[{"publication":"Cell","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"       187","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","issue":"1","oa":1,"date_updated":"2024-01-22T13:43:40Z","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","type":"journal_article","status":"public","pmid":1,"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"month":"01","file":[{"file_id":"14874","file_name":"2024_Cell_Kuhn.pdf","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","success":1,"date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-22T13:41:41Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":13194060,"access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"04","author":[{"last_name":"Kuhn","first_name":"Andre","full_name":"Kuhn, Andre"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"last_name":"Mutte","first_name":"Sumanth","full_name":"Mutte, Sumanth"},{"last_name":"Dubey","first_name":"Shiv Mani","full_name":"Dubey, Shiv Mani"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"first_name":"Sjef","full_name":"Boeren, Sjef","last_name":"Boeren"},{"last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","full_name":"Monzer, Aline"},{"first_name":"Jasper","full_name":"Koehorst, Jasper","last_name":"Koehorst"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"last_name":"Nishihama","first_name":"Ryuichi","full_name":"Nishihama, Ryuichi"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych"},{"full_name":"Sprakel, Joris","first_name":"Joris","last_name":"Sprakel"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"doi":"10.1016/j.cell.2023.11.021","_id":"14826","article_type":"original","file_date_updated":"2024-01-22T13:41:41Z","ec_funded":1,"year":"2024","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.","keyword":["General Biochemistry","Genetics and Molecular Biology"],"citation":{"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>.","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>.","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.","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.","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>","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>"},"date_created":"2024-01-17T12:45:40Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2024-01-04T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":187,"department":[{"_id":"JiFr"}],"page":"130-148.e17","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["580"],"abstract":[{"lang":"eng","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."}],"external_id":{"pmid":["38128538"]},"publication_status":"published"},{"intvolume":"        13","has_accepted_license":"1","oa":1,"date_updated":"2024-02-28T12:29:43Z","article_processing_charge":"Yes","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","publication":"eLife","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["2050-084X"]},"day":"21","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257"},{"first_name":"Ivana","full_name":"Matijevic, Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"status":"public","type":"journal_article","ec_funded":1,"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","year":"2024","date_created":"2024-02-27T07:10:11Z","citation":{"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>","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>.","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>","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024)."},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"doi":"10.7554/elife.68993","article_type":"original","_id":"15033","ddc":["580"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","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."}],"publication_status":"epub_ahead","publisher":"eLife Sciences Publications","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2024-02-21T00:00:00Z","department":[{"_id":"JiFr"}],"volume":13,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}]},{"language":[{"iso":"eng"}],"publication":"FEBS Letters","title":"In vitro reconstitution of small GTPase regulation","date_updated":"2023-08-16T08:32:29Z","oa":1,"issue":"6","article_processing_charge":"Yes (via OA deal)","intvolume":"       597","has_accepted_license":"1","scopus_import":"1","isi":1,"pmid":1,"type":"journal_article","status":"public","author":[{"first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Albert","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","last_name":"Auer"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel"},{"full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","last_name":"Budiman","id":"55380f95-15b2-11ec-abd3-aff8e230696b"},{"full_name":"Kowalski, Lukasz M","first_name":"Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","last_name":"Kowalski"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","first_name":"Ivana","full_name":"Matijevic, Ivana"}],"oa_version":"Published Version","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":3148143,"relation":"main_file","creator":"dernst","date_updated":"2023-08-16T08:31:04Z","date_created":"2023-08-16T08:31:04Z","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","file_name":"2023_FEBSLetters_Loose.pdf","file_id":"14063","success":1}],"month":"03","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"file_date_updated":"2023-08-16T08:31:04Z","_id":"12163","article_type":"review","doi":"10.1002/1873-3468.14540","date_created":"2023-01-12T12:09:58Z","citation":{"apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>."},"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","year":"2023","page":"762-777","department":[{"_id":"MaLo"}],"quality_controlled":"1","volume":597,"publisher":"Wiley","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2023-03-01T00:00:00Z","publication_status":"published","external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"}},{"author":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","first_name":"Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"month":"02","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"file":[{"file_size":10045006,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_updated":"2023-03-16T07:58:16Z","date_created":"2023-03-16T07:58:16Z","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","checksum":"4e7069845e3dad22bb44fb71ec624c60","file_id":"12728","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"01","status":"public","type":"journal_article","issue":"1","article_processing_charge":"No","oa":1,"date_updated":"2023-08-01T12:55:32Z","title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"        51","language":[{"iso":"eng"}],"publication":"Biochemical Society Transactions","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"external_id":{"isi":["000926043100001"]},"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"date_published":"2023-02-01T00:00:00Z","publisher":"Portland Press","quality_controlled":"1","volume":51,"department":[{"_id":"FlSc"}],"page":"87-99","year":"2023","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","keyword":["Biochemistry"],"citation":{"apa":"Fäßler, F., Javoor, M., &#38; Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” <i>Biochemical Society Transactions</i>, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. <i>Biochemical Society Transactions</i>. 2023;51(1):87-99. doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:<a href=\"https://doi.org/10.1042/bst20220221\">10.1042/bst20220221</a>.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” <i>Biochemical Society Transactions</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/bst20220221\">https://doi.org/10.1042/bst20220221</a>."},"date_created":"2023-01-27T10:08:19Z","_id":"12421","article_type":"original","file_date_updated":"2023-03-16T07:58:16Z","doi":"10.1042/bst20220221"},{"status":"public","type":"journal_article","file":[{"date_updated":"2023-05-02T09:26:21Z","date_created":"2023-05-02T09:26:21Z","checksum":"47e94fbe19e86505b429cb7a5b503ce6","file_name":"2023_Cell_Knaus.pdf","file_id":"12889","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":15712841,"creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"27","month":"04","publication_identifier":{"issn":["0092-8674"]},"author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"},{"first_name":"Bernadette","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","orcid":"0000-0003-1843-3173"},{"full_name":"Malzl, Daniel","first_name":"Daniel","last_name":"Malzl"},{"first_name":"Maria","full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova"},{"first_name":"Mateja","full_name":"Smogavec, Mateja","last_name":"Smogavec"},{"full_name":"Schwarz, Lena A.","first_name":"Lena A.","last_name":"Schwarz"},{"first_name":"Sarah","full_name":"Gorkiewicz, Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"last_name":"Knittl-Frank","first_name":"Christian","full_name":"Knittl-Frank, Christian"},{"id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","last_name":"Tassinari","first_name":"Marianna","full_name":"Tassinari, Marianna"},{"last_name":"Maulide","first_name":"Nuno","full_name":"Maulide, Nuno"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"first_name":"Jörg","full_name":"Menche, Jörg","last_name":"Menche"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"publication":"Cell","language":[{"iso":"eng"}],"intvolume":"       186","scopus_import":"1","has_accepted_license":"1","isi":1,"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","issue":"9","article_processing_charge":"Yes (via OA deal)","oa":1,"date_updated":"2024-02-07T08:03:32Z","quality_controlled":"1","volume":186,"page":"1950-1967.e25","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"date_published":"2023-04-27T00:00:00Z","publisher":"Elsevier","project":[{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"}],"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"}],"external_id":{"isi":["000991468700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","doi":"10.1016/j.cell.2023.02.037","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"article_type":"original","_id":"12802","file_date_updated":"2023-05-02T09:26:21Z","related_material":{"record":[{"id":"13107","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}]},"ec_funded":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"citation":{"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>","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>","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.","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.","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>.","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.","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>."},"date_created":"2023-04-05T08:15:40Z","year":"2023","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."},{"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"06","file":[{"creator":"cchlebak","file_size":3155843,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"e07d5323f9c0e5cbd1ad6453f29440ab","file_name":"2023_JACS_Bunting.pdf","file_id":"13219","success":1,"date_updated":"2023-07-12T10:22:04Z","date_created":"2023-07-12T10:22:04Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"30","oa_version":"Published Version","author":[{"full_name":"Bunting, Rhys","first_name":"Rhys","orcid":"0000-0001-6928-074X","last_name":"Bunting","id":"91deeae8-1207-11ec-b130-c194ad5b50c6"},{"last_name":"Wodaczek","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","orcid":"0009-0000-1457-795X","first_name":"Felix","full_name":"Wodaczek, Felix"},{"first_name":"Tina","full_name":"Torabi, Tina","last_name":"Torabi"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"status":"public","type":"journal_article","pmid":1,"isi":1,"intvolume":"       145","has_accepted_license":"1","issue":"27","article_processing_charge":"Yes (via OA deal)","oa":1,"date_updated":"2023-10-11T08:45:10Z","title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["540"],"abstract":[{"lang":"eng","text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude."}],"external_id":{"isi":["001020623900001"],"pmid":["37390457"]},"publication_status":"published","date_published":"2023-06-30T00:00:00Z","publisher":"American Chemical Society","volume":145,"quality_controlled":"1","page":"14894-14902","department":[{"_id":"MaIb"},{"_id":"BiCh"}],"year":"2023","acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_created":"2023-07-12T09:16:40Z","citation":{"ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. 2023;145(27):14894-14902. doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>.","mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>.","ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.","apa":"Bunting, R., Wodaczek, F., Torabi, T., &#38; Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>"},"doi":"10.1021/jacs.3c04030","_id":"13216","article_type":"original","file_date_updated":"2023-07-12T10:22:04Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c11973"}],"oa_version":"Published Version","day":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"author":[{"first_name":"Jinhua","full_name":"Wang, Jinhua","last_name":"Wang"},{"first_name":"Tzuf Shay","full_name":"Peled, Tzuf Shay","last_name":"Peled"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal"}],"pmid":1,"status":"public","type":"journal_article","intvolume":"       145","scopus_import":"1","title":"Photocleavable anionic glues for light-responsive nanoparticle aggregates","oa":1,"date_updated":"2023-08-02T10:44:22Z","issue":"7","article_processing_charge":"No","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"external_id":{"pmid":["36757850"]},"abstract":[{"lang":"eng","text":"Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus."}],"publication_status":"published","page":"4098-4108","extern":"1","volume":145,"quality_controlled":"1","publisher":"American Chemical Society","date_published":"2023-02-09T00:00:00Z","citation":{"chicago":"Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.2c11973\">https://doi.org/10.1021/jacs.2c11973</a>.","mla":"Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 7, American Chemical Society, 2023, pp. 4098–108, doi:<a href=\"https://doi.org/10.1021/jacs.2c11973\">10.1021/jacs.2c11973</a>.","ista":"Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108.","short":"J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145 (2023) 4098–4108.","ieee":"J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive nanoparticle aggregates,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 7. American Chemical Society, pp. 4098–4108, 2023.","ama":"Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive nanoparticle aggregates. <i>Journal of the American Chemical Society</i>. 2023;145(7):4098-4108. doi:<a href=\"https://doi.org/10.1021/jacs.2c11973\">10.1021/jacs.2c11973</a>","apa":"Wang, J., Peled, T. S., &#38; Klajn, R. (2023). Photocleavable anionic glues for light-responsive nanoparticle aggregates. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.2c11973\">https://doi.org/10.1021/jacs.2c11973</a>"},"date_created":"2023-08-01T09:33:08Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"year":"2023","doi":"10.1021/jacs.2c11973","article_type":"original","_id":"13354"},{"publication_status":"published","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."}],"external_id":{"pmid":["37316515"],"arxiv":["2209.02283"]},"quality_controlled":"1","volume":14,"extern":"1","date_published":"2023-06-14T00:00:00Z","publisher":"Springer Nature","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"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>.","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.","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>.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","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.","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>","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>"},"date_created":"2023-08-09T13:06:59Z","year":"2023","article_number":"3512","_id":"13989","article_type":"original","doi":"10.1038/s41467-023-38540-3","arxiv":1,"author":[{"full_name":"Hales, Jordyn","first_name":"Jordyn","last_name":"Hales"},{"last_name":"Bajpai","full_name":"Bajpai, Utkarsh","first_name":"Utkarsh"},{"last_name":"Liu","full_name":"Liu, Tongtong","first_name":"Tongtong"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova"},{"full_name":"Li, Mingda","first_name":"Mingda","last_name":"Li"},{"last_name":"Mitrano","first_name":"Matteo","full_name":"Mitrano, Matteo"},{"full_name":"Wang, Yao","first_name":"Yao","last_name":"Wang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"oa_version":"Published Version","month":"06","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","status":"public","pmid":1,"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","article_processing_charge":"No","date_updated":"2023-08-22T06:50:04Z","oa":1,"scopus_import":"1","intvolume":"        14","language":[{"iso":"eng"}],"publication":"Nature Communications"},{"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","issue":"1","article_processing_charge":"No","oa":1,"date_updated":"2023-12-18T08:06:14Z","scopus_import":"1","intvolume":"         5","language":[{"iso":"eng"}],"publication":"STAR Protocols","author":[{"full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giselle T","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"day":"08","oa_version":"Submitted Version","month":"12","publication_identifier":{"issn":["2666-1667"]},"status":"public","type":"journal_article","pmid":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"citation":{"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.","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>","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>.","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>.","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.","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>"},"date_created":"2023-12-13T11:48:05Z","year":"2023","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.","article_number":"102771","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"_id":"14683","article_type":"review","doi":"10.1016/j.xpro.2023.102771","publication_status":"epub_ahead","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"}],"external_id":{"pmid":["38070137"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"volume":5,"quality_controlled":"1","department":[{"_id":"SiHi"}],"date_published":"2023-12-08T00:00:00Z","publisher":"Elsevier"},{"article_number":"a041447","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_created":"2024-01-08T12:43:48Z","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.","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).","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.","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>.","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>.","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>"},"year":"2023","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.","doi":"10.1101/cshperspect.a041447","_id":"14742","article_type":"original","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."}],"external_id":{"pmid":["37604585"]},"publication_status":"published","quality_controlled":"1","volume":15,"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_published":"2023-11-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory","scopus_import":"1","intvolume":"        15","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","article_processing_charge":"No","issue":"11","oa":1,"date_updated":"2024-01-08T12:52:29Z","publication":"Cold Spring Harbor Perspectives in Biology","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"day":"01","oa_version":"Published Version","publication_identifier":{"issn":["1943-0264"]},"month":"11","author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"last_name":"Giménez","full_name":"Giménez, Mabel D.","first_name":"Mabel D."},{"last_name":"Joron","first_name":"Mathieu","full_name":"Joron, Mathieu"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"first_name":"Jeremy B.","full_name":"Searle, Jeremy B.","last_name":"Searle"},{"full_name":"Walden, Nora","first_name":"Nora","last_name":"Walden"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"}],"status":"public","type":"journal_article","pmid":1},{"citation":{"chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","apa":"Danzl, J. G., &#38; Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>"},"date_created":"2024-01-10T08:07:15Z","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"year":"2023","related_material":{"record":[{"status":"public","relation":"extended_version","id":"13267"}]},"_id":"14770","article_type":"letter_note","doi":"10.1038/s41592-023-01937-5","publication_status":"published","external_id":{"isi":["001025621500002"]},"abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"department":[{"_id":"JoDa"}],"page":"1141-1142","volume":20,"quality_controlled":"1","publisher":"Springer Nature","date_published":"2023-08-01T00:00:00Z","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","date_updated":"2024-01-10T08:37:48Z","article_processing_charge":"No","issue":"8","scopus_import":"1","intvolume":"        20","isi":1,"language":[{"iso":"eng"}],"publication":"Nature Methods","author":[{"first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431"}],"oa_version":"None","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"month":"08","status":"public","type":"journal_article"},{"month":"09","publication_identifier":{"issn":["1534-5807"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"day":"11","oa_version":"Preprint","author":[{"full_name":"Westerich, Kim Joana","first_name":"Kim Joana","last_name":"Westerich"},{"full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna","last_name":"Tarbashevich"},{"first_name":"Jan","full_name":"Schick, Jan","last_name":"Schick"},{"first_name":"Antra","full_name":"Gupta, Antra","last_name":"Gupta"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"first_name":"Kenneth","full_name":"Hull, Kenneth","last_name":"Hull"},{"last_name":"Romo","full_name":"Romo, Daniel","first_name":"Daniel"},{"first_name":"Dagmar","full_name":"Zeuschner, Dagmar","last_name":"Zeuschner"},{"full_name":"Goudarzi, Mohammad","first_name":"Mohammad","last_name":"Goudarzi","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross-Thebing","full_name":"Gross-Thebing, Theresa","first_name":"Theresa"},{"last_name":"Raz","first_name":"Erez","full_name":"Raz, Erez"}],"status":"public","type":"journal_article","pmid":1,"intvolume":"        58","issue":"17","article_processing_charge":"No","oa":1,"date_updated":"2024-01-16T08:56:36Z","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","publication":"Developmental Cell","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"external_id":{"pmid":["37463577"]},"publication_status":"published","date_published":"2023-09-11T00:00:00Z","publisher":"Elsevier","volume":58,"quality_controlled":"1","page":"1578-1592.e5","department":[{"_id":"Bio"}],"year":"2023","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.","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"date_created":"2024-01-10T09:41:21Z","citation":{"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>.","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>.","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.","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.","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.","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>","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>"},"doi":"10.1016/j.devcel.2023.06.009","article_type":"original","_id":"14781"},{"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"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.","lang":"eng"}],"publication_status":"published","publisher":"Elsevier","date_published":"2022-09-01T00:00:00Z","department":[{"_id":"GaTk"}],"volume":31,"quality_controlled":"1","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"article_number":"100435","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. ","year":"2022","date_created":"2023-01-12T12:08:51Z","citation":{"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>","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","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.","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>","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>.","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>."},"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"doi":"10.1016/j.coisb.2022.100435","file_date_updated":"2023-01-24T12:14:10Z","article_type":"original","_id":"12156","month":"09","publication_identifier":{"issn":["2452-3100"]},"oa_version":"Published Version","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2022_CurrentBiology_Zoller.pdf","file_id":"12362","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","success":1,"date_updated":"2023-01-24T12:14:10Z","date_created":"2023-01-24T12:14:10Z","creator":"dernst","relation":"main_file","file_size":2214944,"access_level":"open_access","content_type":"application/pdf"}],"author":[{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"type":"journal_article","status":"public","has_accepted_license":"1","intvolume":"        31","scopus_import":"1","date_updated":"2023-02-13T09:20:34Z","oa":1,"issue":"9","article_processing_charge":"Yes (via OA deal)","title":"Eukaryotic gene regulation at equilibrium, or non?","publication":"Current Opinion in Systems Biology","language":[{"iso":"eng"}]},{"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_created":"2023-01-12T12:09:00Z","citation":{"short":"L. Hayward, G. Sella, ELife 11 (2022).","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","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>","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>.","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>.","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","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>"},"year":"2022","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","article_number":"66697","_id":"12157","article_type":"original","file_date_updated":"2023-01-24T12:21:32Z","doi":"10.7554/elife.66697","publication_status":"published","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."}],"external_id":{"isi":["000890735600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"volume":11,"quality_controlled":"1","department":[{"_id":"NiBa"}],"date_published":"2022-09-26T00:00:00Z","publisher":"eLife Sciences Publications","title":"Polygenic adaptation after a sudden change in environment","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:04:58Z","scopus_import":"1","intvolume":"        11","has_accepted_license":"1","isi":1,"language":[{"iso":"eng"}],"publication":"eLife","author":[{"last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura","full_name":"Hayward, Laura"},{"last_name":"Sella","first_name":"Guy","full_name":"Sella, Guy"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"28de155b231ac1c8d4501c98b2fb359a","file_id":"12363","file_name":"2022_eLife_Hayward.pdf","date_created":"2023-01-24T12:21:32Z","date_updated":"2023-01-24T12:21:32Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":18935612}],"oa_version":"Published Version","day":"26","publication_identifier":{"eissn":["2050-084X"]},"month":"09","status":"public","type":"journal_article"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["540"],"abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000871563700006"],"pmid":["36280671"]},"publication_status":"published","date_published":"2022-10-24T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","volume":13,"department":[{"_id":"StFr"}],"article_number":"6326","year":"2022","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. ","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"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>","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.","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>.","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>.","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>","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.","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)."},"date_created":"2023-01-16T09:45:09Z","doi":"10.1038/s41467-022-33931-4","_id":"12208","article_type":"original","file_date_updated":"2023-01-27T07:19:11Z","month":"10","publication_identifier":{"issn":["2041-1723"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":4216931,"creator":"dernst","date_created":"2023-01-27T07:19:11Z","date_updated":"2023-01-27T07:19:11Z","success":1,"file_name":"2022_NatureCommunications_Prehal.pdf","checksum":"5034336dbf0f860030ef745c08df9e0e","file_id":"12411"}],"oa_version":"Published Version","day":"24","author":[{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"first_name":"Jean-Marc","full_name":"von Mentlen, Jean-Marc","last_name":"von Mentlen"},{"last_name":"Drvarič Talian","first_name":"Sara","full_name":"Drvarič Talian, Sara"},{"last_name":"Vizintin","first_name":"Alen","full_name":"Vizintin, Alen"},{"last_name":"Dominko","full_name":"Dominko, Robert","first_name":"Robert"},{"last_name":"Amenitsch","full_name":"Amenitsch, Heinz","first_name":"Heinz"},{"full_name":"Porcar, Lionel","first_name":"Lionel","last_name":"Porcar"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Wood, Vanessa","first_name":"Vanessa","last_name":"Wood"}],"status":"public","type":"journal_article","pmid":1,"isi":1,"has_accepted_license":"1","intvolume":"        13","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-08-04T09:15:31Z","oa":1,"title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","publication":"Nature Communications","language":[{"iso":"eng"}]},{"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"}],"external_id":{"isi":["000850348400025"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","quality_controlled":"1","volume":13,"department":[{"_id":"EdHa"}],"date_published":"2022-09-05T00:00:00Z","publisher":"Springer Nature","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"related_material":{"record":[{"status":"public","id":"13068","relation":"research_data"}]},"article_number":"5219","ec_funded":1,"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_created":"2023-01-16T09:46:53Z","citation":{"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.","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>","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).","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>.","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.","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>"},"year":"2022","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","article_type":"original","_id":"12217","file_date_updated":"2023-01-27T08:14:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":22645149,"relation":"main_file","creator":"dernst","date_updated":"2023-01-27T08:14:48Z","date_created":"2023-01-27T08:14:48Z","checksum":"295261b5172274fd5b8f85a6a6058828","file_id":"12416","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","success":1}],"oa_version":"Published Version","day":"05","month":"09","publication_identifier":{"issn":["2041-1723"]},"author":[{"last_name":"Randriamanantsoa","full_name":"Randriamanantsoa, S.","first_name":"S."},{"first_name":"A.","full_name":"Papargyriou, A.","last_name":"Papargyriou"},{"first_name":"H. C.","full_name":"Maurer, H. C.","last_name":"Maurer"},{"first_name":"K.","full_name":"Peschke, K.","last_name":"Peschke"},{"last_name":"Schuster","full_name":"Schuster, M.","first_name":"M."},{"last_name":"Zecchin","full_name":"Zecchin, G.","first_name":"G."},{"last_name":"Steiger","full_name":"Steiger, K.","first_name":"K."},{"first_name":"R.","full_name":"Öllinger, R.","last_name":"Öllinger"},{"first_name":"D.","full_name":"Saur, D.","last_name":"Saur"},{"last_name":"Scheel","first_name":"C.","full_name":"Scheel, C."},{"last_name":"Rad","first_name":"R.","full_name":"Rad, R."},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"full_name":"Reichert, M.","first_name":"M.","last_name":"Reichert"},{"last_name":"Bausch","first_name":"A. R.","full_name":"Bausch, A. R."}],"type":"journal_article","status":"public","intvolume":"        13","scopus_import":"1","has_accepted_license":"1","isi":1,"title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:25:23Z","publication":"Nature Communications","language":[{"iso":"eng"}]},{"date_published":"2022-06-15T00:00:00Z","publisher":"Springer Nature","volume":5,"quality_controlled":"1","department":[{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000811777900003"]},"publication_status":"published","doi":"10.1038/s42003-022-03446-1","article_type":"original","_id":"12224","file_date_updated":"2023-01-27T08:23:46Z","article_number":"589","year":"2022","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.","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"date_created":"2023-01-16T09:48:19Z","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>","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>.","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.","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>.","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.","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)."},"type":"journal_article","status":"public","month":"06","publication_identifier":{"issn":["2399-3642"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":3968356,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"bd95be1e77090208b79bc45ea8785d0b","file_id":"12417","file_name":"2022_CommBiology_Muhia.pdf","success":1,"date_updated":"2023-01-27T08:23:46Z","date_created":"2023-01-27T08:23:46Z"}],"day":"15","oa_version":"Published Version","author":[{"full_name":"Muhia, Mary W","first_name":"Mary W","last_name":"Muhia","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d"},{"full_name":"YuanXiang, PingAn","first_name":"PingAn","last_name":"YuanXiang"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"last_name":"Schwarz","first_name":"Jürgen R.","full_name":"Schwarz, Jürgen R."},{"first_name":"Frank F.","full_name":"Heisler, Frank F.","last_name":"Heisler"},{"last_name":"Gromova","full_name":"Gromova, Kira V.","first_name":"Kira V."},{"first_name":"Edda","full_name":"Thies, Edda","last_name":"Thies"},{"last_name":"Breiden","first_name":"Petra","full_name":"Breiden, Petra"},{"last_name":"Pechmann","full_name":"Pechmann, Yvonne","first_name":"Yvonne"},{"last_name":"Kreutz","first_name":"Michael R.","full_name":"Kreutz, Michael R."},{"first_name":"Matthias","full_name":"Kneussel, Matthias","last_name":"Kneussel"}],"publication":"Communications Biology","language":[{"iso":"eng"}],"isi":1,"intvolume":"         5","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:25:59Z","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes"},{"external_id":{"pmid":["36174555"],"isi":["000898428700006"]},"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."}],"publication_status":"published","page":"2290-2304.e7","department":[{"_id":"CaHe"}],"quality_controlled":"1","volume":57,"publisher":"Elsevier","date_published":"2022-10-01T00:00:00Z","citation":{"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.","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>","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>.","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.","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>.","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>"},"date_created":"2023-01-16T09:51:39Z","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"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.","year":"2022","doi":"10.1016/j.devcel.2022.09.003","_id":"12238","article_type":"original","oa_version":"None","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","publication_identifier":{"issn":["1534-5807"]},"author":[{"first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"last_name":"Matsuda","full_name":"Matsuda, Kimiya","first_name":"Kimiya"},{"full_name":"Jikko, Yuya","first_name":"Yuya","last_name":"Jikko"},{"last_name":"Maryu","full_name":"Maryu, Gembu","first_name":"Gembu"},{"first_name":"Katsuya","full_name":"Sakai, Katsuya","last_name":"Sakai"},{"full_name":"Imamura, Ryu","first_name":"Ryu","last_name":"Imamura"},{"last_name":"Tsukiji","full_name":"Tsukiji, Shinya","first_name":"Shinya"},{"full_name":"Aoki, Kazuhiro","first_name":"Kazuhiro","last_name":"Aoki"},{"full_name":"Terai, Kenta","first_name":"Kenta","last_name":"Terai"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"first_name":"Michiyuki","full_name":"Matsuda, Michiyuki","last_name":"Matsuda"}],"pmid":1,"status":"public","type":"journal_article","intvolume":"        57","scopus_import":"1","isi":1,"title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","date_updated":"2023-08-04T09:38:53Z","issue":"19","article_processing_charge":"No","publication":"Developmental Cell","language":[{"iso":"eng"}]},{"date_created":"2023-01-16T09:58:34Z","citation":{"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>.","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.","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).","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>"},"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"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.","year":"2022","article_number":"e10490","acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2023-01-30T09:49:55Z","_id":"12261","article_type":"original","doi":"10.15252/msb.202110490","publication_status":"published","external_id":{"isi":["000856482800001"]},"abstract":[{"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.","lang":"eng"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ToBo"}],"quality_controlled":"1","volume":18,"publisher":"Embo Press","date_published":"2022-09-01T00:00:00Z","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","oa":1,"date_updated":"2023-08-04T09:51:49Z","article_processing_charge":"No","issue":"9","has_accepted_license":"1","scopus_import":"1","intvolume":"        18","isi":1,"language":[{"iso":"eng"}],"publication":"Molecular Systems Biology","author":[{"first_name":"Andreas","full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr"},{"first_name":"Tin Yau","full_name":"Pang, Tin Yau","last_name":"Pang"},{"last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","first_name":"Karin","full_name":"Mitosch, Karin"},{"last_name":"Lercher","first_name":"Martin J","full_name":"Lercher, Martin J"},{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"oa_version":"Published Version","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"file_id":"12446","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","date_created":"2023-01-30T09:49:55Z","date_updated":"2023-01-30T09:49:55Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_size":1098812,"relation":"main_file"}],"publication_identifier":{"eissn":["1744-4292"]},"month":"09","type":"journal_article","status":"public"},{"type":"journal_article","status":"public","pmid":1,"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.15252/embr.202154163","open_access":"1"}],"author":[{"first_name":"Maisha","full_name":"Rahman, Maisha","last_name":"Rahman"},{"first_name":"Nelson","full_name":"Ramirez, Nelson","last_name":"Ramirez","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"full_name":"Diaz‐Balzac, Carlos A","first_name":"Carlos A","last_name":"Diaz‐Balzac"},{"full_name":"Bülow, Hannes E","first_name":"Hannes E","last_name":"Bülow"}],"publication":"EMBO Reports","language":[{"iso":"eng"}],"isi":1,"has_accepted_license":"1","intvolume":"        23","scopus_import":"1","article_processing_charge":"No","issue":"7","oa":1,"date_updated":"2023-10-03T11:25:54Z","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","date_published":"2022-07-05T00:00:00Z","publisher":"Embo Press","quality_controlled":"1","volume":23,"department":[{"_id":"MaDe"}],"abstract":[{"lang":"eng","text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system."}],"external_id":{"pmid":["35586945"],"isi":["000797302700001"]},"publication_status":"published","doi":"10.15252/embr.202154163","_id":"12275","article_type":"original","article_number":"e54163","year":"2022","acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship","keyword":["Genetics","Molecular Biology","Biochemistry"],"date_created":"2023-01-16T10:01:44Z","citation":{"mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>, vol. 23, no. 7, e54163, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>.","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163.","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>.","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” <i>EMBO Reports</i>, vol. 23, no. 7. Embo Press, 2022.","ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. 2022;23(7). doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., &#38; Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>"}}]