[{"file_date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-17T12:45:40Z","volume":187,"month":"01","type":"journal_article","oa_version":"Published Version","abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"date_updated":"2024-01-22T13:43:40Z","page":"130-148.e17","_id":"14826","year":"2024","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","date_published":"2024-01-04T00:00:00Z","ddc":["580"],"has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"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.","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>.","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>","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>","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.","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.","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>."},"intvolume":"       187","external_id":{"pmid":["38128538"]},"status":"public","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"04","file":[{"date_updated":"2024-01-22T13:41:41Z","file_id":"14874","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","date_created":"2024-01-22T13:41:41Z","access_level":"open_access","success":1,"file_name":"2024_Cell_Kuhn.pdf","relation":"main_file","content_type":"application/pdf","file_size":13194060,"creator":"dernst"}],"author":[{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"first_name":"Sumanth","last_name":"Mutte","full_name":"Mutte, Sumanth"},{"full_name":"Dubey, Shiv Mani","last_name":"Dubey","first_name":"Shiv Mani"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"last_name":"Koehorst","first_name":"Jasper","full_name":"Koehorst, Jasper"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"full_name":"Nishihama, Ryuichi","last_name":"Nishihama","first_name":"Ryuichi"},{"last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"last_name":"Sprakel","first_name":"Joris","full_name":"Sprakel, Joris"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","publication":"Cell","department":[{"_id":"JiFr"}],"pmid":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1016/j.cell.2023.11.021","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"issue":"1","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}]},{"status":"public","external_id":{"pmid":["38054353"]},"citation":{"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.","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>","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>."},"related_material":{"link":[{"relation":"software","url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling"}]},"intvolume":"       227","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570"],"date_published":"2024-01-10T00:00:00Z","year":"2024","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.","_id":"14850","month":"01","type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","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>"}],"date_updated":"2024-01-23T12:13:08Z","date_created":"2024-01-22T08:14:49Z","file_date_updated":"2024-01-23T12:08:24Z","volume":227,"issue":"1","language":[{"iso":"eng"}],"keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"quality_controlled":"1","doi":"10.1242/jeb.246217","department":[{"_id":"NiBa"}],"pmid":1,"publisher":"The Company of Biologists","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Experimental Biology","file":[{"date_created":"2024-01-23T12:08:24Z","access_level":"open_access","file_id":"14877","date_updated":"2024-01-23T12:08:24Z","checksum":"136325372f6f45abaa62a71e2d23bfb6","file_size":594128,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2024_JourExperimBiology_Pal.pdf","success":1}],"day":"10","author":[{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","first_name":"Arka","last_name":"Pal"},{"first_name":"Mihir","last_name":"Joshi","full_name":"Joshi, Mihir"},{"full_name":"Thaker, Maria","first_name":"Maria","last_name":"Thaker"}],"article_number":"jeb246217","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise"},{"citation":{"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.","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>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology (2024).","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>","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.","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>.","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>"},"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release"}]},"status":"public","external_id":{"pmid":["38316877"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"date_published":"2024-02-05T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"epub_ahead","_id":"14979","year":"2024","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.","date_created":"2024-02-12T09:59:45Z","type":"journal_article","month":"02","oa_version":"Published Version","date_updated":"2024-03-05T09:27:47Z","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"}],"language":[{"iso":"eng"}],"keyword":["Molecular Biology","Structural Biology"],"project":[{"grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"quality_controlled":"1","doi":"10.1038/s41594-023-01201-6","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","publication":"Nature Structural & Molecular Biology","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","day":"05","author":[{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"},{"first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse"},{"last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas"},{"first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"last_name":"Bauer","first_name":"Lukas W","full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM"}]},{"publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.68993","quality_controlled":"1","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"author":[{"first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matijevic","first_name":"Ivana","full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"day":"21","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"}],"publication":"eLife","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes","ec_funded":1,"publication_status":"epub_ahead","oa":1,"has_accepted_license":"1","ddc":["580"],"date_published":"2024-02-21T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"status":"public","intvolume":"        13","citation":{"short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","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>.","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.","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","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>"},"oa_version":"Published Version","month":"02","type":"journal_article","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_updated":"2024-02-28T12:29:43Z","volume":13,"date_created":"2024-02-27T07:10:11Z","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","year":"2024","_id":"15033"},{"intvolume":"        40","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}],"record":[{"relation":"research_data","status":"public","id":"14614"}]},"citation":{"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.","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>.","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>","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>.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023)."},"external_id":{"pmid":["37988296"]},"status":"public","date_published":"2023-12-01T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","oa":1,"has_accepted_license":"1","_id":"14613","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).","year":"2023","volume":40,"file_date_updated":"2024-01-02T11:39:38Z","date_created":"2023-11-27T16:14:37Z","abstract":[{"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.","lang":"eng"}],"date_updated":"2024-02-21T12:18:35Z","oa_version":"Published Version","month":"12","type":"journal_article","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"issue":"12","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461"}],"doi":"10.1093/molbev/msad245","quality_controlled":"1","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication":"Molecular Biology and Evolution","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","pmid":1,"department":[{"_id":"BeVi"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","article_number":"msad245","author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","first_name":"Clementine","last_name":"Lasne"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N"},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"first_name":"Lorena Alexandra","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"day":"01","file":[{"file_size":8623505,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2023_MolecularBioEvo_Lasne.pdf","success":1,"date_created":"2024-01-02T11:39:38Z","access_level":"open_access","file_id":"14727","date_updated":"2024-01-02T11:39:38Z","checksum":"47c1c72fb499f26ea52d216b242208c8"}]},{"volume":15,"date_created":"2023-12-04T08:10:55Z","file_date_updated":"2023-12-04T08:15:43Z","oa_version":"Published Version","type":"journal_article","month":"11","date_updated":"2023-12-04T08:17:22Z","abstract":[{"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”.","lang":"eng"}],"_id":"14639","year":"2023","date_published":"2023-11-23T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"        15","extern":"1","citation":{"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>","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.","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>.","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>","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.","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>.","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)."},"status":"public","article_number":"102","title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","author":[{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"last_name":"Vona","first_name":"Barbara","full_name":"Vona, Barbara"},{"full_name":"Lau, Tracy","last_name":"Lau","first_name":"Tracy"},{"last_name":"Huang","first_name":"Kevin","full_name":"Huang, Kevin","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3"},{"last_name":"Zaki","first_name":"Maha S.","full_name":"Zaki, Maha S."},{"full_name":"Aldeen, Huda Shujaa","last_name":"Aldeen","first_name":"Huda Shujaa"},{"last_name":"Karimiani","first_name":"Ehsan Ghayoor","full_name":"Karimiani, Ehsan Ghayoor"},{"last_name":"Rocca","first_name":"Clarissa","full_name":"Rocca, Clarissa"},{"first_name":"Mahmoud M.","last_name":"Noureldeen","full_name":"Noureldeen, Mahmoud M."},{"full_name":"Saad, Ahmed K.","last_name":"Saad","first_name":"Ahmed K."},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"full_name":"Bartolomaeus, Tobias","first_name":"Tobias","last_name":"Bartolomaeus"},{"full_name":"Abou Jamra, Rami","last_name":"Abou Jamra","first_name":"Rami"},{"full_name":"Zifarelli, Giovanni","first_name":"Giovanni","last_name":"Zifarelli"},{"last_name":"Gotkhindikar","first_name":"Aditi","full_name":"Gotkhindikar, Aditi"},{"last_name":"Wentzensen","first_name":"Ingrid M.","full_name":"Wentzensen, Ingrid M."},{"full_name":"Liao, Mingjuan","last_name":"Liao","first_name":"Mingjuan"},{"first_name":"Emalyn Elise","last_name":"Cork","full_name":"Cork, Emalyn Elise"},{"full_name":"Varshney, Pratishtha","first_name":"Pratishtha","last_name":"Varshney"},{"full_name":"Hashemi, Narges","first_name":"Narges","last_name":"Hashemi"},{"full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan","last_name":"Mohammadi"},{"full_name":"Rad, Aboulfazl","last_name":"Rad","first_name":"Aboulfazl"},{"full_name":"Neira, Juanita","last_name":"Neira","first_name":"Juanita"},{"full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi","last_name":"Toosi"},{"first_name":"Cordula","last_name":"Knopp","full_name":"Knopp, Cordula"},{"full_name":"Kurth, Ingo","last_name":"Kurth","first_name":"Ingo"},{"full_name":"Challman, Thomas D.","first_name":"Thomas D.","last_name":"Challman"},{"full_name":"Smith, Rebecca","first_name":"Rebecca","last_name":"Smith"},{"first_name":"Asmahan","last_name":"Abdalla","full_name":"Abdalla, Asmahan"},{"full_name":"Haaf, Thomas","first_name":"Thomas","last_name":"Haaf"},{"full_name":"Suri, Mohnish","first_name":"Mohnish","last_name":"Suri"},{"full_name":"Joshi, Manali","last_name":"Joshi","first_name":"Manali"},{"last_name":"Chung","first_name":"Wendy K.","full_name":"Chung, Wendy K."},{"first_name":"Andres","last_name":"Moreno-De-Luca","full_name":"Moreno-De-Luca, Andres"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"last_name":"Maroofian","first_name":"Reza","full_name":"Maroofian, Reza"},{"first_name":"Gaurav K.","last_name":"Varshney","full_name":"Varshney, Gaurav K."}],"day":"23","file":[{"creator":"dernst","file_size":14791081,"relation":"main_file","content_type":"application/pdf","file_name":"2023_GenomeMed_Lin.pdf","success":1,"access_level":"open_access","date_created":"2023-12-04T08:15:43Z","checksum":"279efd212005549aba817a487d56d363","file_id":"14640","date_updated":"2023-12-04T08:15:43Z"}],"publication":"Genome Medicine","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1186/s13073-023-01258-4","quality_controlled":"1","publication_identifier":{"issn":["1756-994X"]},"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"language":[{"iso":"eng"}]},{"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.","year":"2023","_id":"14683","type":"journal_article","oa_version":"Submitted Version","month":"12","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"}],"date_updated":"2023-12-18T08:06:14Z","volume":5,"date_created":"2023-12-13T11:48:05Z","status":"public","external_id":{"pmid":["38070137"]},"intvolume":"         5","citation":{"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>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","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>.","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.","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023)."},"oa":1,"publication_status":"epub_ahead","date_published":"2023-12-08T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2023.102771"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"pmid":1,"publication":"STAR Protocols","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"day":"08","article_number":"102771","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","project":[{"grant_number":"T0101031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2666-1667"]},"doi":"10.1016/j.xpro.2023.102771","quality_controlled":"1"},{"title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","article_number":"a041447","day":"01","author":[{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"full_name":"Giménez, Mabel D.","first_name":"Mabel D.","last_name":"Giménez"},{"full_name":"Joron, Mathieu","last_name":"Joron","first_name":"Mathieu"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Jeremy B.","last_name":"Searle","full_name":"Searle, Jeremy B."},{"first_name":"Nora","last_name":"Walden","full_name":"Walden, Nora"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"}],"article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Cold Spring Harbor Perspectives in Biology","pmid":1,"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1101/cshperspect.a041447","publication_identifier":{"issn":["1943-0264"]},"language":[{"iso":"eng"}],"issue":"11","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_created":"2024-01-08T12:43:48Z","volume":15,"abstract":[{"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.","lang":"eng"}],"date_updated":"2024-01-08T12:52:29Z","month":"11","oa_version":"Published Version","type":"journal_article","_id":"14742","year":"2023","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"date_published":"2023-11-01T00:00:00Z","oa":1,"publication_status":"published","citation":{"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.","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>.","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>","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>.","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.","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>"},"intvolume":"        15","status":"public","external_id":{"pmid":["37604585"]}},{"quality_controlled":"1","doi":"10.1038/s41592-023-01937-5","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"language":[{"iso":"eng"}],"issue":"8","isi":1,"keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","day":"01","author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"}],"article_processing_charge":"No","scopus_import":"1","article_type":"letter_note","publication":"Nature Methods","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-08-01T00:00:00Z","publication_status":"published","citation":{"ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","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>","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>","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 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.","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>."},"intvolume":"        20","related_material":{"record":[{"status":"public","id":"13267","relation":"extended_version"}]},"external_id":{"isi":["001025621500002"]},"status":"public","date_created":"2024-01-10T08:07:15Z","volume":20,"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"}],"date_updated":"2024-01-10T08:37:48Z","month":"08","oa_version":"None","type":"journal_article","page":"1141-1142","_id":"14770","year":"2023"},{"doi":"10.1242/dev.201559","quality_controlled":"1","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"keyword":["Developmental Biology","Molecular Biology"],"isi":1,"issue":"19","language":[{"iso":"eng"}],"article_number":"dev201559","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","author":[{"last_name":"Harish","first_name":"Rohit K","full_name":"Harish, Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d"},{"full_name":"Gupta, Mansi","first_name":"Mansi","last_name":"Gupta"},{"first_name":"Daniela","last_name":"Zöller","full_name":"Zöller, Daniela"},{"full_name":"Hartmann, Hella","first_name":"Hella","last_name":"Hartmann"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"first_name":"Anja","last_name":"Machate","full_name":"Machate, Anja"},{"last_name":"Hans","first_name":"Stefan","full_name":"Hans, Stefan"},{"full_name":"Brand, Michael","first_name":"Michael","last_name":"Brand"}],"file":[{"success":1,"file_name":"2023_Development_Harish.pdf","content_type":"application/pdf","relation":"main_file","file_size":12836306,"creator":"dernst","date_updated":"2024-01-10T12:41:13Z","file_id":"14790","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","date_created":"2024-01-10T12:41:13Z","access_level":"open_access"}],"day":"01","publication":"Development","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","publisher":"The Company of Biologists","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnKi"}],"pmid":1,"ddc":["570"],"date_published":"2023-10-01T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"       150","citation":{"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>","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.","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>.","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>","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","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."},"status":"public","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"volume":150,"date_created":"2024-01-10T09:18:54Z","file_date_updated":"2024-01-10T12:41:13Z","month":"10","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_updated":"2024-01-10T12:45:25Z","_id":"14774","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.","year":"2023"},{"intvolume":"        24","citation":{"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>","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.","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>.","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>","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).","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>.","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."},"external_id":{"pmid":["38003717"],"isi":["001113792600001"]},"status":"public","ddc":["580"],"date_published":"2023-11-01T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","_id":"14776","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.","year":"2023","volume":24,"date_created":"2024-01-10T09:24:35Z","file_date_updated":"2024-01-10T13:39:42Z","month":"11","type":"journal_article","oa_version":"Published Version","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."}],"date_updated":"2024-01-10T13:41:10Z","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"isi":1,"issue":"22","language":[{"iso":"eng"}],"doi":"10.3390/ijms242216527","quality_controlled":"1","publication_identifier":{"issn":["1422-0067"]},"publication":"International Journal of Molecular Sciences","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"Yes","publisher":"MDPI","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"pmid":1,"article_number":"16527","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","author":[{"first_name":"Anastasiia","last_name":"Teplova","full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"last_name":"Serebryakova","first_name":"Marina V.","full_name":"Serebryakova, Marina V."},{"last_name":"Golyshev","first_name":"Sergei A.","full_name":"Golyshev, Sergei A."},{"full_name":"Galiullina, Raisa A.","first_name":"Raisa A.","last_name":"Galiullina"},{"full_name":"Chichkova, Nina V.","last_name":"Chichkova","first_name":"Nina V."},{"full_name":"Vartapetian, Andrey B.","first_name":"Andrey B.","last_name":"Vartapetian"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":2637784,"creator":"dernst","success":1,"file_name":"2023_IJMS_Teplova.pdf","date_created":"2024-01-10T13:39:42Z","access_level":"open_access","date_updated":"2024-01-10T13:39:42Z","file_id":"14791","checksum":"4df7d206ba022b7f54eff1f0aec1659a"}],"day":"01"},{"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"date_published":"2023-09-11T00:00:00Z","oa":1,"publication_status":"published","citation":{"ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","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>.","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>","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.","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>.","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."},"intvolume":"        58","external_id":{"pmid":["37463577"]},"status":"public","date_created":"2024-01-10T09:41:21Z","volume":58,"abstract":[{"text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency.","lang":"eng"}],"date_updated":"2024-01-16T08:56:36Z","oa_version":"Preprint","type":"journal_article","month":"09","page":"1578-1592.e5","_id":"14781","year":"2023","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","quality_controlled":"1","doi":"10.1016/j.devcel.2023.06.009","publication_identifier":{"issn":["1534-5807"]},"language":[{"iso":"eng"}],"issue":"17","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","day":"11","author":[{"last_name":"Westerich","first_name":"Kim Joana","full_name":"Westerich, Kim Joana"},{"full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna","last_name":"Tarbashevich"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"full_name":"Gupta, Antra","first_name":"Antra","last_name":"Gupta"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"first_name":"Kenneth","last_name":"Hull","full_name":"Hull, Kenneth"},{"first_name":"Daniel","last_name":"Romo","full_name":"Romo, Daniel"},{"last_name":"Zeuschner","first_name":"Dagmar","full_name":"Zeuschner, Dagmar"},{"full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","first_name":"Mohammad","last_name":"Goudarzi"},{"last_name":"Gross-Thebing","first_name":"Theresa","full_name":"Gross-Thebing, Theresa"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"article_processing_charge":"No","article_type":"original","publication":"Developmental Cell","pmid":1,"department":[{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier"},{"date_published":"2023-06-14T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"oa":1,"publication_status":"published","intvolume":"        14","extern":"1","citation":{"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>","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>.","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>","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (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>.","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."},"status":"public","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"volume":14,"date_created":"2023-08-09T13:06:59Z","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_updated":"2023-08-22T06:50:04Z","month":"06","type":"journal_article","oa_version":"Published Version","_id":"13989","year":"2023","doi":"10.1038/s41467-023-38540-3","quality_controlled":"1","publication_identifier":{"eissn":["2041-1723"]},"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"arxiv":1,"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","article_number":"3512","author":[{"full_name":"Hales, Jordyn","first_name":"Jordyn","last_name":"Hales"},{"full_name":"Bajpai, Utkarsh","last_name":"Bajpai","first_name":"Utkarsh"},{"full_name":"Liu, Tongtong","last_name":"Liu","first_name":"Tongtong"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Li","first_name":"Mingda","full_name":"Li, Mingda"},{"last_name":"Mitrano","first_name":"Matteo","full_name":"Mitrano, Matteo"},{"last_name":"Wang","first_name":"Yao","full_name":"Wang, Yao"}],"day":"14","publication":"Nature Communications","article_processing_charge":"No","scopus_import":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","pmid":1},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"language":[{"iso":"eng"}],"issue":"8","publication_identifier":{"issn":["2160-1836"]},"doi":"10.1093/g3journal/jkad121","quality_controlled":"1","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publication":"G3: Genes, Genomes, Genetics","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"day":"01","file":[{"date_updated":"2023-11-07T09:00:19Z","file_id":"14498","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_created":"2023-11-07T09:00:19Z","access_level":"open_access","success":1,"file_name":"2023_G3_Puixeu.pdf","content_type":"application/pdf","relation":"main_file","file_size":845642,"creator":"dernst"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","external_id":{"isi":["001002997200001"]},"status":"public","intvolume":"        13","related_material":{"record":[{"status":"public","id":"12933","relation":"research_data"},{"status":"public","id":"14058","relation":"dissertation_contains"}]},"citation":{"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>.","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.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","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>","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>","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).","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>."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2023-08-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"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).","year":"2023","_id":"14077","date_updated":"2023-12-13T12:15:37Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","month":"08","type":"journal_article","volume":13,"file_date_updated":"2023-11-07T09:00:19Z","date_created":"2023-08-18T06:52:14Z"},{"_id":"12163","acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","year":"2023","volume":597,"date_created":"2023-01-12T12:09:58Z","file_date_updated":"2023-08-16T08:31:04Z","page":"762-777","oa_version":"Published Version","type":"journal_article","month":"03","abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"date_updated":"2023-08-16T08:32:29Z","intvolume":"       597","citation":{"ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>"},"status":"public","external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"ddc":["570"],"date_published":"2023-03-01T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","publication":"FEBS Letters","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"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"},"article_type":"review","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaLo"}],"pmid":1,"title":"In vitro reconstitution of small GTPase regulation","author":[{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","last_name":"Auer","first_name":"Albert"},{"last_name":"Brognara","first_name":"Gabriel","full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"full_name":"Budiman, Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","first_name":"Hanifatul R","last_name":"Budiman"},{"id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M","first_name":"Lukasz M","last_name":"Kowalski"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"}],"day":"01","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"date_created":"2023-08-16T08:31:04Z","access_level":"open_access","date_updated":"2023-08-16T08:31:04Z","file_id":"14063","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","content_type":"application/pdf","relation":"main_file","file_size":3148143,"creator":"dernst","success":1,"file_name":"2023_FEBSLetters_Loose.pdf"}],"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"isi":1,"issue":"6","language":[{"iso":"eng"}],"doi":"10.1002/1873-3468.14540","quality_controlled":"1","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]}},{"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2023-04-27T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","external_id":{"isi":["000991468700001"]},"intvolume":"       186","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","relation":"press_release"}],"record":[{"status":"public","id":"13107","relation":"dissertation_contains"}]},"citation":{"short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>"},"page":"1950-1967.e25","month":"04","oa_version":"Published Version","type":"journal_article","date_updated":"2024-02-07T08:03:32Z","abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"volume":186,"file_date_updated":"2023-05-02T09:26:21Z","date_created":"2023-04-05T08:15:40Z","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","year":"2023","_id":"12802","publication_identifier":{"issn":["0092-8674"]},"doi":"10.1016/j.cell.2023.02.037","quality_controlled":"1","project":[{"grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"isi":1,"issue":"9","language":[{"iso":"eng"}],"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"},{"last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"full_name":"Malzl, Daniel","last_name":"Malzl","first_name":"Daniel"},{"first_name":"Maria","last_name":"Gerykova Bujalkova","full_name":"Gerykova Bujalkova, Maria"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"last_name":"Schwarz","first_name":"Lena A.","full_name":"Schwarz, Lena A."},{"full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","last_name":"Gorkiewicz","first_name":"Sarah"},{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Knittl-Frank, Christian","last_name":"Knittl-Frank","first_name":"Christian"},{"last_name":"Tassinari","first_name":"Marianna","full_name":"Tassinari, Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e"},{"full_name":"Maulide, Nuno","first_name":"Nuno","last_name":"Maulide"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"day":"27","file":[{"success":1,"file_name":"2023_Cell_Knaus.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":15712841,"checksum":"47e94fbe19e86505b429cb7a5b503ce6","date_updated":"2023-05-02T09:26:21Z","file_id":"12889","access_level":"open_access","date_created":"2023-05-02T09:26:21Z"}],"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"publication":"Cell","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (via OA deal)"},{"year":"2022","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","_id":"10787","month":"04","type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"date_updated":"2025-05-26T09:05:09Z","date_created":"2022-02-21T16:08:10Z","file_date_updated":"2022-08-02T06:14:32Z","volume":377,"external_id":{"pmid":["35184588"],"isi":["000758140300001"]},"status":"public","citation":{"ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>"},"intvolume":"       377","related_material":{"record":[{"id":"14711","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2022-04-11T00:00:00Z","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"The Royal Society","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","day":"11","file":[{"file_size":1349672,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","success":1,"date_created":"2022-08-02T06:14:32Z","access_level":"open_access","file_id":"11719","date_updated":"2022-08-02T06:14:32Z","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d"}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Oluwafunmilola O","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"title":"The response of a metapopulation to a changing environment","project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"}],"issue":"1848","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"isi":1,"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"quality_controlled":"1","doi":"10.1098/rstb.2021.0009"},{"status":"public","external_id":{"isi":["000785983900003"],"pmid":["35385734"]},"intvolume":"        39","related_material":{"record":[{"id":"12364","status":"public","relation":"dissertation_contains"}]},"citation":{"ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022.","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>"},"oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2022-04-05T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","year":"2022","_id":"11160","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"date_updated":"2024-03-25T23:30:25Z","oa_version":"Published Version","type":"journal_article","month":"04","volume":39,"date_created":"2022-04-15T09:03:10Z","file_date_updated":"2022-04-15T09:06:25Z","project":[{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205"}],"isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"issue":"1","publication_identifier":{"issn":["2211-1247"]},"doi":"10.1016/j.celrep.2022.110615","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","pmid":1,"department":[{"_id":"JoDa"},{"_id":"GaNo"}],"publication":"Cell Reports","article_processing_charge":"Yes","ec_funded":1,"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"first_name":"Carlo Emanuele","last_name":"Villa","full_name":"Villa, Carlo Emanuele"},{"first_name":"Cristina","last_name":"Cheroni","full_name":"Cheroni, Cristina"},{"first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"López-Tóbon, Alejandro","first_name":"Alejandro","last_name":"López-Tóbon"},{"full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","first_name":"Bárbara"},{"first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yahya, Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87","last_name":"Yahya","first_name":"Aysan Çerağ"},{"last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"full_name":"Gabriele, Michele","last_name":"Gabriele","first_name":"Michele"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Gabitto, Mariano","first_name":"Mariano","last_name":"Gabitto"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Testa, Giuseppe","first_name":"Giuseppe","last_name":"Testa"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"day":"05","file":[{"creator":"dernst","file_size":"7808644","relation":"main_file","content_type":"application/pdf","file_name":"2022_CellReports_Villa.pdf","success":1,"access_level":"open_access","date_created":"2022-04-15T09:06:25Z","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","file_id":"11164","date_updated":"2022-04-15T09:06:25Z"}],"title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","article_number":"110615"},{"year":"2022","_id":"11167","date_updated":"2023-08-03T06:31:06Z","abstract":[{"text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.","lang":"eng"}],"type":"journal_article","month":"06","oa_version":"Published Version","date_created":"2022-04-15T09:32:35Z","file_date_updated":"2022-08-05T05:56:03Z","volume":74,"status":"public","external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"citation":{"ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>"},"intvolume":"        74","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570"],"date_published":"2022-06-01T00:00:00Z","pmid":1,"department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Current Opinion in Structural Biology","day":"01","file":[{"creator":"dernst","file_size":815607,"relation":"main_file","content_type":"application/pdf","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","success":1,"access_level":"open_access","date_created":"2022-08-05T05:56:03Z","checksum":"72bdde48853643a32d42b75f54965c44","file_id":"11725","date_updated":"2022-08-05T05:56:03Z"}],"author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"}],"title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","article_number":"102350","language":[{"iso":"eng"}],"isi":1,"keyword":["Molecular Biology","Structural Biology"],"publication_identifier":{"issn":["0959-440X"]},"quality_controlled":"1","doi":"10.1016/j.sbi.2022.102350"},{"_id":"11351","acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","year":"2022","volume":32,"date_created":"2022-05-04T06:22:06Z","file_date_updated":"2022-08-05T06:29:18Z","page":"P2375-2389","month":"06","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"date_updated":"2023-08-03T07:05:36Z","intvolume":"        32","citation":{"short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>"},"status":"public","external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"ddc":["570"],"date_published":"2022-06-06T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","publication":"Current Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","department":[{"_id":"FlSc"}],"pmid":1,"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","author":[{"first_name":"William J.","last_name":"Nicolas","full_name":"Nicolas, William J."},{"first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"last_name":"Meyerowitz","first_name":"Elliot","full_name":"Meyerowitz, Elliot"}],"day":"06","file":[{"file_name":"2022_CurrentBiology_Nicolas.pdf","success":1,"creator":"dernst","file_size":12827717,"relation":"main_file","content_type":"application/pdf","checksum":"af3f24d97c016d844df237abef987639","file_id":"11730","date_updated":"2022-08-05T06:29:18Z","access_level":"open_access","date_created":"2022-08-05T06:29:18Z"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"isi":1,"issue":"11","language":[{"iso":"eng"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"doi":"10.1016/j.cub.2022.04.024","quality_controlled":"1","publication_identifier":{"issn":["0960-9822"]}}]