[{"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"}],"month":"10","publication":"Plant Cell Division","series_title":"MIMB","status":"public","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.","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"}],"publisher":"Humana Press","_id":"10268","date_created":"2021-11-11T10:03:30Z","page":"105-114","scopus_import":"1","volume":2382,"title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","citation":{"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>.","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.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","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>","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>.","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.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_published":"2021-10-28T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1940-6029"],"eisbn":["978-1-0716-1744-1"],"isbn":["978-1-0716-1743-4"],"issn":["1064-3745"]},"type":"book_chapter","year":"2021","day":"28","date_updated":"2022-06-03T06:47:06Z","intvolume":"      2382","alternative_title":["Methods in Molecular Biology"],"publication_status":"published","pmid":1,"external_id":{"pmid":["34705235"]},"oa_version":"None","doi":"10.1007/978-1-0716-1744-1_6","author":[{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","last_name":"Glanc","full_name":"Glanc, Matous"}]},{"pmid":1,"external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"oa_version":"Published Version","doi":"10.7554/elife.72132","author":[{"last_name":"Marconi","full_name":"Marconi, Marco","first_name":"Marco"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","last_name":"Gallemi"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Krzysztof","last_name":"Wabnik","full_name":"Wabnik, Krzysztof"}],"file":[{"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"11372","file_size":14137503,"creator":"dernst","file_name":"2021_eLife_Marconi.pdf","date_updated":"2022-05-13T09:00:29Z","success":1,"date_created":"2022-05-13T09:00:29Z"}],"intvolume":"        10","publication_status":"published","article_number":"72132","volume":10,"citation":{"short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","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.","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>.","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>","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>.","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>","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."},"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","department":[{"_id":"EvBe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2021-11-01T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"type":"journal_article","year":"2021","date_updated":"2023-08-14T11:49:23Z","day":"01","file_date_updated":"2022-05-13T09:00:29Z","quality_controlled":"1","ddc":["570"],"isi":1,"oa":1,"status":"public","publication":"eLife","month":"11","abstract":[{"lang":"eng","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."}],"article_type":"original","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).","publisher":"eLife Sciences Publications","scopus_import":"1","date_created":"2021-11-11T10:05:18Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"10270"},{"external_id":{"isi":["000715997300001"],"pmid":["34745067"]},"pmid":1,"author":[{"last_name":"Qi","orcid":"0000-0002-6148-2416","full_name":"Qi, Qin","first_name":"Qin","id":"3B22D412-F248-11E8-B48F-1D18A9856A87"},{"first_name":"S. Andreas","full_name":"Angermayr, S. Andreas","last_name":"Angermayr"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"file":[{"creator":"cchlebak","file_name":"2021_FrontiersMicrob_Qi.pdf","success":1,"date_updated":"2021-11-11T10:54:40Z","date_created":"2021-11-11T10:54:40Z","checksum":"d41321748e9588dd3cf03e9a7222127f","access_level":"open_access","relation":"main_file","file_id":"10272","file_size":2397203,"content_type":"application/pdf"}],"doi":"10.3389/fmicb.2021.760017","oa_version":"Published Version","article_number":"760017","publication_status":"published","intvolume":"        12","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","citation":{"short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","ista":"Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017.","mla":"Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” <i>Frontiers in Microbiology</i>, vol. 12, 760017, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmicb.2021.760017\">10.3389/fmicb.2021.760017</a>.","chicago":"Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmicb.2021.760017\">https://doi.org/10.3389/fmicb.2021.760017</a>.","apa":"Qi, Q., Angermayr, S. A., &#38; Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2021.760017\">https://doi.org/10.3389/fmicb.2021.760017</a>","ama":"Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fmicb.2021.760017\">10.3389/fmicb.2021.760017</a>","ieee":"Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021."},"project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"volume":12,"file_date_updated":"2021-11-11T10:54:40Z","date_updated":"2025-04-14T09:40:44Z","day":"20","year":"2021","type":"journal_article","publication_identifier":{"eissn":["1664-302X"]},"date_published":"2021-10-20T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"10","publication":"Frontiers in Microbiology","oa":1,"status":"public","isi":1,"ddc":["610"],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"10271","scopus_import":"1","date_created":"2021-11-11T10:39:37Z","keyword":["microbiology"],"publisher":"Frontiers","ec_funded":1,"abstract":[{"lang":"eng","text":"Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions."}],"acknowledgement":"High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support.","article_type":"original"},{"isi":1,"oa":1,"status":"public","publication":"Nature Communications","month":"11","ddc":["530"],"quality_controlled":"1","scopus_import":"1","date_created":"2021-11-14T23:01:23Z","_id":"10280","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_type":"original","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."}],"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.","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","volume":12,"citation":{"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>","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","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>.","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>","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","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>."},"title":"Metamachines of pluripotent colloids","type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"year":"2021","date_updated":"2023-08-14T11:48:37Z","day":"04","file_date_updated":"2021-11-15T13:25:52Z","has_accepted_license":"1","department":[{"_id":"JePa"}],"language":[{"iso":"eng"}],"date_published":"2021-11-04T00:00:00Z","publication_status":"published","article_number":"6398","issue":"1","intvolume":"        12","external_id":{"pmid":["34737315"],"isi":["000714754400010"]},"pmid":1,"doi":"10.1038/s41467-021-26699-6","author":[{"last_name":"Aubret","full_name":"Aubret, Antoine","first_name":"Antoine"},{"first_name":"Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","orcid":"0000-0002-2916-6632","last_name":"Martinet","full_name":"Martinet, Quentin"},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"}],"file":[{"success":1,"date_updated":"2021-11-15T13:25:52Z","date_created":"2021-11-15T13:25:52Z","creator":"cchlebak","file_name":"2021_NatComm_Aubret.pdf","file_id":"10292","file_size":6282703,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1c392b12b9b7b615d422d9fabe19cdb9"}],"oa_version":"Published Version"},{"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","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>","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>.","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.","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>.","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.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021)."},"project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":12,"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-10-30T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"has_accepted_license":"1","file_date_updated":"2022-05-16T07:02:27Z","day":"30","date_updated":"2025-04-15T07:29:28Z","publication_identifier":{"eissn":["2073-4425"]},"type":"journal_article","year":"2021","quality_controlled":"1","ddc":["570"],"publication":"Genes","month":"10","oa":1,"status":"public","isi":1,"publisher":"MDPI","ec_funded":1,"article_type":"original","abstract":[{"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","lang":"eng"}],"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.","_id":"10281","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","date_created":"2021-11-14T23:01:24Z","external_id":{"isi":["000834044200002"]},"oa_version":"Published Version","author":[{"first_name":"Verica","last_name":"Vasic","full_name":"Vasic, Verica"},{"first_name":"Mattson S.O.","full_name":"Jones, Mattson S.O.","last_name":"Jones"},{"id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","first_name":"Denise","full_name":"Haslinger, Denise","last_name":"Haslinger"},{"first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","full_name":"Knaus, Lisa"},{"first_name":"Michael J.","last_name":"Schmeisser","full_name":"Schmeisser, Michael J."},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia"},{"first_name":"Andreas G.","last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G."}],"file":[{"date_created":"2022-05-16T07:02:27Z","success":1,"date_updated":"2022-05-16T07:02:27Z","creator":"dernst","file_name":"2021_Genes_Vasic.pdf","file_size":1335308,"file_id":"11380","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"256cb832a9c3051c7dc741f6423b8cbd"}],"doi":"10.3390/genes12111746","intvolume":"        12","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"issue":"11","article_number":"1746","publication_status":"published"},{"external_id":{"isi":["000714350000001"]},"doi":"10.15252/embr.202153824","author":[{"first_name":"Leonardo","full_name":"Restivo, Leonardo","last_name":"Restivo"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"first_name":"Michael","full_name":"Tsoory, Michael","last_name":"Tsoory"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"last_name":"Badurek","full_name":"Badurek, Sylvia","first_name":"Sylvia"},{"last_name":"Pitzer","full_name":"Pitzer, Claudia","first_name":"Claudia"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont"},{"first_name":"Jonathan","full_name":"Ward, Jonathan","last_name":"Ward"},{"first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","last_name":"Schunn","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael"},{"first_name":"Lucas P.J.J.","full_name":"Noldus, Lucas P.J.J.","last_name":"Noldus"},{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"last_name":"Voikar","full_name":"Voikar, Vootele","first_name":"Vootele"}],"file":[{"creator":"dernst","file_name":"2021_EmboReports_Restivo.pdf","date_updated":"2022-05-16T07:07:41Z","date_created":"2022-05-16T07:07:41Z","success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":488583,"file_id":"11381"}],"oa_version":"Published Version","publication_status":"published","article_number":"e53824","intvolume":"        22","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","volume":22,"title":"Towards best practices in research: Role of academic core facilities","citation":{"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).","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>.","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>.","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>","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>"},"type":"journal_article","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"year":"2021","file_date_updated":"2022-05-16T07:07:41Z","date_updated":"2023-08-14T11:47:35Z","day":"04","department":[{"_id":"PreCl"}],"has_accepted_license":"1","date_published":"2021-11-04T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"month":"11","publication":"EMBO Reports","oa":1,"status":"public","quality_controlled":"1","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"10283","date_created":"2021-11-14T23:01:24Z","scopus_import":"1","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.","article_type":"original","abstract":[{"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.","lang":"eng"}],"publisher":"EMBO Press"},{"doi":"10.1214/21-EJP686","author":[{"id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","full_name":"Dubach, Guillaume","orcid":"0000-0001-6892-8137","last_name":"Dubach"}],"file":[{"file_name":"2021_ElecJournalProb_Dubach.pdf","creator":"cchlebak","date_updated":"2021-11-15T10:10:17Z","date_created":"2021-11-15T10:10:17Z","success":1,"checksum":"1c975afb31460277ce4d22b93538e5f9","file_size":735940,"content_type":"application/pdf","file_id":"10288","access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","article_number":"124","publication_status":"published","intvolume":"        26","year":"2021","type":"journal_article","publication_identifier":{"eissn":["1083-6489"]},"file_date_updated":"2021-11-15T10:10:17Z","date_updated":"2025-04-14T07:43:47Z","day":"28","department":[{"_id":"LaEr"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2021-09-28T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"volume":26,"title":"On eigenvector statistics in the spherical and truncated unitary ensembles","citation":{"ista":"Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary ensembles. Electronic Journal of Probability. 26, 124.","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>.","short":"G. Dubach, Electronic Journal of Probability 26 (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>","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.","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>.","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>"},"_id":"10285","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2021-11-14T23:01:25Z","scopus_import":"1","ec_funded":1,"article_type":"original","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.","abstract":[{"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.","lang":"eng"}],"publisher":"Institute of Mathematical Statistics","publication":"Electronic Journal of Probability","month":"09","status":"public","oa":1,"quality_controlled":"1","ddc":["519"]},{"publication_status":"published","article_number":"e71575","intvolume":"        10","doi":"10.7554/elife.71575","author":[{"last_name":"Conde-Dusman","full_name":"Conde-Dusman, María J","first_name":"María J"},{"first_name":"Partha N","full_name":"Dey, Partha N","last_name":"Dey"},{"last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar","first_name":"Óscar"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","full_name":"García-Lira, Carmen","last_name":"García-Lira"},{"first_name":"Teddy","last_name":"Grand","full_name":"Grand, Teddy"},{"last_name":"Briz","full_name":"Briz, Victor","first_name":"Victor"},{"last_name":"Velasco","full_name":"Velasco, Eric R","first_name":"Eric R"},{"first_name":"Raül","last_name":"Andero Galí","full_name":"Andero Galí, Raül"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"last_name":"Barco","full_name":"Barco, Angel","first_name":"Angel"},{"full_name":"Paoletti, Pierre","last_name":"Paoletti","first_name":"Pierre"},{"first_name":"John F","full_name":"Wesseling, John F","last_name":"Wesseling"},{"first_name":"Fabrizio","full_name":"Gardoni, Fabrizio","last_name":"Gardoni"},{"first_name":"Steven J","full_name":"Tavalin, Steven J","last_name":"Tavalin"},{"full_name":"Perez-Otaño, Isabel","last_name":"Perez-Otaño","first_name":"Isabel"}],"file":[{"file_size":2477302,"content_type":"application/pdf","file_id":"10302","access_level":"open_access","relation":"main_file","checksum":"59318e9e41507cec83c2f4070e6ad540","date_updated":"2021-11-18T07:02:02Z","date_created":"2021-11-18T07:02:02Z","success":1,"creator":"lgarciar","file_name":"elife-71575-v1.pdf"}],"oa_version":"Published Version","external_id":{"isi":["000720945900001"]},"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"10301","scopus_import":"1","date_created":"2021-11-18T06:59:45Z","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).","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"}],"article_type":"original","publisher":"eLife Sciences Publications","isi":1,"month":"11","publication":"eLife","status":"public","oa":1,"ddc":["570"],"quality_controlled":"1","type":"journal_article","publication_identifier":{"issn":["2050-084X"]},"year":"2021","file_date_updated":"2021-11-18T07:02:02Z","date_updated":"2024-10-21T06:02:05Z","day":"17","has_accepted_license":"1","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"date_published":"2021-11-17T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","volume":10,"title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","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).","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>.","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.","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>","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.","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>","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>."}},{"ddc":["570"],"quality_controlled":"1","isi":1,"oa":1,"status":"public","publication":"Communications Biology","month":"03","article_type":"original","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.","abstract":[{"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.","lang":"eng"}],"publisher":"Springer ","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"scopus_import":"1","date_created":"2021-11-19T11:37:29Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"10310","volume":4,"citation":{"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).","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>.","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.","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>.","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.","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>"},"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"LeSa"}],"has_accepted_license":"1","date_published":"2021-03-08T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"issn":["2399-3642"]},"year":"2021","date_updated":"2023-08-14T11:51:19Z","day":"08","file_date_updated":"2021-11-19T15:09:18Z","intvolume":"         4","article_number":"304","publication_status":"published","issue":"1","pmid":1,"external_id":{"pmid":["33686186"],"isi":["000627440700001"]},"oa_version":"Published Version","doi":"10.1038/s42003-021-01808-9","author":[{"orcid":"0000-0002-3219-2022","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"first_name":"Anna","full_name":"Frank, Anna","last_name":"Frank"},{"first_name":"Hideaki","last_name":"Tanaka","full_name":"Tanaka, Hideaki"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"first_name":"Eithar","last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar"},{"last_name":"Kato","full_name":"Kato, Takayuki","first_name":"Takayuki"},{"first_name":"Keiichi","full_name":"Namba, Keiichi","last_name":"Namba"},{"last_name":"Gerle","full_name":"Gerle, Christoph","first_name":"Christoph"},{"first_name":"Marc M.","last_name":"Nowaczyk","full_name":"Nowaczyk, Marc M."},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"}],"file":[{"creator":"cchlebak","file_name":"2021_CommBio_Çoruh.pdf","date_updated":"2021-11-19T15:09:18Z","success":1,"date_created":"2021-11-19T15:09:18Z","checksum":"8ffd39f2bba7152a2441802ff313bf0b","access_level":"open_access","relation":"main_file","file_size":6030261,"content_type":"application/pdf","file_id":"10318"}]},{"intvolume":"         2","issue":"4","article_number":"100939","publication_status":"published","oa_version":"Published Version","doi":"10.1016/j.xpro.2021.100939","file":[{"creator":"cchlebak","file_name":"2021_STARProtocols_Amberg.pdf","date_updated":"2021-11-22T08:23:58Z","date_created":"2021-11-22T08:23:58Z","success":1,"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","access_level":"open_access","relation":"main_file","file_size":7309464,"content_type":"application/pdf","file_id":"10329"}],"author":[{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","last_name":"Amberg","full_name":"Amberg, Nicole"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"abstract":[{"lang":"eng","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)."}],"article_type":"original","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.","publisher":"Cell Press","_id":"10321","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","date_created":"2021-11-21T23:01:28Z","ddc":["573"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"corr_author":"1","month":"11","publication":"STAR Protocols","status":"public","oa":1,"department":[{"_id":"SiHi"}],"has_accepted_license":"1","date_published":"2021-11-10T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"eissn":["2666-1667"]},"year":"2021","file_date_updated":"2021-11-22T08:23:58Z","day":"10","date_updated":"2025-04-15T08:23:07Z","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"volume":2,"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","citation":{"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>","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>.","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>","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).","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.","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>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes"},{"intvolume":"        19","issue":"11","publication_status":"published","article_number":"e3001431","pmid":1,"related_material":{"record":[{"id":"13069","relation":"research_data","status":"public"}]},"external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"oa_version":"Published Version","doi":"10.1371/journal.pbio.3001431","author":[{"last_name":"Chauve","full_name":"Chauve, Laetitia","first_name":"Laetitia"},{"first_name":"Francesca","full_name":"Hodge, Francesca","last_name":"Hodge"},{"last_name":"Murdoch","full_name":"Murdoch, Sharlene","first_name":"Sharlene"},{"first_name":"Fatemah","last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah"},{"last_name":"Mann","full_name":"Mann, Harry Jack","first_name":"Harry Jack"},{"first_name":"Andrea","full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo"},{"first_name":"Hanneke","full_name":"Okkenhaug, Hanneke","last_name":"Okkenhaug"},{"first_name":"Greg","last_name":"West","full_name":"West, 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"},{"last_name":"Li","full_name":"Li, Cheryl","first_name":"Cheryl"},{"first_name":"Steven","full_name":"Wingett, Steven","last_name":"Wingett"},{"first_name":"Hermine","last_name":"Kienberger","full_name":"Kienberger, Hermine"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}],"file":[{"checksum":"0c61b667f814fd9435b3ac42036fc36d","relation":"main_file","access_level":"open_access","file_size":4069215,"file_id":"10330","content_type":"application/pdf","success":1,"date_created":"2021-11-22T09:34:03Z","date_updated":"2021-11-22T09:34:03Z","file_name":"2021_PLoSBio_Chauve.pdf","creator":"cchlebak"}],"quality_controlled":"1","ddc":["570"],"isi":1,"publication":"PLoS Biology","month":"11","status":"public","oa":1,"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.","abstract":[{"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.","lang":"eng"}],"article_type":"original","publisher":"Public Library of Science","_id":"10322","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","date_created":"2021-11-21T23:01:28Z","volume":19,"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","citation":{"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>.","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.","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>","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.","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>.","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>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"date_published":"2021-11-01T00:00:00Z","year":"2021","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"type":"journal_article","file_date_updated":"2021-11-22T09:34:03Z","date_updated":"2023-08-14T11:53:27Z","day":"01"},{"publication_status":"published","article_number":"762005","intvolume":"         8","external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"pmid":1,"doi":"10.3389/fmolb.2021.762005","file":[{"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","file_id":"10333","file_size":4700798,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","file_name":"2021_FrontiersMolBioSc_Sučec.pdf","date_updated":"2021-11-23T15:06:58Z","success":1,"date_created":"2021-11-23T15:06:58Z"}],"author":[{"full_name":"Sučec, Iva","last_name":"Sučec","first_name":"Iva"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"oa_version":"Published Version","isi":1,"corr_author":"1","status":"public","oa":1,"publication":"Frontiers in Molecular Biosciences","month":"10","ddc":["547"],"quality_controlled":"1","date_created":"2021-11-21T23:01:29Z","scopus_import":"1","_id":"10323","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"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).","article_type":"original","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."}],"publisher":"Frontiers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","volume":8,"citation":{"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>","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>.","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.","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).","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","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>."},"title":"How do chaperones bind (partly) unfolded client proteins?","type":"journal_article","publication_identifier":{"eissn":["2296-889X"]},"year":"2021","day":"25","date_updated":"2024-10-09T21:01:12Z","file_date_updated":"2021-11-23T15:06:58Z","has_accepted_license":"1","department":[{"_id":"PaSc"}],"language":[{"iso":"eng"}],"date_published":"2021-10-25T00:00:00Z"},{"publication_status":"published","alternative_title":["LNCS"],"arxiv":1,"external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]},"oa_version":"Preprint","doi":"10.1007/978-3-662-64331-0_11","author":[{"first_name":"Zeta","last_name":"Avarikioti","full_name":"Avarikioti, Zeta"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Roger","full_name":"Wattenhofer, Roger","last_name":"Wattenhofer"},{"first_name":"Dionysis","last_name":"Zindros","full_name":"Zindros, Dionysis"}],"quality_controlled":"1","isi":1,"oa":1,"status":"public","month":"10","publication":"25th International Conference on Financial Cryptography and Data Security","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","abstract":[{"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.","lang":"eng"}],"publisher":"Springer Nature","page":"209-230","scopus_import":"1","date_created":"2021-11-21T23:01:29Z","_id":"10324","volume":"12675 ","citation":{"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>","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>.","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>","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.","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>.","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.","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."},"title":"Brick: Asynchronous incentive-compatible payment channels","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","conference":{"location":"Virtual","name":"FC: Financial Cryptography","end_date":"2021-03-05","start_date":"2021-03-01"},"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"department":[{"_id":"ElKo"}],"date_published":"2021-10-23T00:00:00Z","language":[{"iso":"eng"}],"year":"2021","type":"conference","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-6626-4330-3"],"eisbn":["978-3-662-64331-0"],"eissn":["1611-3349"]},"date_updated":"2023-08-14T12:59:58Z","day":"23"},{"publication_status":"published","intvolume":"         7","file":[{"date_created":"2025-01-21T12:41:43Z","success":1,"date_updated":"2025-01-21T12:41:43Z","creator":"dernst","file_name":"Accepted version_Xu et al.,2021 Catabolism of strigolactones by a carboxylesterase.pdf","checksum":"d20231806bea67f0fd19e96a94a048f4","file_id":"18864","file_size":41109943,"content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"first_name":"Liang","last_name":"Chai","full_name":"Chai, Liang"},{"full_name":"Zhang, Shiqi","last_name":"Zhang","first_name":"Shiqi"},{"last_name":"Yu","full_name":"Yu, Ruixue","first_name":"Ruixue"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"first_name":"Chongyi","full_name":"Xu, Chongyi","last_name":"Xu"},{"full_name":"Hu, Yuxin","last_name":"Hu","first_name":"Yuxin"}],"doi":"10.1038/s41477-021-01011-y","oa_version":"Submitted Version","external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"pmid":1,"scopus_import":"1","page":"1495–1504 ","date_created":"2021-11-21T23:01:30Z","OA_place":"repository","_id":"10326","publisher":"Springer Nature","article_type":"original","acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants."}],"oa":1,"status":"public","publication":"Nature Plants","month":"11","isi":1,"quality_controlled":"1","ddc":["580"],"date_updated":"2025-01-21T12:42:52Z","day":"11","file_date_updated":"2025-01-21T12:41:43Z","type":"journal_article","year":"2021","publication_identifier":{"eissn":["2055-0278"]},"date_published":"2021-11-11T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"JiFr"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","citation":{"apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., &#38; Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>.","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. 2021;7:1495–1504. doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>","ieee":"E. Xu <i>et al.</i>, “Catabolism of strigolactones by a carboxylesterase,” <i>Nature Plants</i>, vol. 7. Springer Nature, pp. 1495–1504, 2021.","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504."},"title":"Catabolism of strigolactones by a carboxylesterase","volume":7},{"intvolume":"       220","article_number":"e202009154","publication_status":"published","issue":"6","extern":"1","pmid":1,"external_id":{"pmid":["33929486"]},"oa_version":"None","author":[{"last_name":"Zeng","full_name":"Zeng, Longhui","first_name":"Longhui"},{"first_name":"Ivan","last_name":"Palaia","full_name":"Palaia, Ivan"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Xiaolei","last_name":"Su","full_name":"Su, Xiaolei"}],"doi":"10.1083/jcb.202009154","quality_controlled":"1","status":"public","month":"04","publication":"Journal of Cell Biology","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publisher":"Rockefeller University Press","article_type":"original","acknowledgement":"Charles H. Hood Foundation (NO AWARD) ; Rally Foundation (NO AWARD)","abstract":[{"lang":"eng","text":"The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction."}],"scopus_import":"1","date_created":"2021-11-25T15:21:30Z","_id":"10337","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"keyword":["cell biology"],"citation":{"apa":"Zeng, L., Palaia, I., Šarić, A., &#38; Su, X. (2021). PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>","ama":"Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. 2021;220(6). doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>","chicago":"Zeng, Longhui, Ivan Palaia, Anđela Šarić, and Xiaolei Su. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>.","ieee":"L. Zeng, I. Palaia, A. Šarić, and X. Su, “PLCγ1 promotes phase separation of T cell signaling components,” <i>Journal of Cell Biology</i>, vol. 220, no. 6. Rockefeller University Press, 2021.","short":"L. Zeng, I. Palaia, A. Šarić, X. Su, Journal of Cell Biology 220 (2021).","mla":"Zeng, Longhui, et al. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>, vol. 220, no. 6, e202009154, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>.","ista":"Zeng L, Palaia I, Šarić A, Su X. 2021. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 220(6), e202009154."},"title":"PLCγ1 promotes phase separation of T cell signaling components","volume":220,"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2021-04-30T00:00:00Z","language":[{"iso":"eng"}],"day":"30","date_updated":"2021-11-25T15:33:08Z","year":"2021","type":"journal_article","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]}},{"_id":"10338","scopus_import":"1","page":"1565-1577","date_created":"2021-11-25T15:36:36Z","keyword":["biophysics"],"publisher":"Elsevier","abstract":[{"text":"In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.","lang":"eng"}],"article_type":"original","month":"02","publication":"Biophysical Journal","oa":1,"status":"public","quality_controlled":"1","date_updated":"2022-04-01T10:34:38Z","day":"19","year":"2021","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"language":[{"iso":"eng"}],"date_published":"2021-02-19T00:00:00Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2020.10.01.322156","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Physical modeling of multivalent interactions in the nuclear pore complex","citation":{"short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","mla":"Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>, vol. 120, no. 9, Elsevier, 2021, pp. 1565–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>.","ista":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.","apa":"Davis, L. K., Šarić, A., Hoogenboom, B. W., &#38; Zilman, A. (2021). Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>","chicago":"Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>.","ama":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. 2021;120(9):1565-1577. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>","ieee":"L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling of multivalent interactions in the nuclear pore complex,” <i>Biophysical Journal</i>, vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021."},"volume":120,"extern":"1","issue":"9","publication_status":"published","intvolume":"       120","author":[{"last_name":"Davis","full_name":"Davis, Luke K.","first_name":"Luke K."},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela"},{"full_name":"Hoogenboom, Bart W.","last_name":"Hoogenboom","first_name":"Bart W."},{"first_name":"Anton","last_name":"Zilman","full_name":"Zilman, Anton"}],"doi":"10.1016/j.bpj.2021.01.039","oa_version":"Preprint","external_id":{"pmid":["33617830"]},"pmid":1},{"keyword":["condensed matter physics","general chemistry"],"_id":"10339","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)"},"OA_place":"publisher","scopus_import":"1","page":"3798-3806","date_created":"2021-11-25T16:06:42Z","acknowledgement":"We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.), the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council (Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan Palaia for fruitful discussions.","article_type":"original","abstract":[{"lang":"eng","text":"We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation."}],"publisher":"Royal Society of Chemistry","license":"https://creativecommons.org/licenses/by-nc/3.0/","publication":"Soft Matter","month":"02","status":"public","oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"type":"journal_article","year":"2021","date_updated":"2024-10-14T14:20:59Z","day":"16","language":[{"iso":"eng"}],"date_published":"2021-02-16T00:00:00Z","OA_type":"hybrid","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e","open_access":"1"}],"article_processing_charge":"No","volume":17,"title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","citation":{"mla":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>.","ista":"Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.","short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>.","apa":"Vanhille-Campos, C., &#38; Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>","ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” <i>Soft Matter</i>, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. 2021;17(14):3798-3806. doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>"},"extern":"1","issue":"14","publication_status":"published","intvolume":"        17","doi":"10.1039/d0sm02012e","author":[{"first_name":"Christian","full_name":"Vanhille-Campos, Christian","last_name":"Vanhille-Campos"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"oa_version":"Published Version","external_id":{"pmid":["33629089"]},"pmid":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2"}]}},{"year":"2021","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"day":"16","date_updated":"2024-10-14T11:13:03Z","language":[{"iso":"eng"}],"date_published":"2021-01-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2020.07.28.224741","open_access":"1"}],"article_processing_charge":"No","volume":120,"citation":{"ista":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 120(4), 598–606.","mla":"Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>.","short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606.","ieee":"A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A. Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,” <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.","apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38; Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. 2021;120(4):598-606. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>","chicago":"Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>."},"title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","keyword":["biophysics"],"page":"598-606","scopus_import":"1","date_created":"2021-11-25T16:18:23Z","_id":"10340","acknowledgement":"We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1 to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant from Paris Sciences et Lettres Research University and support from the Institut Curie.","article_type":"original","abstract":[{"lang":"eng","text":"The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales."}],"publisher":"Cell Press","oa":1,"status":"public","publication":"Biophysical Journal","month":"01","quality_controlled":"1","doi":"10.1016/j.bpj.2020.12.028","author":[{"full_name":"Paraschiv, Alexandru","last_name":"Paraschiv","first_name":"Alexandru"},{"first_name":"Thibaut J.","last_name":"Lagny","full_name":"Lagny, Thibaut J."},{"first_name":"Christian Vanhille","last_name":"Campos","full_name":"Campos, Christian Vanhille"},{"first_name":"Evelyne","last_name":"Coudrier","full_name":"Coudrier, Evelyne"},{"first_name":"Patricia","last_name":"Bassereau","full_name":"Bassereau, Patricia"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"oa_version":"Preprint","external_id":{"pmid":["33460596"]},"pmid":1,"extern":"1","publication_status":"published","issue":"4","intvolume":"       120"},{"ddc":["530"],"quality_controlled":"1","isi":1,"corr_author":"1","oa":1,"status":"public","publication":"Nature Physics","month":"11","article_type":"original","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","ec_funded":1,"publisher":"Springer Nature","scopus_import":"1","page":"1382–1390","date_created":"2021-11-28T23:01:29Z","_id":"10365","volume":17,"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"citation":{"apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>","ieee":"M. Luciano <i>et al.</i>, “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” <i>Nature Physics</i>, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>.","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. <i>Nature Physics</i>. 2021;17(12):1382–1390. doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>","short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” <i>Nature Physics</i>, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390."},"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"EdHa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2021-11-18T00:00:00Z","year":"2021","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"type":"journal_article","day":"18","date_updated":"2025-04-14T07:52:26Z","file_date_updated":"2023-10-11T09:31:43Z","intvolume":"        17","publication_status":"published","issue":"12","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/"}]},"external_id":{"isi":["000720204300004"]},"oa_version":"Submitted Version","doi":"10.1038/s41567-021-01374-1","author":[{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"last_name":"Xue","full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Winnok H.","last_name":"De Vos","full_name":"De Vos, Winnok H."},{"first_name":"Lorena","full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata"},{"full_name":"Surin, Mathieu","last_name":"Surin","first_name":"Mathieu"},{"first_name":"Frank","full_name":"Lafont, Frank","last_name":"Lafont"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"file":[{"date_updated":"2023-10-11T09:31:43Z","success":1,"date_created":"2023-10-11T09:31:43Z","file_name":"50145_4_merged_1630498627.pdf","creator":"channezo","file_id":"14420","file_size":40285498,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5d6d76750a71d7cb632bb15417c38ef7"}]},{"volume":168,"citation":{"ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>, vol. 168, no. 12, 203758, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. 2021;168(12). doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., &#38; Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” <i>Cells and Development</i>, vol. 168, no. 12. Elsevier, 2021.","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>."},"title":"Special rebranding issue: “Quantitative cell and developmental biology”","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"date_published":"2021-11-17T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2667-2901"]},"year":"2021","day":"17","date_updated":"2026-06-18T08:37:21Z","ddc":["570"],"quality_controlled":"1","isi":1,"corr_author":"1","oa":1,"status":"public","publication":"Cells and Development","month":"11","article_type":"letter_note","publisher":"Elsevier","date_created":"2021-11-28T23:01:30Z","scopus_import":"1","_id":"10366","pmid":1,"external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"oa_version":"Published Version","doi":"10.1016/j.cdev.2021.203758","author":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lennon, Ana Maria","last_name":"Lennon","first_name":"Ana Maria"},{"last_name":"Mayor","full_name":"Mayor, Roberto","first_name":"Roberto"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"}],"intvolume":"       168","article_number":"203758","publication_status":"published","issue":"12"}]