[{"intvolume":"       187","publication":"Cell","date_updated":"2024-01-22T13:43:40Z","ec_funded":1,"department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kuhn","first_name":"Andre","full_name":"Kuhn, Andre"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"last_name":"Mutte","first_name":"Sumanth","full_name":"Mutte, Sumanth"},{"first_name":"Shiv Mani","last_name":"Dubey","full_name":"Dubey, Shiv Mani"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"first_name":"Sjef","last_name":"Boeren","full_name":"Boeren, Sjef"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"},{"last_name":"Koehorst","first_name":"Jasper","full_name":"Koehorst, Jasper"},{"full_name":"Kohchi, Takayuki","first_name":"Takayuki","last_name":"Kohchi"},{"full_name":"Nishihama, Ryuichi","first_name":"Ryuichi","last_name":"Nishihama"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Sprakel, Joris","last_name":"Sprakel","first_name":"Joris"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"oa":1,"volume":187,"abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"year":"2024","citation":{"ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>."},"_id":"14826","file":[{"file_name":"2024_Cell_Kuhn.pdf","access_level":"open_access","success":1,"file_size":13194060,"date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-22T13:41:41Z","relation":"main_file","creator":"dernst","file_id":"14874","content_type":"application/pdf","checksum":"06fd236a9ee0b46ccb05f44695bfc34b"}],"date_created":"2024-01-17T12:45:40Z","article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","doi":"10.1016/j.cell.2023.11.021","scopus_import":"1","file_date_updated":"2024-01-22T13:41:41Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["580"],"status":"public","month":"01","publisher":"Elsevier","pmid":1,"external_id":{"pmid":["38128538"]},"date_published":"2024-01-04T00:00:00Z","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"}],"has_accepted_license":"1","issue":"1","day":"04","page":"130-148.e17","quality_controlled":"1"},{"date_updated":"2024-02-28T12:29:43Z","ec_funded":1,"publication":"eLife","department":[{"_id":"JiFr"}],"intvolume":"        13","volume":13,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski"},{"last_name":"Matijevic","first_name":"Ivana","full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"date_created":"2024-02-27T07:10:11Z","_id":"15033","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"citation":{"chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>"},"year":"2024","oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"epub_ahead","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","publication_identifier":{"issn":["2050-084X"]},"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","article_type":"original","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"doi":"10.7554/elife.68993","status":"public","month":"02","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"ddc":["580"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2024-02-21T00:00:00Z","publisher":"eLife Sciences Publications","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","quality_controlled":"1","day":"21"},{"date_published":"2023-04-27T00:00:00Z","external_id":{"isi":["000991468700001"]},"type":"journal_article","publisher":"Elsevier","month":"04","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"quality_controlled":"1","page":"1950-1967.e25","day":"27","issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"},{"grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13107"}],"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","description":"News on ISTA Website","relation":"press_release"}]},"oa":1,"volume":186,"author":[{"last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"last_name":"Gerykova Bujalkova","first_name":"Maria","full_name":"Gerykova Bujalkova, Maria"},{"full_name":"Smogavec, Mateja","first_name":"Mateja","last_name":"Smogavec"},{"full_name":"Schwarz, Lena A.","first_name":"Lena A.","last_name":"Schwarz"},{"last_name":"Gorkiewicz","first_name":"Sarah","full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"last_name":"Knittl-Frank","first_name":"Christian","full_name":"Knittl-Frank, Christian"},{"id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","full_name":"Tassinari, Marianna","first_name":"Marianna","last_name":"Tassinari"},{"last_name":"Maulide","first_name":"Nuno","full_name":"Maulide, Nuno"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"publication":"Cell","date_updated":"2024-02-07T08:03:32Z","ec_funded":1,"intvolume":"       186","publication_status":"published","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","file_date_updated":"2023-05-02T09:26:21Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","doi":"10.1016/j.cell.2023.02.037","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["0092-8674"]},"acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","_id":"12802","file":[{"checksum":"47e94fbe19e86505b429cb7a5b503ce6","file_id":"12889","creator":"dernst","content_type":"application/pdf","date_updated":"2023-05-02T09:26:21Z","relation":"main_file","file_size":15712841,"date_created":"2023-05-02T09:26:21Z","success":1,"access_level":"open_access","file_name":"2023_Cell_Knaus.pdf"}],"date_created":"2023-04-05T08:15:40Z","year":"2023","citation":{"mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>"},"abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}]},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"doi":"10.1038/s41467-023-38540-3","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","publication_status":"published","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","oa_version":"Published Version","article_processing_charge":"No","citation":{"ieee":"J. Hales <i>et al.</i>, “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","ama":"Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &#38; Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>."},"year":"2023","article_number":"3512","abstract":[{"lang":"eng","text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements."}],"date_created":"2023-08-09T13:06:59Z","_id":"13989","author":[{"full_name":"Hales, Jordyn","last_name":"Hales","first_name":"Jordyn"},{"full_name":"Bajpai, Utkarsh","last_name":"Bajpai","first_name":"Utkarsh"},{"full_name":"Liu, Tongtong","first_name":"Tongtong","last_name":"Liu"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"full_name":"Li, Mingda","first_name":"Mingda","last_name":"Li"},{"full_name":"Mitrano, Matteo","first_name":"Matteo","last_name":"Mitrano"},{"last_name":"Wang","first_name":"Yao","full_name":"Wang, Yao"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":14,"oa":1,"arxiv":1,"intvolume":"        14","date_updated":"2023-08-22T06:50:04Z","publication":"Nature Communications","day":"14","quality_controlled":"1","pmid":1,"publisher":"Springer Nature","type":"journal_article","date_published":"2023-06-14T00:00:00Z","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"language":[{"iso":"eng"}],"extern":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"month":"06","status":"public"},{"quality_controlled":"1","day":"08","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020"}],"external_id":{"pmid":["38070137"]},"date_published":"2023-12-08T00:00:00Z","type":"journal_article","publisher":"Elsevier","pmid":1,"month":"12","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"publication_status":"epub_ahead","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","oa_version":"Submitted Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"doi":"10.1016/j.xpro.2023.102771","scopus_import":"1","article_type":"review","publication_identifier":{"issn":["2666-1667"]},"acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. 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.","_id":"14683","date_created":"2023-12-13T11:48:05Z","article_number":"102771","year":"2023","citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2023). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2023.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>"},"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa":1,"volume":5,"author":[{"last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"publication":"STAR Protocols","ec_funded":1,"date_updated":"2023-12-18T08:06:14Z","intvolume":"         5"},{"day":"01","quality_controlled":"1","issue":"11","pmid":1,"publisher":"Cold Spring Harbor Laboratory","type":"journal_article","date_published":"2023-11-01T00:00:00Z","external_id":{"pmid":["37604585"]},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"status":"public","month":"11","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","publication_identifier":{"issn":["1943-0264"]},"article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"doi":"10.1101/cshperspect.a041447","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","abstract":[{"lang":"eng","text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life."}],"citation":{"ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>."},"article_number":"a041447","year":"2023","date_created":"2024-01-08T12:43:48Z","_id":"14742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"full_name":"Giménez, Mabel D.","last_name":"Giménez","first_name":"Mabel D."},{"first_name":"Mathieu","last_name":"Joron","full_name":"Joron, Mathieu"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"volume":15,"oa":1,"intvolume":"        15","date_updated":"2024-01-08T12:52:29Z","publication":"Cold Spring Harbor Perspectives in Biology","department":[{"_id":"NiBa"},{"_id":"BeVi"}]},{"intvolume":"        58","date_updated":"2024-01-16T08:56:36Z","publication":"Developmental Cell","department":[{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Westerich","first_name":"Kim Joana","full_name":"Westerich, Kim Joana"},{"last_name":"Tarbashevich","first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna"},{"full_name":"Schick, Jan","first_name":"Jan","last_name":"Schick"},{"first_name":"Antra","last_name":"Gupta","full_name":"Gupta, Antra"},{"full_name":"Zhu, Mingzhao","last_name":"Zhu","first_name":"Mingzhao"},{"full_name":"Hull, Kenneth","last_name":"Hull","first_name":"Kenneth"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"full_name":"Zeuschner, Dagmar","last_name":"Zeuschner","first_name":"Dagmar"},{"last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross-Thebing","first_name":"Theresa","full_name":"Gross-Thebing, Theresa"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"volume":58,"oa":1,"abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"citation":{"ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>."},"year":"2023","date_created":"2024-01-10T09:41:21Z","_id":"14781","publication_identifier":{"issn":["1534-5807"]},"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","article_type":"original","doi":"10.1016/j.devcel.2023.06.009","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"oa_version":"Preprint","article_processing_charge":"No","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","publication_status":"published","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"language":[{"iso":"eng"}],"status":"public","month":"09","pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2023-09-11T00:00:00Z","external_id":{"pmid":["37463577"]},"issue":"17","day":"11","page":"1578-1592.e5","quality_controlled":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27"}],"issue":"9","day":"01","quality_controlled":"1","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"09","publisher":"Elsevier","date_published":"2022-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code."}],"article_number":"100435","year":"2022","citation":{"ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>"},"_id":"12156","date_created":"2023-01-12T12:08:51Z","file":[{"file_size":2214944,"date_updated":"2023-01-24T12:14:10Z","date_created":"2023-01-24T12:14:10Z","relation":"main_file","file_name":"2022_CurrentBiology_Zoller.pdf","access_level":"open_access","success":1,"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","content_type":"application/pdf","file_id":"12362","creator":"dernst"}],"article_type":"original","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","publication_identifier":{"issn":["2452-3100"]},"doi":"10.1016/j.coisb.2022.100435","scopus_import":"1","file_date_updated":"2023-01-24T12:14:10Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","title":"Eukaryotic gene regulation at equilibrium, or non?","publication_status":"published","intvolume":"        31","publication":"Current Opinion in Systems Biology","date_updated":"2023-02-13T09:20:34Z","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"oa":1,"volume":31},{"article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-01-24T12:21:32Z","publication_status":"published","title":"Polygenic adaptation after a sudden change in environment","acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","publication_identifier":{"eissn":["2050-084X"]},"article_type":"original","scopus_import":"1","doi":"10.7554/elife.66697","date_created":"2023-01-12T12:09:00Z","file":[{"creator":"dernst","file_id":"12363","content_type":"application/pdf","checksum":"28de155b231ac1c8d4501c98b2fb359a","success":1,"access_level":"open_access","file_name":"2022_eLife_Hayward.pdf","relation":"main_file","file_size":18935612,"date_created":"2023-01-24T12:21:32Z","date_updated":"2023-01-24T12:21:32Z"}],"_id":"12157","abstract":[{"lang":"eng","text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species."}],"citation":{"ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"year":"2022","article_number":"66697","volume":11,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Laura","last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura"},{"first_name":"Guy","last_name":"Sella","full_name":"Sella, Guy"}],"date_updated":"2023-08-04T09:04:58Z","publication":"eLife","department":[{"_id":"NiBa"}],"intvolume":"        11","quality_controlled":"1","day":"26","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","type":"journal_article","external_id":{"isi":["000890735600001"]},"date_published":"2022-09-26T00:00:00Z","publisher":"eLife Sciences Publications","status":"public","isi":1,"month":"09","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"ddc":["570"],"language":[{"iso":"eng"}]},{"citation":{"ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326.","ieee":"C. Prehal <i>et al.</i>, “On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>","mla":"Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>, vol. 13, 6326, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>.","short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).","chicago":"Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin, Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger, and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>.","apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>"},"article_number":"6326","year":"2022","abstract":[{"text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells.","lang":"eng"}],"date_created":"2023-01-16T09:45:09Z","file":[{"creator":"dernst","file_id":"12411","content_type":"application/pdf","checksum":"5034336dbf0f860030ef745c08df9e0e","access_level":"open_access","success":1,"file_name":"2022_NatureCommunications_Prehal.pdf","file_size":4216931,"date_created":"2023-01-27T07:19:11Z","date_updated":"2023-01-27T07:19:11Z","relation":"main_file"}],"_id":"12208","scopus_import":"1","doi":"10.1038/s41467-022-33931-4","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for the access to the Austrian SAXS beamline and TU Graz for support through the Lead Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition, the authors acknowledge access to the D-22SANS beamline at the ILL neutron source. Electron microscopy measurements were performed at the Scientific Scenter for Optical and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P. and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F. is indebted to IST Austria for support. ","publication_identifier":{"issn":["2041-1723"]},"article_type":"original","title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-01-27T07:19:11Z","intvolume":"        13","department":[{"_id":"StFr"}],"date_updated":"2023-08-04T09:15:31Z","publication":"Nature Communications","author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"first_name":"Jean-Marc","last_name":"von Mentlen","full_name":"von Mentlen, Jean-Marc"},{"first_name":"Sara","last_name":"Drvarič Talian","full_name":"Drvarič Talian, Sara"},{"last_name":"Vizintin","first_name":"Alen","full_name":"Vizintin, Alen"},{"full_name":"Dominko, Robert","last_name":"Dominko","first_name":"Robert"},{"last_name":"Amenitsch","first_name":"Heinz","full_name":"Amenitsch, Heinz"},{"last_name":"Porcar","first_name":"Lionel","full_name":"Porcar, Lionel"},{"first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Wood","first_name":"Vanessa","full_name":"Wood, Vanessa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":13,"oa":1,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"24","quality_controlled":"1","ddc":["540"],"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"isi":1,"month":"10","status":"public","pmid":1,"publisher":"Springer Nature","type":"journal_article","date_published":"2022-10-24T00:00:00Z","external_id":{"pmid":["36280671"],"isi":["000871563700006"]}},{"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"09","isi":1,"publisher":"Springer Nature","date_published":"2022-09-05T00:00:00Z","external_id":{"isi":["000850348400025"]},"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288"}],"day":"05","quality_controlled":"1","intvolume":"        13","publication":"Nature Communications","date_updated":"2023-08-04T09:25:23Z","ec_funded":1,"department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Randriamanantsoa","first_name":"S.","full_name":"Randriamanantsoa, S."},{"full_name":"Papargyriou, A.","last_name":"Papargyriou","first_name":"A."},{"full_name":"Maurer, H. C.","last_name":"Maurer","first_name":"H. C."},{"first_name":"K.","last_name":"Peschke","full_name":"Peschke, K."},{"full_name":"Schuster, M.","last_name":"Schuster","first_name":"M."},{"full_name":"Zecchin, G.","first_name":"G.","last_name":"Zecchin"},{"first_name":"K.","last_name":"Steiger","full_name":"Steiger, K."},{"first_name":"R.","last_name":"Öllinger","full_name":"Öllinger, R."},{"last_name":"Saur","first_name":"D.","full_name":"Saur, D."},{"full_name":"Scheel, C.","first_name":"C.","last_name":"Scheel"},{"full_name":"Rad, R.","last_name":"Rad","first_name":"R."},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Reichert","first_name":"M.","full_name":"Reichert, M."},{"last_name":"Bausch","first_name":"A. R.","full_name":"Bausch, A. R."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13068"}]},"oa":1,"volume":13,"abstract":[{"text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis.","lang":"eng"}],"article_number":"5219","year":"2022","citation":{"mla":"Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>, vol. 13, 5219, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>.","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>","chicago":"Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>.","short":"S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, Nature Communications 13 (2022).","ieee":"S. Randriamanantsoa <i>et al.</i>, “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 13, 5219.","ama":"Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>"},"_id":"12217","file":[{"content_type":"application/pdf","file_id":"12416","creator":"dernst","checksum":"295261b5172274fd5b8f85a6a6058828","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","success":1,"access_level":"open_access","relation":"main_file","date_created":"2023-01-27T08:14:48Z","file_size":22645149,"date_updated":"2023-01-27T08:14:48Z"}],"date_created":"2023-01-16T09:46:53Z","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"acknowledgement":"A.R.B. acknowledges the financial support of the European Research Council (ERC) through the funding of the grant Principles of Integrin Mechanics and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project ID 201269156). E.H. was supported by the European Union (European Research Council Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project 12, project ID 329628492). M.R. was supported by the German Research Foundation (DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt DEAL.","doi":"10.1038/s41467-022-32806-y","scopus_import":"1","file_date_updated":"2023-01-27T08:14:48Z","article_processing_charge":"No","oa_version":"Published Version","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","publication_status":"published"},{"intvolume":"         5","publication":"Communications Biology","date_updated":"2023-08-04T09:25:59Z","department":[{"_id":"PreCl"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","full_name":"Muhia, Mary W","first_name":"Mary W","last_name":"Muhia"},{"last_name":"YuanXiang","first_name":"PingAn","full_name":"YuanXiang, PingAn"},{"last_name":"Sedlacik","first_name":"Jan","full_name":"Sedlacik, Jan"},{"first_name":"Jürgen R.","last_name":"Schwarz","full_name":"Schwarz, Jürgen R."},{"full_name":"Heisler, Frank F.","first_name":"Frank F.","last_name":"Heisler"},{"full_name":"Gromova, Kira V.","first_name":"Kira V.","last_name":"Gromova"},{"first_name":"Edda","last_name":"Thies","full_name":"Thies, Edda"},{"last_name":"Breiden","first_name":"Petra","full_name":"Breiden, Petra"},{"full_name":"Pechmann, Yvonne","first_name":"Yvonne","last_name":"Pechmann"},{"full_name":"Kreutz, Michael R.","first_name":"Michael R.","last_name":"Kreutz"},{"last_name":"Kneussel","first_name":"Matthias","full_name":"Kneussel, Matthias"}],"oa":1,"volume":5,"abstract":[{"lang":"eng","text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine <jats:italic>Mkln1</jats:italic> knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that <jats:italic>Mkln1</jats:italic> deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from <jats:italic>Mkln1</jats:italic> ablation."}],"year":"2022","article_number":"589","citation":{"apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>.","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>, vol. 5, 589, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>.","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>","ieee":"M. W. Muhia <i>et al.</i>, “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589."},"_id":"12224","file":[{"date_created":"2023-01-27T08:23:46Z","file_size":3968356,"date_updated":"2023-01-27T08:23:46Z","relation":"main_file","success":1,"access_level":"open_access","file_name":"2022_CommBiology_Muhia.pdf","checksum":"bd95be1e77090208b79bc45ea8785d0b","content_type":"application/pdf","creator":"dernst","file_id":"12417"}],"date_created":"2023-01-16T09:48:19Z","article_type":"original","acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"issn":["2399-3642"]},"doi":"10.1038/s42003-022-03446-1","scopus_import":"1","file_date_updated":"2023-01-27T08:23:46Z","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"06","isi":1,"publisher":"Springer Nature","date_published":"2022-06-15T00:00:00Z","external_id":{"isi":["000811777900003"]},"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"15","quality_controlled":"1"},{"author":[{"first_name":"Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","full_name":"Hino, Naoya"},{"first_name":"Kimiya","last_name":"Matsuda","full_name":"Matsuda, Kimiya"},{"full_name":"Jikko, Yuya","first_name":"Yuya","last_name":"Jikko"},{"last_name":"Maryu","first_name":"Gembu","full_name":"Maryu, Gembu"},{"last_name":"Sakai","first_name":"Katsuya","full_name":"Sakai, Katsuya"},{"last_name":"Imamura","first_name":"Ryu","full_name":"Imamura, Ryu"},{"full_name":"Tsukiji, Shinya","first_name":"Shinya","last_name":"Tsukiji"},{"last_name":"Aoki","first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro"},{"first_name":"Kenta","last_name":"Terai","full_name":"Terai, Kenta"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"full_name":"Matsuda, Michiyuki","first_name":"Michiyuki","last_name":"Matsuda"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":57,"intvolume":"        57","department":[{"_id":"CaHe"}],"publication":"Developmental Cell","date_updated":"2023-08-04T09:38:53Z","doi":"10.1016/j.devcel.2022.09.003","scopus_import":"1","article_type":"original","acknowledgement":"We thank the members of the Matsuda Laboratory for their helpful discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical assistance. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107 and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no. JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER (no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739 to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO. This work was partly supported by an Extramural Collaborative Research Grant of Cancer Research Institute, Kanazawa University.","publication_identifier":{"issn":["1534-5807"]},"publication_status":"published","title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","article_processing_charge":"No","oa_version":"None","year":"2022","citation":{"ista":"Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K, Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 57(19), 2290–2304.e7.","ieee":"N. Hino <i>et al.</i>, “A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration,” <i>Developmental Cell</i>, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.","ama":"Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. 2022;57(19):2290-2304.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>","mla":"Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>.","short":"N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji, K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57 (2022) 2290–2304.e7.","apa":"Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda, M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>","chicago":"Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>."},"abstract":[{"lang":"eng","text":"Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration."}],"_id":"12238","date_created":"2023-01-16T09:51:39Z","publisher":"Elsevier","pmid":1,"external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"date_published":"2022-10-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"month":"10","isi":1,"status":"public","page":"2290-2304.e7","day":"01","quality_controlled":"1","issue":"19"},{"quality_controlled":"1","day":"01","issue":"9","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"isi":["000856482800001"]},"date_published":"2022-09-01T00:00:00Z","type":"journal_article","publisher":"Embo Press","month":"09","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","publication_status":"published","file_date_updated":"2023-01-30T09:49:55Z","oa_version":"Published Version","article_processing_charge":"No","doi":"10.15252/msb.202110490","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1744-4292"]},"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","_id":"12261","date_created":"2023-01-16T09:58:34Z","file":[{"checksum":"8b1d8f5ea20c8408acf466435fb6ae01","content_type":"application/pdf","creator":"dernst","file_id":"12446","file_size":1098812,"relation":"main_file","date_updated":"2023-01-30T09:49:55Z","date_created":"2023-01-30T09:49:55Z","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","success":1,"access_level":"open_access"}],"article_number":"e10490","year":"2022","citation":{"ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” <i>Molecular Systems Biology</i>, vol. 18, no. 9. Embo Press, 2022.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. 2022;18(9). doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &#38; Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>, vol. 18, no. 9, e10490, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>."},"abstract":[{"lang":"eng","text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"volume":18,"author":[{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","first_name":"Andreas","last_name":"Angermayr"},{"first_name":"Tin Yau","last_name":"Pang","full_name":"Pang, Tin Yau"},{"full_name":"Chevereau, Guillaume","first_name":"Guillaume","last_name":"Chevereau"},{"last_name":"Mitosch","first_name":"Karin","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lercher, Martin J","last_name":"Lercher","first_name":"Martin J"},{"last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToBo"}],"publication":"Molecular Systems Biology","date_updated":"2023-08-04T09:51:49Z","intvolume":"        18"},{"publisher":"eLife Sciences Publications","pmid":1,"date_published":"2022-09-15T00:00:00Z","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"month":"09","isi":1,"status":"public","day":"15","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus"}],"author":[{"last_name":"Sumser","first_name":"Anton L","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881"},{"first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa":1,"volume":11,"intvolume":"        11","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"publication":"eLife","date_updated":"2023-08-04T10:29:48Z","ec_funded":1,"doi":"10.7554/elife.79848","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["2050-084X"]},"acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","publication_status":"published","file_date_updated":"2023-01-30T11:50:53Z","article_processing_charge":"No","oa_version":"Published Version","article_number":"79848","year":"2022","citation":{"ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>."},"abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"_id":"12288","date_created":"2023-01-16T10:04:15Z","file":[{"relation":"main_file","file_size":8506811,"date_created":"2023-01-30T11:50:53Z","date_updated":"2023-01-30T11:50:53Z","file_name":"2022_eLife_Sumser.pdf","access_level":"open_access","success":1,"checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","file_id":"12463","creator":"dernst","content_type":"application/pdf"}]},{"abstract":[{"text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.","lang":"eng"}],"year":"2022","citation":{"short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>.","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022.","ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>"},"_id":"12670","date_created":"2023-02-23T09:15:57Z","article_type":"review","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"main_file_link":[{"url":"https://doi.org/10.1111/jipb.13422","open_access":"1"}],"doi":"10.1111/jipb.13422","scopus_import":"1","article_processing_charge":"No","oa_version":"Published Version","title":"DNA methylation dynamics during germline development","publication_status":"published","intvolume":"        64","publication":"Journal of Integrative Plant Biology","date_updated":"2023-05-08T10:59:00Z","department":[{"_id":"XiFe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"oa":1,"volume":64,"issue":"12","day":"07","page":"2240-2251","quality_controlled":"1","keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"extern":"1","language":[{"iso":"eng"}],"status":"public","month":"12","publisher":"Wiley","pmid":1,"external_id":{"pmid":["36478632"]},"date_published":"2022-12-07T00:00:00Z","type":"journal_article"},{"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"04","pmid":1,"publisher":"The Royal Society","type":"journal_article","date_published":"2022-04-11T00:00:00Z","external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"has_accepted_license":"1","issue":"1848","day":"11","quality_controlled":"1","intvolume":"       377","date_updated":"2025-05-26T09:05:09Z","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya"}],"volume":377,"oa":1,"related_material":{"record":[{"id":"14711","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"citation":{"ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>."},"year":"2022","date_created":"2022-02-21T16:08:10Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","date_updated":"2022-08-02T06:14:32Z","date_created":"2022-08-02T06:14:32Z","relation":"main_file","file_size":1349672,"file_id":"11719","creator":"dernst","content_type":"application/pdf","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d"}],"_id":"10787","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"article_type":"original","scopus_import":"1","doi":"10.1098/rstb.2021.0009","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2022-08-02T06:14:32Z","publication_status":"published","title":"The response of a metapopulation to a changing environment"},{"status":"public","month":"04","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"date_published":"2022-04-05T00:00:00Z","type":"journal_article","publisher":"Elsevier","pmid":1,"project":[{"_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","call_identifier":"H2020"},{"grant_number":"I04205","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"1","quality_controlled":"1","day":"05","publication":"Cell Reports","ec_funded":1,"date_updated":"2024-03-25T23:30:25Z","department":[{"_id":"JoDa"},{"_id":"GaNo"}],"intvolume":"        39","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12364"}]},"oa":1,"volume":39,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Carlo Emanuele","last_name":"Villa","full_name":"Villa, Carlo Emanuele"},{"last_name":"Cheroni","first_name":"Cristina","full_name":"Cheroni, Cristina"},{"first_name":"Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"last_name":"López-Tóbon","first_name":"Alejandro","full_name":"López-Tóbon, Alejandro"},{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara","first_name":"Bárbara","last_name":"Oliveira"},{"first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto"},{"id":"365A65F8-F248-11E8-B48F-1D18A9856A87","full_name":"Yahya, Aysan Çerağ","first_name":"Aysan Çerağ","last_name":"Yahya"},{"first_name":"Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"last_name":"Gabriele","first_name":"Michele","full_name":"Gabriele, Michele"},{"last_name":"Tavakoli","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"first_name":"Mariano","last_name":"Gabitto","full_name":"Gabitto, Mariano"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"first_name":"Giuseppe","last_name":"Testa","full_name":"Testa, Giuseppe"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"_id":"11160","file":[{"checksum":"b4e8d68f0268dec499af333e6fd5d8e1","content_type":"application/pdf","creator":"dernst","file_id":"11164","file_size":"7808644","date_updated":"2022-04-15T09:06:25Z","relation":"main_file","date_created":"2022-04-15T09:06:25Z","file_name":"2022_CellReports_Villa.pdf","access_level":"open_access","success":1}],"date_created":"2022-04-15T09:03:10Z","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"year":"2022","article_number":"110615","citation":{"mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022."},"file_date_updated":"2022-04-15T09:06:25Z","oa_version":"Published Version","article_processing_charge":"Yes","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","publication_status":"published","article_type":"original","publication_identifier":{"issn":["2211-1247"]},"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","doi":"10.1016/j.celrep.2022.110615"},{"day":"06","page":"P2375-2389","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"issue":"11","publisher":"Elsevier","pmid":1,"date_published":"2022-06-06T00:00:00Z","external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"type":"journal_article","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"06","isi":1,"article_type":"original","acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","publication_identifier":{"issn":["0960-9822"]},"doi":"10.1016/j.cub.2022.04.024","scopus_import":"1","file_date_updated":"2022-08-05T06:29:18Z","oa_version":"Published Version","article_processing_charge":"No","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","publication_status":"published","abstract":[{"lang":"eng","text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall."}],"year":"2022","citation":{"ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>."},"_id":"11351","date_created":"2022-05-04T06:22:06Z","file":[{"date_updated":"2022-08-05T06:29:18Z","relation":"main_file","date_created":"2022-08-05T06:29:18Z","file_size":12827717,"file_name":"2022_CurrentBiology_Nicolas.pdf","access_level":"open_access","success":1,"checksum":"af3f24d97c016d844df237abef987639","content_type":"application/pdf","creator":"dernst","file_id":"11730"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Nicolas, William J.","last_name":"Nicolas","first_name":"William J."},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","last_name":"Fäßler","first_name":"Florian"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jensen, Grant","last_name":"Jensen","first_name":"Grant"},{"last_name":"Meyerowitz","first_name":"Elliot","full_name":"Meyerowitz, Elliot"}],"oa":1,"volume":32,"intvolume":"        32","publication":"Current Biology","date_updated":"2023-08-03T07:05:36Z","department":[{"_id":"FlSc"}]},{"doi":"10.1038/s41467-022-30301-y","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","title":"In vitro reconstitution of Escherichia coli divisome activation","publication_status":"published","file_date_updated":"2022-05-13T09:10:51Z","oa_version":"Published Version","article_processing_charge":"No","article_number":"2635","year":"2022","citation":{"short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"_id":"11373","file":[{"creator":"dernst","file_id":"11374","content_type":"application/pdf","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","access_level":"open_access","success":1,"file_name":"2022_NatureCommunications_Radler.pdf","date_updated":"2022-05-13T09:10:51Z","date_created":"2022-05-13T09:10:51Z","relation":"main_file","file_size":6945191}],"date_created":"2022-05-13T09:06:28Z","author":[{"last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "},{"last_name":"Baranova","first_name":"Natalia S.","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","first_name":"Paulo R","last_name":"Dos Santos Caldas"},{"last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lopez Pelegrin","first_name":"Maria D","full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David","first_name":"David","last_name":"Michalik"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"id":"14280","relation":"dissertation_contains","status":"public"},{"relation":"research_data","status":"public","id":"10934"}]},"volume":13,"intvolume":"        13","department":[{"_id":"MaLo"}],"publication":"Nature Communications","ec_funded":1,"date_updated":"2024-02-21T12:35:18Z","day":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"publisher":"Springer Nature","date_published":"2022-05-12T00:00:00Z","external_id":{"isi":["000795171100037"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"month":"05","isi":1,"status":"public"}]