":"public","relation":"later_version"},{"id":"10307","status":"public","relation":"dissertation_contains"}]},"month":"10","year":"2021","publication_status":"submitted","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"type":"preprint","date_created":"2021-11-19T12:24:16Z","date_updated":"2024-03-25T23:30:19Z","_id":"10316","oa_version":"Preprint","publisher":"Cold Spring Harbor Laboratory","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","author":[{"first_name":"Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivana","last_name":"Glatzová","full_name":"Glatzová, Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d"},{"full_name":"Lukesch, Michael S.","last_name":"Lukesch","first_name":"Michael S."},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C"},{"first_name":"Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"doi":"10.1101/2021.10.18.464770","day":"18","article_processing_charge":"No"},{"publisher":"Cell Press","doi":"10.1016/j.xpro.2021.100939","article_processing_charge":"Yes","type":"journal_article","date_updated":"2023-11-16T13:08:03Z","_id":"10321","ddc":["573"],"quality_controlled":"1","year":"2021","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"}],"status":"public","publication":"STAR Protocols","date_published":"2021-11-10T00:00:00Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","ec_funded":1,"oa_version":"Published Version","title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","author":[{"orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","last_name":"Amberg"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"scopus_import":"1","day":"10","article_type":"original","date_created":"2021-11-21T23:01:28Z","volume":2,"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).","lang":"eng"}],"intvolume":"         2","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","publication_identifier":{"eissn":["2666-1667"]},"publication_status":"published","file_date_updated":"2021-11-22T08:23:58Z","month":"11","article_number":"100939","file":[{"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_STARProtocols_Amberg.pdf","file_id":"10329","creator":"cchlebak","date_updated":"2021-11-22T08:23:58Z","file_size":7309464,"date_created":"2021-11-22T08:23:58Z"}],"department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","citation":{"ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 2, no. 4. Cell Press, 2021.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>","apa":"Amberg, N., &#38; Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 2, no. 4, 100939, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>.","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>."}},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"13069"}]},"external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"year":"2021","isi":1,"date_published":"2021-11-01T00:00:00Z","acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","pmid":1,"status":"public","publication":"PLoS Biology","type":"journal_article","_id":"10322","date_updated":"2023-08-14T11:53:27Z","publisher":"Public Library of Science","article_processing_charge":"No","doi":"10.1371/journal.pbio.3001431","quality_controlled":"1","ddc":["570"],"file":[{"file_id":"10330","date_created":"2021-11-22T09:34:03Z","file_size":4069215,"creator":"cchlebak","date_updated":"2021-11-22T09:34:03Z","relation":"main_file","checksum":"0c61b667f814fd9435b3ac42036fc36d","file_name":"2021_PLoSBio_Chauve.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"article_number":"e3001431","department":[{"_id":"MaDe"}],"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"L. Chauve <i>et al.</i>, “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” <i>PLoS Biology</i>, vol. 19, no. 11. Public Library of Science, 2021.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. <i>PLoS Biology</i>. 2021;19(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001431\">10.1371/journal.pbio.3001431</a>","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001431\">https://doi.org/10.1371/journal.pbio.3001431</a>","mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” <i>PLoS Biology</i>, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001431\">10.1371/journal.pbio.3001431</a>.","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pbio.3001431\">https://doi.org/10.1371/journal.pbio.3001431</a>.","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431."},"issue":"11","language":[{"iso":"eng"}],"oa":1,"date_created":"2021-11-21T23:01:28Z","article_type":"original","volume":19,"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","oa_version":"Published Version","scopus_import":"1","day":"01","author":[{"first_name":"Laetitia","last_name":"Chauve","full_name":"Chauve, Laetitia"},{"first_name":"Francesca","last_name":"Hodge","full_name":"Hodge, Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"first_name":"Fatemah","last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah"},{"first_name":"Harry Jack","full_name":"Mann, Harry Jack","last_name":"Mann"},{"full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo","first_name":"Andrea"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"last_name":"West","full_name":"West, Greg","first_name":"Greg"},{"full_name":"Sousa, Bebiana C.","last_name":"Sousa","first_name":"Bebiana C."},{"first_name":"Anne","full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"first_name":"Steven","full_name":"Wingett, Steven","last_name":"Wingett"},{"last_name":"Kienberger","full_name":"Kienberger, Hermine","first_name":"Hermine"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario"},{"first_name":"Michael","full_name":"Wakelam, Michael","last_name":"Wakelam"},{"first_name":"Olivia","last_name":"Casanueva","full_name":"Casanueva, Olivia"}],"file_date_updated":"2021-11-22T09:34:03Z","publication_status":"published","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        19","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” <i>Frontiers in Molecular Biosciences</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmolb.2021.762005\">https://doi.org/10.3389/fmolb.2021.762005</a>.","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” <i>Frontiers in Molecular Biosciences</i>, vol. 8, 762005, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmolb.2021.762005\">10.3389/fmolb.2021.762005</a>.","apa":"Sučec, I., Bersch, B., &#38; Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? <i>Frontiers in Molecular Biosciences</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmolb.2021.762005\">https://doi.org/10.3389/fmolb.2021.762005</a>","ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? <i>Frontiers in Molecular Biosciences</i>. 2021;8. doi:<a href=\"https://doi.org/10.3389/fmolb.2021.762005\">10.3389/fmolb.2021.762005</a>","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” <i>Frontiers in Molecular Biosciences</i>, vol. 8. Frontiers, 2021."},"month":"10","file":[{"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_FrontiersMolBioSc_Sučec.pdf","file_id":"10333","creator":"cchlebak","date_updated":"2021-11-23T15:06:58Z","date_created":"2021-11-23T15:06:58Z","file_size":4700798}],"article_number":"762005","department":[{"_id":"PaSc"}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity."}],"intvolume":"         8","has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["2296-889X"]},"file_date_updated":"2021-11-23T15:06:58Z","title":"How do chaperones bind (partly) unfolded client proteins?","oa_version":"Published Version","author":[{"first_name":"Iva","full_name":"Sučec, Iva","last_name":"Sučec"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"day":"25","scopus_import":"1","article_type":"original","date_created":"2021-11-21T23:01:29Z","volume":8,"status":"public","publication":"Frontiers in Molecular Biosciences","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","date_published":"2021-10-25T00:00:00Z","pmid":1,"external_id":{"pmid":["34760928"],"isi":["000717241700001"]},"year":"2021","isi":1,"ddc":["547"],"quality_controlled":"1","publisher":"Frontiers","doi":"10.3389/fmolb.2021.762005","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-08-14T11:55:04Z","_id":"10323"},{"_id":"10324","date_updated":"2023-08-14T12:59:58Z","type":"conference","alternative_title":["LNCS"],"article_processing_charge":"No","doi":"10.1007/978-3-662-64331-0_11","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"quality_controlled":"1","page":"209-230","isi":1,"year":"2021","external_id":{"arxiv":["1905.11360"],"isi":["000712016200011"]},"conference":{"name":"FC: Financial Cryptography","end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual"},"date_published":"2021-10-23T00:00:00Z","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","publication":"25th International Conference on Financial Cryptography and Data Security","status":"public","volume":"12675 ","date_created":"2021-11-21T23:01:29Z","day":"23","scopus_import":"1","author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"},{"first_name":"Dionysis","full_name":"Zindros, Dionysis","last_name":"Zindros"}],"title":"Brick: Asynchronous incentive-compatible payment channels","oa_version":"Preprint","publication_identifier":{"isbn":["9-783-6626-4330-3"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-662-64331-0"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity."}],"department":[{"_id":"ElKo"}],"month":"10","arxiv":1,"citation":{"chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In <i>25th International Conference on Financial Cryptography and Data Security</i>, 12675:209–30. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">https://doi.org/10.1007/978-3-662-64331-0_11</a>.","ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” <i>25th International Conference on Financial Cryptography and Data Security</i>, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">10.1007/978-3-662-64331-0_11</a>.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., &#38; Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In <i>25th International Conference on Financial Cryptography and Data Security</i> (Vol. 12675, pp. 209–230). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">https://doi.org/10.1007/978-3-662-64331-0_11</a>","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: <i>25th International Conference on Financial Cryptography and Data Security</i>. Vol 12675. Springer Nature; 2021:209-230. doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_11\">10.1007/978-3-662-64331-0_11</a>","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230.","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in <i>25th International Conference on Financial Cryptography and Data Security</i>, Virtual, 2021, vol. 12675, pp. 209–230."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]}]