[{"article_type":"original","year":"2024","has_accepted_license":"1","oa_version":"Published Version","date_updated":"2024-01-22T13:43:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38128538"]},"scopus_import":"1","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"issue":"1","article_processing_charge":"Yes (in subscription journal)","file":[{"access_level":"open_access","date_updated":"2024-01-22T13:41:41Z","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","file_size":13194060,"creator":"dernst","file_name":"2024_Cell_Kuhn.pdf","success":1,"date_created":"2024-01-22T13:41:41Z","relation":"main_file","file_id":"14874","content_type":"application/pdf"}],"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."}],"_id":"14826","date_published":"2024-01-04T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2024-01-22T13:41:41Z","volume":187,"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"ec_funded":1,"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.","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.","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>","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17."},"title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","day":"04","author":[{"last_name":"Kuhn","full_name":"Kuhn, Andre","first_name":"Andre"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"first_name":"Sumanth","full_name":"Mutte, Sumanth","last_name":"Mutte"},{"full_name":"Dubey, Shiv Mani","first_name":"Shiv Mani","last_name":"Dubey"},{"full_name":"Carrillo Carrasco, Vanessa Polet","first_name":"Vanessa Polet","last_name":"Carrillo Carrasco"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline"},{"first_name":"Jasper","full_name":"Koehorst, Jasper","last_name":"Koehorst"},{"first_name":"Takayuki","full_name":"Kohchi, Takayuki","last_name":"Kohchi"},{"full_name":"Nishihama, Ryuichi","first_name":"Ryuichi","last_name":"Nishihama"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"full_name":"Sprakel, Joris","first_name":"Joris","last_name":"Sprakel"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"type":"journal_article","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.","pmid":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"ddc":["580"],"doi":"10.1016/j.cell.2023.11.021","page":"130-148.e17","month":"01","date_created":"2024-01-17T12:45:40Z","publisher":"Elsevier","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication":"Cell","intvolume":"       187","status":"public"},{"day":"12","type":"journal_article","author":[{"first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"citation":{"ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” <i>European Journal of Cell Biology</i>, vol. 103, no. 1. Elsevier, 2024.","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380.","chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>.","mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>, vol. 103, no. 1, 151380, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>.","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","apa":"Radler, P., &#38; Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. 2024;103(1). doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>"},"title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","language":[{"iso":"eng"}],"keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"ddc":["570"],"doi":"10.1016/j.ejcb.2023.151380","acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"pmid":1,"month":"01","date_created":"2024-01-18T08:16:43Z","department":[{"_id":"MaLo"}],"quality_controlled":"1","publication":"European Journal of Cell Biology","intvolume":"       103","status":"public","publisher":"Elsevier","article_type":"review","year":"2024","has_accepted_license":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-23T08:37:13Z","scopus_import":"1","external_id":{"pmid":["38218128"]},"publication_identifier":{"issn":["0171-9335"]},"article_number":"151380","_id":"14834","date_published":"2024-01-12T00:00:00Z","abstract":[{"text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.","lang":"eng"}],"issue":"1","article_processing_charge":"Yes","volume":103,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"epub_ahead","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.ejcb.2023.151380","open_access":"1"}]},{"month":"01","date_created":"2024-01-22T08:14:49Z","publisher":"The Company of Biologists","publication":"Journal of Experimental Biology","quality_controlled":"1","department":[{"_id":"NiBa"}],"status":"public","intvolume":"       227","citation":{"short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","ama":"Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels using more signal modalities than females utilise. <i>Journal of Experimental Biology</i>. 2024;227(1). doi:<a href=\"https://doi.org/10.1242/jeb.246217\">10.1242/jeb.246217</a>","apa":"Pal, A., Joshi, M., &#38; Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. <i>Journal of Experimental Biology</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>","chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>.","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” <i>Journal of Experimental Biology</i>, vol. 227, no. 1. The Company of Biologists, 2024.","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jeb.246217\">10.1242/jeb.246217</a>."},"title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","day":"10","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","full_name":"Pal, Arka","last_name":"Pal"},{"last_name":"Joshi","first_name":"Mihir","full_name":"Joshi, Mihir"},{"first_name":"Maria","full_name":"Thaker, Maria","last_name":"Thaker"}],"type":"journal_article","pmid":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling"}]},"acknowledgement":"We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions, and help with sampling and colour analyses. We thank Muralidhar and the central LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch funding was provided by the Department of Science and Technology Fund for Improvement of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute of Science (DBT-IISc) partnership program and a Science and Engineering Research Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian Institute of Science. Deposited in PMC for immediate release.","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"doi":"10.1242/jeb.246217","ddc":["570"],"article_processing_charge":"Yes (via OA deal)","issue":"1","file":[{"date_created":"2024-01-23T12:08:24Z","success":1,"content_type":"application/pdf","file_id":"14877","relation":"main_file","checksum":"136325372f6f45abaa62a71e2d23bfb6","date_updated":"2024-01-23T12:08:24Z","access_level":"open_access","file_name":"2024_JourExperimBiology_Pal.pdf","file_size":594128,"creator":"dernst"}],"article_number":"jeb246217","_id":"14850","abstract":[{"text":"Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals.</jats:p>","lang":"eng"}],"date_published":"2024-01-10T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2024-01-23T12:08:24Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":227,"article_type":"original","has_accepted_license":"1","year":"2024","oa_version":"Published Version","external_id":{"pmid":["38054353"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-23T12:13:08Z","publication_identifier":{"issn":["1477-9145"],"eissn":["0022-0949"]}},{"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology (2024)."},"author":[{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia","full_name":"Datler, Julia"},{"last_name":"Hansen","first_name":"Jesse","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"first_name":"Andreas","full_name":"Thader, Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W","first_name":"Lukas W","last_name":"Bauer"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"type":"journal_article","day":"05","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"pmid":1,"ddc":["570"],"doi":"10.1038/s41594-023-01201-6","language":[{"iso":"eng"}],"keyword":["Molecular Biology","Structural Biology"],"date_created":"2024-02-12T09:59:45Z","month":"02","publisher":"Springer Nature","status":"public","quality_controlled":"1","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publication":"Nature Structural & Molecular Biology","has_accepted_license":"1","oa_version":"Published Version","year":"2024","article_type":"original","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-05T09:27:47Z","external_id":{"pmid":["38316877"]},"article_processing_charge":"Yes (in subscription journal)","_id":"14979","date_published":"2024-02-05T00:00:00Z","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"oa":1,"publication_status":"epub_ahead","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"file_date_updated":"2024-02-23T14:20:16Z","publication_status":"published","oa":1,"file":[{"checksum":"b2d3da47c98d481577a4baf68944fe41","date_updated":"2024-02-23T13:50:53Z","access_level":"open_access","file_name":"hledik thesis pdfa 2b.pdf","creator":"mhledik","file_size":7102089,"date_created":"2024-02-23T13:50:53Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"15021"},{"date_created":"2024-02-23T13:50:54Z","content_type":"application/zip","file_id":"15022","relation":"source_file","date_updated":"2024-02-23T14:20:16Z","access_level":"closed","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","file_size":14014790,"creator":"mhledik"}],"date_published":"2024-02-23T00:00:00Z","_id":"15020","abstract":[{"lang":"eng","text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal."}],"article_processing_charge":"No","date_updated":"2025-06-30T13:21:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663 - 337X"]},"year":"2024","oa_version":"Published Version","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","publisher":"Institute of Science and Technology Austria","month":"02","date_created":"2024-02-23T14:02:04Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"}],"page":"158","language":[{"iso":"eng"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"],"doi":"10.15479/at:ista:15020","ddc":["576","519"],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"related_material":{"record":[{"status":"public","id":"7553","relation":"part_of_dissertation"},{"id":"7606","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"12081","relation":"part_of_dissertation"}]},"day":"23","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","ec_funded":1,"citation":{"ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>"},"title":"Genetic information and biological optimization"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:29:43Z","publication_identifier":{"issn":["2050-084X"]},"article_type":"original","oa_version":"Published Version","year":"2024","has_accepted_license":"1","publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68993","open_access":"1"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":13,"article_processing_charge":"Yes","_id":"15033","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."}],"date_published":"2024-02-21T00:00:00Z","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"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","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"ddc":["580"],"doi":"10.7554/elife.68993","citation":{"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.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","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>.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","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>"},"ec_funded":1,"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","day":"21","type":"journal_article","author":[{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","first_name":"Maciek"},{"full_name":"Matijevic, Ivana","first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"}],"publisher":"eLife Sciences Publications","publication":"eLife","department":[{"_id":"JiFr"}],"quality_controlled":"1","status":"public","intvolume":"        13","month":"02","date_created":"2024-02-27T07:10:11Z"},{"publisher":"Oxford University Press","intvolume":"        40","status":"public","publication":"Molecular Biology and Evolution","department":[{"_id":"BeVi"}],"quality_controlled":"1","date_created":"2023-11-27T16:14:37Z","month":"12","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"},{"grant_number":"ESP39 49461","name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"pmid":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}],"record":[{"relation":"research_data","id":"14614","status":"public"}]},"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","ddc":["570"],"doi":"10.1093/molbev/msad245","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","citation":{"short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>."},"author":[{"orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","last_name":"Lasne","first_name":"Clementine","full_name":"Lasne, Clementine"},{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"first_name":"Lorena Alexandra","full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco","orcid":"0000-0002-1253-6297","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"type":"journal_article","day":"01","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":40,"file_date_updated":"2024-01-02T11:39:38Z","article_processing_charge":"Yes (via OA deal)","issue":"12","_id":"14613","date_published":"2023-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"file":[{"relation":"main_file","file_id":"14727","content_type":"application/pdf","success":1,"date_created":"2024-01-02T11:39:38Z","file_size":8623505,"creator":"dernst","file_name":"2023_MolecularBioEvo_Lasne.pdf","access_level":"open_access","date_updated":"2024-01-02T11:39:38Z","checksum":"47c1c72fb499f26ea52d216b242208c8"}],"article_number":"msad245","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"external_id":{"pmid":["37988296"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:18:35Z","year":"2023","has_accepted_license":"1","oa_version":"Published Version","article_type":"original"},{"oa_version":"Published Version","has_accepted_license":"1","year":"2023","article_type":"original","publication_identifier":{"issn":["1756-994X"]},"date_updated":"2023-12-04T08:17:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"_id":"14639","date_published":"2023-11-23T00:00:00Z","article_number":"102","file":[{"creator":"dernst","file_size":14791081,"file_name":"2023_GenomeMed_Lin.pdf","checksum":"279efd212005549aba817a487d56d363","access_level":"open_access","date_updated":"2023-12-04T08:15:43Z","file_id":"14640","relation":"main_file","content_type":"application/pdf","date_created":"2023-12-04T08:15:43Z","success":1}],"article_processing_charge":"Yes","volume":15,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-12-04T08:15:43Z","oa":1,"publication_status":"published","type":"journal_article","author":[{"last_name":"Lin","full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"last_name":"Lau","full_name":"Lau, Tracy","first_name":"Tracy"},{"orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin","first_name":"Kevin","last_name":"Huang"},{"last_name":"Zaki","first_name":"Maha S.","full_name":"Zaki, Maha S."},{"last_name":"Aldeen","full_name":"Aldeen, Huda Shujaa","first_name":"Huda Shujaa"},{"full_name":"Karimiani, Ehsan Ghayoor","first_name":"Ehsan Ghayoor","last_name":"Karimiani"},{"last_name":"Rocca","first_name":"Clarissa","full_name":"Rocca, Clarissa"},{"last_name":"Noureldeen","first_name":"Mahmoud M.","full_name":"Noureldeen, Mahmoud M."},{"first_name":"Ahmed K.","full_name":"Saad, Ahmed K.","last_name":"Saad"},{"last_name":"Petree","full_name":"Petree, Cassidy","first_name":"Cassidy"},{"last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias","first_name":"Tobias"},{"last_name":"Abou Jamra","first_name":"Rami","full_name":"Abou Jamra, Rami"},{"full_name":"Zifarelli, Giovanni","first_name":"Giovanni","last_name":"Zifarelli"},{"first_name":"Aditi","full_name":"Gotkhindikar, Aditi","last_name":"Gotkhindikar"},{"last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M.","first_name":"Ingrid M."},{"full_name":"Liao, Mingjuan","first_name":"Mingjuan","last_name":"Liao"},{"full_name":"Cork, Emalyn Elise","first_name":"Emalyn Elise","last_name":"Cork"},{"last_name":"Varshney","full_name":"Varshney, Pratishtha","first_name":"Pratishtha"},{"last_name":"Hashemi","first_name":"Narges","full_name":"Hashemi, Narges"},{"full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan","last_name":"Mohammadi"},{"first_name":"Aboulfazl","full_name":"Rad, Aboulfazl","last_name":"Rad"},{"last_name":"Neira","full_name":"Neira, Juanita","first_name":"Juanita"},{"last_name":"Toosi","first_name":"Mehran Beiraghi","full_name":"Toosi, Mehran Beiraghi"},{"full_name":"Knopp, Cordula","first_name":"Cordula","last_name":"Knopp"},{"last_name":"Kurth","first_name":"Ingo","full_name":"Kurth, Ingo"},{"last_name":"Challman","first_name":"Thomas D.","full_name":"Challman, Thomas D."},{"first_name":"Rebecca","full_name":"Smith, Rebecca","last_name":"Smith"},{"full_name":"Abdalla, Asmahan","first_name":"Asmahan","last_name":"Abdalla"},{"last_name":"Haaf","full_name":"Haaf, Thomas","first_name":"Thomas"},{"full_name":"Suri, Mohnish","first_name":"Mohnish","last_name":"Suri"},{"first_name":"Manali","full_name":"Joshi, Manali","last_name":"Joshi"},{"first_name":"Wendy K.","full_name":"Chung, Wendy K.","last_name":"Chung"},{"first_name":"Andres","full_name":"Moreno-De-Luca, Andres","last_name":"Moreno-De-Luca"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"first_name":"Reza","full_name":"Maroofian, Reza","last_name":"Maroofian"},{"last_name":"Varshney","full_name":"Varshney, Gaurav K.","first_name":"Gaurav K."}],"day":"23","title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","citation":{"mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>, vol. 15, 102, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>.","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023)."},"ddc":["570"],"doi":"10.1186/s13073-023-01258-4","language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"date_created":"2023-12-04T08:10:55Z","extern":"1","month":"11","status":"public","intvolume":"        15","quality_controlled":"1","publication":"Genome Medicine","publisher":"Springer Nature"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":5,"publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"oa":1,"article_number":"102771","_id":"14683","date_published":"2023-12-08T00:00:00Z","abstract":[{"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","lang":"eng"}],"article_processing_charge":"No","issue":"1","external_id":{"pmid":["38070137"]},"scopus_import":"1","date_updated":"2023-12-18T08:06:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2666-1667"]},"article_type":"review","oa_version":"Submitted Version","year":"2023","publication":"STAR Protocols","quality_controlled":"1","department":[{"_id":"SiHi"}],"status":"public","intvolume":"         5","publisher":"Elsevier","month":"12","date_created":"2023-12-13T11:48:05Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"language":[{"iso":"eng"}],"doi":"10.1016/j.xpro.2023.102771","ddc":["570"],"pmid":1,"project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"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.","day":"08","type":"journal_article","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"citation":{"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>.","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.","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.","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>.","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (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>","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>"},"ec_funded":1,"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry"},{"article_processing_charge":"No","_id":"14726","date_published":"2023-12-23T00:00:00Z","abstract":[{"lang":"eng","text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants."}],"article_number":"koad324","oa":1,"main_file_link":[{"url":"https://doi.org/10.1093/plcell/koad324","open_access":"1"}],"publication_status":"epub_ahead","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","year":"2023","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-03T12:43:41Z","date_created":"2024-01-02T11:19:37Z","extern":"1","month":"12","publisher":"Oxford University Press","status":"public","quality_controlled":"1","publication":"The Plant Cell","title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","citation":{"ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. 2023. doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>","apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>","short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023).","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>, koad324, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>.","chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>.","ieee":"L.-Z. Zhou <i>et al.</i>, “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” <i>The Plant Cell</i>. Oxford University Press, 2023.","ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324."},"type":"journal_article","author":[{"last_name":"Zhou","first_name":"Liang-Zi","full_name":"Zhou, Liang-Zi"},{"last_name":"Wang","first_name":"Lele","full_name":"Wang, Lele"},{"last_name":"Chen","first_name":"Xia","full_name":"Chen, Xia"},{"first_name":"Zengxiang","full_name":"Ge, Zengxiang","last_name":"Ge","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8"},{"last_name":"Mergner","first_name":"Julia","full_name":"Mergner, Julia"},{"last_name":"Li","full_name":"Li, Xingli","first_name":"Xingli"},{"last_name":"Küster","first_name":"Bernhard","full_name":"Küster, Bernhard"},{"first_name":"Gernot","full_name":"Längst, Gernot","last_name":"Längst"},{"full_name":"Qu, Li-Jia","first_name":"Li-Jia","last_name":"Qu"},{"last_name":"Dresselhaus","first_name":"Thomas","full_name":"Dresselhaus, Thomas"}],"day":"23","ddc":["580"],"doi":"10.1093/plcell/koad324","language":[{"iso":"eng"}],"keyword":["Cell Biology","Plant Science"]},{"type":"journal_article","author":[{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"first_name":"Mabel D.","full_name":"Giménez, Mabel D.","last_name":"Giménez"},{"first_name":"Mathieu","full_name":"Joron, Mathieu","last_name":"Joron"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"last_name":"Walden","first_name":"Nora","full_name":"Walden, Nora"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"day":"01","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","citation":{"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).","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>","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","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.","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.","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>."},"doi":"10.1101/cshperspect.a041447","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"pmid":1,"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.","date_created":"2024-01-08T12:43:48Z","month":"11","status":"public","intvolume":"        15","publication":"Cold Spring Harbor Perspectives in Biology","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory","oa_version":"Published Version","year":"2023","article_type":"original","publication_identifier":{"issn":["1943-0264"]},"external_id":{"pmid":["37604585"]},"scopus_import":"1","date_updated":"2024-01-08T12:52:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"_id":"14742","date_published":"2023-11-01T00:00:00Z","article_number":"a041447","article_processing_charge":"No","issue":"11","volume":15,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"oa":1,"publication_status":"published"},{"publication_status":"published","volume":20,"article_processing_charge":"No","issue":"8","date_published":"2023-08-01T00:00:00Z","_id":"14770","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","external_id":{"isi":["001025621500002"]},"date_updated":"2024-01-10T08:37:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"article_type":"letter_note","year":"2023","oa_version":"None","publisher":"Springer Nature","isi":1,"publication":"Nature Methods","quality_controlled":"1","department":[{"_id":"JoDa"}],"intvolume":"        20","status":"public","page":"1141-1142","month":"08","date_created":"2024-01-10T08:07:15Z","related_material":{"record":[{"status":"public","id":"13267","relation":"extended_version"}]},"keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"language":[{"iso":"eng"}],"doi":"10.1038/s41592-023-01937-5","citation":{"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>.","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.","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.","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>","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>","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142."},"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","day":"01","type":"journal_article","author":[{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"}]},{"pmid":1,"acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","keyword":["Developmental Biology","Molecular Biology"],"language":[{"iso":"eng"}],"doi":"10.1242/dev.201559","ddc":["570"],"citation":{"ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. The Company of Biologists, 2023.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559."},"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","day":"01","type":"journal_article","author":[{"last_name":"Harish","full_name":"Harish, Rohit K","first_name":"Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d"},{"last_name":"Gupta","full_name":"Gupta, Mansi","first_name":"Mansi"},{"last_name":"Zöller","full_name":"Zöller, Daniela","first_name":"Daniela"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"full_name":"Machate, Anja","first_name":"Anja","last_name":"Machate"},{"last_name":"Hans","first_name":"Stefan","full_name":"Hans, Stefan"},{"last_name":"Brand","first_name":"Michael","full_name":"Brand, Michael"}],"publisher":"The Company of Biologists","isi":1,"publication":"Development","department":[{"_id":"AnKi"}],"quality_controlled":"1","intvolume":"       150","status":"public","month":"10","date_created":"2024-01-10T09:18:54Z","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-10T12:45:25Z","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"article_type":"original","has_accepted_license":"1","year":"2023","oa_version":"Published Version","publication_status":"published","oa":1,"file_date_updated":"2024-01-10T12:41:13Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":150,"article_processing_charge":"Yes (via OA deal)","issue":"19","article_number":"dev201559","file":[{"file_name":"2023_Development_Harish.pdf","file_size":12836306,"creator":"dernst","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","date_updated":"2024-01-10T12:41:13Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"14790","date_created":"2024-01-10T12:41:13Z","success":1}],"date_published":"2023-10-01T00:00:00Z","_id":"14774","abstract":[{"lang":"eng","text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential."}]},{"has_accepted_license":"1","year":"2023","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["1422-0067"]},"external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-10T13:41:10Z","abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"_id":"14776","date_published":"2023-11-01T00:00:00Z","article_number":"16527","file":[{"content_type":"application/pdf","file_id":"14791","relation":"main_file","success":1,"date_created":"2024-01-10T13:39:42Z","file_name":"2023_IJMS_Teplova.pdf","creator":"dernst","file_size":2637784,"date_updated":"2024-01-10T13:39:42Z","access_level":"open_access","checksum":"4df7d206ba022b7f54eff1f0aec1659a"}],"article_processing_charge":"Yes","issue":"22","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":24,"file_date_updated":"2024-01-10T13:39:42Z","oa":1,"publication_status":"published","author":[{"last_name":"Teplova","full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"first_name":"Artemii A.","full_name":"Pigidanov, Artemii A.","last_name":"Pigidanov"},{"first_name":"Marina V.","full_name":"Serebryakova, Marina V.","last_name":"Serebryakova"},{"last_name":"Golyshev","full_name":"Golyshev, Sergei A.","first_name":"Sergei A."},{"first_name":"Raisa A.","full_name":"Galiullina, Raisa A.","last_name":"Galiullina"},{"last_name":"Chichkova","full_name":"Chichkova, Nina V.","first_name":"Nina V."},{"first_name":"Andrey B.","full_name":"Vartapetian, Andrey B.","last_name":"Vartapetian"}],"type":"journal_article","day":"01","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","citation":{"short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>.","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22, 16527, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>."},"ddc":["580"],"doi":"10.3390/ijms242216527","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"language":[{"iso":"eng"}],"pmid":1,"acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","date_created":"2024-01-10T09:24:35Z","month":"11","status":"public","intvolume":"        24","publication":"International Journal of Molecular Sciences","quality_controlled":"1","department":[{"_id":"JiFr"}],"isi":1,"publisher":"MDPI"},{"type":"journal_article","author":[{"last_name":"Westerich","full_name":"Westerich, Kim Joana","first_name":"Kim Joana"},{"last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna"},{"full_name":"Schick, Jan","first_name":"Jan","last_name":"Schick"},{"first_name":"Antra","full_name":"Gupta, Antra","last_name":"Gupta"},{"first_name":"Mingzhao","full_name":"Zhu, Mingzhao","last_name":"Zhu"},{"last_name":"Hull","first_name":"Kenneth","full_name":"Hull, Kenneth"},{"first_name":"Daniel","full_name":"Romo, Daniel","last_name":"Romo"},{"first_name":"Dagmar","full_name":"Zeuschner, Dagmar","last_name":"Zeuschner"},{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Theresa","full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"day":"11","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","citation":{"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>","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>","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.","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>.","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.","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.","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>."},"doi":"10.1016/j.devcel.2023.06.009","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"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.","pmid":1,"date_created":"2024-01-10T09:41:21Z","month":"09","page":"1578-1592.e5","status":"public","intvolume":"        58","department":[{"_id":"Bio"}],"quality_controlled":"1","publication":"Developmental Cell","publisher":"Elsevier","year":"2023","oa_version":"Preprint","article_type":"original","publication_identifier":{"issn":["1534-5807"]},"date_updated":"2024-01-16T08:56:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37463577"]},"_id":"14781","date_published":"2023-09-11T00:00:00Z","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"issue":"17","article_processing_charge":"No","volume":58,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"oa":1,"publication_status":"published"},{"ddc":["570"],"doi":"10.1083/jcb.202206038","keyword":["Cell Biology"],"language":[{"iso":"eng"}],"pmid":1,"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","author":[{"full_name":"Mund, Markus","first_name":"Markus","last_name":"Mund"},{"full_name":"Tschanz, Aline","first_name":"Aline","last_name":"Tschanz"},{"full_name":"Wu, Yu-Le","first_name":"Yu-Le","last_name":"Wu"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey"},{"last_name":"Mehl","first_name":"Johanna L.","full_name":"Mehl, Johanna L."},{"first_name":"Marko","full_name":"Kaksonen, Marko","last_name":"Kaksonen"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S.","last_name":"Schwarz"},{"last_name":"Ries","first_name":"Jonas","full_name":"Ries, Jonas"}],"type":"journal_article","day":"03","title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","citation":{"short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>."},"intvolume":"       222","status":"public","publication":"Journal of Cell Biology","department":[{"_id":"AnSa"}],"quality_controlled":"1","isi":1,"publisher":"Rockefeller University Press","date_created":"2024-01-10T10:45:55Z","month":"02","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"date_updated":"2024-01-16T10:17:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":222,"file_date_updated":"2024-01-16T10:15:09Z","oa":1,"publication_status":"published","_id":"14788","abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"date_published":"2023-02-03T00:00:00Z","file":[{"file_name":"2023_JCB_Mund.pdf","creator":"dernst","file_size":5678069,"date_updated":"2024-01-16T10:15:09Z","access_level":"open_access","checksum":"505d5cac36c14b073b68c7fed1a92bd3","content_type":"application/pdf","relation":"main_file","file_id":"14811","success":1,"date_created":"2024-01-16T10:15:09Z"}],"article_number":"e202206038","article_processing_charge":"No","issue":"3"},{"year":"2023","oa_version":"None","article_type":"original","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"scopus_import":"1","external_id":{"pmid":["38149871"]},"date_updated":"2024-01-22T13:35:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14827","date_published":"2023-12-27T00:00:00Z","abstract":[{"lang":"eng","text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems."}],"article_number":"jcs.261515","article_processing_charge":"No","issue":"24","volume":136,"publication_status":"published","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia","full_name":"Schwayer, Cornelia"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David","full_name":"Brückner, David"}],"type":"journal_article","day":"27","title":"Connecting theory and experiment in cell and tissue mechanics","citation":{"mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>.","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023)."},"doi":"10.1242/jcs.261515","keyword":["Cell Biology"],"language":[{"iso":"eng"}],"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"pmid":1,"acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","date_created":"2024-01-17T12:46:55Z","month":"12","intvolume":"       136","status":"public","publication":"Journal of Cell Science","quality_controlled":"1","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"publisher":"The Company of Biologists"},{"publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2023-08-22T06:50:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"scopus_import":"1","year":"2023","oa_version":"Published Version","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"oa":1,"publication_status":"published","volume":14,"article_processing_charge":"No","arxiv":1,"_id":"13989","abstract":[{"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.","lang":"eng"}],"date_published":"2023-06-14T00:00:00Z","article_number":"3512","pmid":1,"doi":"10.1038/s41467-023-38540-3","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","citation":{"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.","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.","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>.","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).","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>","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>"},"author":[{"last_name":"Hales","full_name":"Hales, Jordyn","first_name":"Jordyn"},{"full_name":"Bajpai, Utkarsh","first_name":"Utkarsh","last_name":"Bajpai"},{"last_name":"Liu","full_name":"Liu, Tongtong","first_name":"Tongtong"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Li","first_name":"Mingda","full_name":"Li, Mingda"},{"last_name":"Mitrano","first_name":"Matteo","full_name":"Mitrano, Matteo"},{"last_name":"Wang","full_name":"Wang, Yao","first_name":"Yao"}],"type":"journal_article","day":"14","publisher":"Springer Nature","status":"public","intvolume":"        14","quality_controlled":"1","publication":"Nature Communications","date_created":"2023-08-09T13:06:59Z","extern":"1","month":"06"},{"status":"public","intvolume":"        13","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"quality_controlled":"1","publication":"G3: Genes, Genomes, Genetics","isi":1,"publisher":"Oxford University Press","date_created":"2023-08-18T06:52:14Z","month":"08","doi":"10.1093/g3journal/jkad121","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","related_material":{"record":[{"id":"12933","relation":"research_data","status":"public"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"type":"journal_article","day":"01","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","ec_funded":1,"citation":{"mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023)."},"volume":13,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-11-07T09:00:19Z","oa":1,"publication_status":"published","date_published":"2023-08-01T00:00:00Z","_id":"14077","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"file":[{"success":1,"date_created":"2023-11-07T09:00:19Z","content_type":"application/pdf","file_id":"14498","relation":"main_file","date_updated":"2023-11-07T09:00:19Z","access_level":"open_access","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_name":"2023_G3_Puixeu.pdf","creator":"dernst","file_size":845642}],"issue":"8","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2160-1836"]},"date_updated":"2023-12-13T12:15:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001002997200001"]},"scopus_import":"1","oa_version":"Published Version","year":"2023","has_accepted_license":"1","article_type":"original"},{"author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"last_name":"Lebedenko","first_name":"Olga O.","full_name":"Lebedenko, Olga O."},{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","first_name":"Lea Marie","last_name":"Becker"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"first_name":"Roman","full_name":"Lichtenecker, Roman","last_name":"Lichtenecker"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"type":"journal_article","day":"01","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","citation":{"mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>, vol. 7, 100079, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>.","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” <i>Journal of Structural Biology: X</i>, vol. 7. Elsevier, 2023.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. 2023;7. doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., &#38; Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023)."},"ddc":["570"],"doi":"10.1016/j.yjsbx.2022.100079","language":[{"iso":"eng"}],"keyword":["Structural Biology"],"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","pmid":1,"date_created":"2023-01-12T11:55:38Z","month":"01","intvolume":"         7","status":"public","quality_controlled":"1","department":[{"_id":"PaSc"}],"publication":"Journal of Structural Biology: X","publisher":"Elsevier","year":"2023","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["2590-1524"]},"date_updated":"2023-08-16T09:37:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["36578472"]},"scopus_import":"1","_id":"12114","date_published":"2023-01-01T00:00:00Z","abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"file":[{"file_size":5132322,"creator":"dernst","file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access","date_updated":"2023-08-16T09:36:28Z","checksum":"b4b1c10a31018aafe053b7d55a470e54","relation":"main_file","file_id":"14064","content_type":"application/pdf","success":1,"date_created":"2023-08-16T09:36:28Z"}],"article_number":"100079","article_processing_charge":"No","volume":7,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2023-08-16T09:36:28Z","oa":1,"publication_status":"published"}]