[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kuhn","first_name":"Andre","full_name":"Kuhn, Andre"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Mutte, Sumanth","last_name":"Mutte","first_name":"Sumanth"},{"first_name":"Shiv Mani","last_name":"Dubey","full_name":"Dubey, Shiv Mani"},{"full_name":"Carrillo Carrasco, Vanessa Polet","last_name":"Carrillo Carrasco","first_name":"Vanessa Polet"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"last_name":"Monzer","first_name":"Aline","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Koehorst, Jasper","last_name":"Koehorst","first_name":"Jasper"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"last_name":"Nishihama","first_name":"Ryuichi","full_name":"Nishihama, Ryuichi"},{"last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"full_name":"Sprakel, Joris","first_name":"Joris","last_name":"Sprakel"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"oa":1,"volume":187,"intvolume":"       187","publication":"Cell","date_updated":"2024-01-22T13:43:40Z","ec_funded":1,"department":[{"_id":"JiFr"}],"article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","doi":"10.1016/j.cell.2023.11.021","scopus_import":"1","file_date_updated":"2024-01-22T13:41:41Z","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","publication_status":"published","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","abstract":[{"text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.","lang":"eng"}],"year":"2024","citation":{"ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","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.","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>.","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>.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17."},"_id":"14826","date_created":"2024-01-17T12:45:40Z","file":[{"checksum":"06fd236a9ee0b46ccb05f44695bfc34b","content_type":"application/pdf","creator":"dernst","file_id":"14874","date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-22T13:41:41Z","file_size":13194060,"relation":"main_file","file_name":"2024_Cell_Kuhn.pdf","success":1,"access_level":"open_access"}],"publisher":"Elsevier","pmid":1,"date_published":"2024-01-04T00:00:00Z","external_id":{"pmid":["38128538"]},"type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["580"],"status":"public","month":"01","day":"04","page":"130-148.e17","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988"}],"has_accepted_license":"1","issue":"1"},{"_id":"14850","file":[{"success":1,"access_level":"open_access","file_name":"2024_JourExperimBiology_Pal.pdf","relation":"main_file","date_created":"2024-01-23T12:08:24Z","date_updated":"2024-01-23T12:08:24Z","file_size":594128,"file_id":"14877","creator":"dernst","content_type":"application/pdf","checksum":"136325372f6f45abaa62a71e2d23bfb6"}],"date_created":"2024-01-22T08:14:49Z","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>"}],"article_number":"jeb246217","year":"2024","citation":{"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.","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.","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>","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","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>.","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>."},"file_date_updated":"2024-01-23T12:08:24Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","publication_status":"published","article_type":"original","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.","publication_identifier":{"issn":["1477-9145"],"eissn":["0022-0949"]},"doi":"10.1242/jeb.246217","publication":"Journal of Experimental Biology","date_updated":"2024-01-23T12:13:08Z","department":[{"_id":"NiBa"}],"intvolume":"       227","related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"oa":1,"volume":227,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"first_name":"Mihir","last_name":"Joshi","full_name":"Joshi, Mihir"},{"first_name":"Maria","last_name":"Thaker","full_name":"Thaker, Maria"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"1","quality_controlled":"1","day":"10","status":"public","month":"01","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"ddc":["570"],"external_id":{"pmid":["38054353"]},"date_published":"2024-01-10T00:00:00Z","type":"journal_article","publisher":"The Company of Biologists","pmid":1},{"date_published":"2024-02-05T00:00:00Z","external_id":{"pmid":["38316877"]},"type":"journal_article","publisher":"Springer Nature","pmid":1,"month":"02","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Molecular Biology","Structural Biology"],"quality_controlled":"1","day":"05","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"oa":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"author":[{"first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse"},{"last_name":"Thader","first_name":"Andreas","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois"},{"last_name":"Bauer","first_name":"Lukas W","full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publication":"Nature Structural & Molecular Biology","date_updated":"2024-03-05T09:27:47Z","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","publication_status":"epub_ahead","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","doi":"10.1038/s41594-023-01201-6","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"article_type":"original","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.","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"_id":"14979","date_created":"2024-02-12T09:59:45Z","year":"2024","citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology (2024).","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>.","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.","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."},"abstract":[{"lang":"eng","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."}]},{"date_created":"2024-02-27T07:10:11Z","_id":"15033","abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"citation":{"ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>","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>.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>"},"year":"2024","oa_version":"Published Version","article_processing_charge":"Yes","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","publication_status":"epub_ahead","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","publication_identifier":{"issn":["2050-084X"]},"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"doi":"10.7554/elife.68993","date_updated":"2024-02-28T12:29:43Z","ec_funded":1,"publication":"eLife","department":[{"_id":"JiFr"}],"intvolume":"        13","volume":13,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"},{"first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"quality_controlled":"1","day":"21","status":"public","month":"02","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"ddc":["580"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2024-02-21T00:00:00Z","publisher":"eLife Sciences Publications"},{"month":"03","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"date_published":"2023-03-01T00:00:00Z","type":"journal_article","publisher":"Wiley","pmid":1,"issue":"6","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"quality_controlled":"1","page":"762-777","day":"01","department":[{"_id":"MaLo"}],"publication":"FEBS Letters","date_updated":"2023-08-16T08:32:29Z","intvolume":"       597","oa":1,"volume":597,"author":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"},{"last_name":"Auer","first_name":"Albert","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","last_name":"Brognara","first_name":"Gabriel"},{"first_name":"Hanifatul R","last_name":"Budiman","id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R"},{"last_name":"Kowalski","first_name":"Lukasz M","full_name":"Kowalski, Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2"},{"first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12163","date_created":"2023-01-12T12:09:58Z","file":[{"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","content_type":"application/pdf","file_id":"14063","creator":"dernst","relation":"main_file","file_size":3148143,"date_created":"2023-08-16T08:31:04Z","date_updated":"2023-08-16T08:31:04Z","file_name":"2023_FEBSLetters_Loose.pdf","access_level":"open_access","success":1}],"year":"2023","citation":{"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.","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.","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>","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.","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>."},"abstract":[{"lang":"eng","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."}],"title":"In vitro reconstitution of small GTPase regulation","publication_status":"published","file_date_updated":"2023-08-16T08:31:04Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","doi":"10.1002/1873-3468.14540","scopus_import":"1","article_type":"review","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"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."},{"quality_controlled":"1","day":"27","page":"1950-1967.e25","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"}],"issue":"9","external_id":{"isi":["000991468700001"]},"date_published":"2023-04-27T00:00:00Z","type":"journal_article","publisher":"Elsevier","status":"public","month":"04","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2023-05-02T09:26:21Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","publication_status":"published","article_type":"original","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","publication_identifier":{"issn":["0092-8674"]},"doi":"10.1016/j.cell.2023.02.037","scopus_import":"1","_id":"12802","file":[{"file_size":15712841,"relation":"main_file","date_updated":"2023-05-02T09:26:21Z","date_created":"2023-05-02T09:26:21Z","file_name":"2023_Cell_Knaus.pdf","success":1,"access_level":"open_access","checksum":"47e94fbe19e86505b429cb7a5b503ce6","content_type":"application/pdf","file_id":"12889","creator":"dernst"}],"date_created":"2023-04-05T08:15:40Z","abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"year":"2023","citation":{"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>","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.","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.","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>","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>.","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."},"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13107"}],"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","relation":"press_release","description":"News on ISTA Website"}]},"volume":186,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa"},{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico"},{"full_name":"Malzl, Daniel","last_name":"Malzl","first_name":"Daniel"},{"full_name":"Gerykova Bujalkova, Maria","first_name":"Maria","last_name":"Gerykova Bujalkova"},{"full_name":"Smogavec, Mateja","last_name":"Smogavec","first_name":"Mateja"},{"first_name":"Lena A.","last_name":"Schwarz","full_name":"Schwarz, Lena A."},{"last_name":"Gorkiewicz","first_name":"Sarah","full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"last_name":"Knittl-Frank","first_name":"Christian","full_name":"Knittl-Frank, Christian"},{"first_name":"Marianna","last_name":"Tassinari","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","full_name":"Tassinari, Marianna"},{"first_name":"Nuno","last_name":"Maulide","full_name":"Maulide, Nuno"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"publication":"Cell","ec_funded":1,"date_updated":"2024-02-07T08:03:32Z","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"intvolume":"       186"},{"quality_controlled":"1","day":"14","status":"public","month":"06","extern":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2023-06-14T00:00:00Z","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"pmid":1,"publisher":"Springer Nature","date_created":"2023-08-09T13:06:59Z","_id":"13989","abstract":[{"lang":"eng","text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements."}],"citation":{"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>","ieee":"J. Hales <i>et al.</i>, “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","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>.","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>","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","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>."},"article_number":"3512","year":"2023","article_processing_charge":"No","oa_version":"Published Version","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","scopus_import":"1","doi":"10.1038/s41467-023-38540-3","main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"date_updated":"2023-08-22T06:50:04Z","publication":"Nature Communications","intvolume":"        14","arxiv":1,"volume":14,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jordyn","last_name":"Hales","full_name":"Hales, Jordyn"},{"full_name":"Bajpai, Utkarsh","first_name":"Utkarsh","last_name":"Bajpai"},{"full_name":"Liu, Tongtong","first_name":"Tongtong","last_name":"Liu"},{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Li","first_name":"Mingda","full_name":"Li, Mingda"},{"first_name":"Matteo","last_name":"Mitrano","full_name":"Mitrano, Matteo"},{"last_name":"Wang","first_name":"Yao","full_name":"Wang, Yao"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"issue":"8","quality_controlled":"1","day":"01","status":"public","month":"08","isi":1,"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["001002997200001"]},"type":"journal_article","publisher":"Oxford University Press","_id":"14077","date_created":"2023-08-18T06:52:14Z","file":[{"file_size":845642,"relation":"main_file","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z","file_name":"2023_G3_Puixeu.pdf","success":1,"access_level":"open_access","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","creator":"dernst","content_type":"application/pdf"}],"abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"year":"2023","citation":{"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>","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","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>.","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023)."},"file_date_updated":"2023-11-07T09:00:19Z","article_processing_charge":"Yes","oa_version":"Published Version","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","publication_status":"published","article_type":"original","publication_identifier":{"issn":["2160-1836"]},"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).","doi":"10.1093/g3journal/jkad121","scopus_import":"1","publication":"G3: Genes, Genomes, Genetics","ec_funded":1,"date_updated":"2023-12-13T12:15:37Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"intvolume":"        13","related_material":{"record":[{"status":"public","relation":"research_data","id":"12933"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"oa":1,"volume":13,"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala"},{"last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}]},{"doi":"10.1093/molbev/msad245","scopus_import":"1","article_type":"original","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).","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","publication_status":"published","file_date_updated":"2024-01-02T11:39:38Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","article_number":"msad245","year":"2023","citation":{"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>.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","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>.","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>","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.","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."},"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"}],"_id":"14613","file":[{"relation":"main_file","file_size":8623505,"date_updated":"2024-01-02T11:39:38Z","date_created":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf","access_level":"open_access","success":1,"checksum":"47c1c72fb499f26ea52d216b242208c8","creator":"dernst","file_id":"14727","content_type":"application/pdf"}],"date_created":"2023-11-27T16:14:37Z","author":[{"orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine","first_name":"Clementine","last_name":"Lasne"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","last_name":"Layana Franco"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14614"}],"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}]},"oa":1,"volume":40,"intvolume":"        40","department":[{"_id":"BeVi"}],"publication":"Molecular Biology and Evolution","date_updated":"2024-02-21T12:18:35Z","day":"01","quality_controlled":"1","issue":"12","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"},{"grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity"}],"publisher":"Oxford University Press","pmid":1,"external_id":{"pmid":["37988296"]},"date_published":"2023-12-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"month":"12","status":"public"},{"_id":"14639","date_created":"2023-12-04T08:10:55Z","file":[{"relation":"main_file","file_size":14791081,"date_updated":"2023-12-04T08:15:43Z","date_created":"2023-12-04T08:15:43Z","success":1,"access_level":"open_access","file_name":"2023_GenomeMed_Lin.pdf","checksum":"279efd212005549aba817a487d56d363","creator":"dernst","file_id":"14640","content_type":"application/pdf"}],"article_number":"102","year":"2023","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.","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.","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>","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)."},"abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","publication_status":"published","file_date_updated":"2023-12-04T08:15:43Z","oa_version":"Published Version","article_processing_charge":"Yes","doi":"10.1186/s13073-023-01258-4","article_type":"original","publication_identifier":{"issn":["1756-994X"]},"publication":"Genome Medicine","date_updated":"2023-12-04T08:17:22Z","intvolume":"        15","oa":1,"volume":15,"author":[{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"first_name":"Barbara","last_name":"Vona","full_name":"Vona, Barbara"},{"last_name":"Lau","first_name":"Tracy","full_name":"Lau, Tracy"},{"first_name":"Kevin","last_name":"Huang","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin"},{"last_name":"Zaki","first_name":"Maha S.","full_name":"Zaki, Maha S."},{"first_name":"Huda Shujaa","last_name":"Aldeen","full_name":"Aldeen, Huda Shujaa"},{"last_name":"Karimiani","first_name":"Ehsan Ghayoor","full_name":"Karimiani, Ehsan Ghayoor"},{"full_name":"Rocca, Clarissa","first_name":"Clarissa","last_name":"Rocca"},{"full_name":"Noureldeen, Mahmoud M.","last_name":"Noureldeen","first_name":"Mahmoud M."},{"first_name":"Ahmed K.","last_name":"Saad","full_name":"Saad, Ahmed K."},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"first_name":"Tobias","last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias"},{"first_name":"Rami","last_name":"Abou Jamra","full_name":"Abou Jamra, Rami"},{"first_name":"Giovanni","last_name":"Zifarelli","full_name":"Zifarelli, Giovanni"},{"full_name":"Gotkhindikar, Aditi","last_name":"Gotkhindikar","first_name":"Aditi"},{"first_name":"Ingrid M.","last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M."},{"last_name":"Liao","first_name":"Mingjuan","full_name":"Liao, Mingjuan"},{"full_name":"Cork, Emalyn Elise","first_name":"Emalyn Elise","last_name":"Cork"},{"full_name":"Varshney, Pratishtha","last_name":"Varshney","first_name":"Pratishtha"},{"first_name":"Narges","last_name":"Hashemi","full_name":"Hashemi, Narges"},{"first_name":"Mohammad Hasan","last_name":"Mohammadi","full_name":"Mohammadi, Mohammad Hasan"},{"last_name":"Rad","first_name":"Aboulfazl","full_name":"Rad, Aboulfazl"},{"first_name":"Juanita","last_name":"Neira","full_name":"Neira, Juanita"},{"last_name":"Toosi","first_name":"Mehran Beiraghi","full_name":"Toosi, Mehran Beiraghi"},{"last_name":"Knopp","first_name":"Cordula","full_name":"Knopp, Cordula"},{"first_name":"Ingo","last_name":"Kurth","full_name":"Kurth, 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","last_name":"Haaf","first_name":"Thomas"},{"last_name":"Suri","first_name":"Mohnish","full_name":"Suri, Mohnish"},{"first_name":"Manali","last_name":"Joshi","full_name":"Joshi, Manali"},{"full_name":"Chung, Wendy K.","last_name":"Chung","first_name":"Wendy K."},{"last_name":"Moreno-De-Luca","first_name":"Andres","full_name":"Moreno-De-Luca, Andres"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"},{"full_name":"Varshney, Gaurav K.","first_name":"Gaurav K.","last_name":"Varshney"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"23","month":"11","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"extern":"1","date_published":"2023-11-23T00:00:00Z","type":"journal_article","publisher":"Springer Nature"},{"department":[{"_id":"SiHi"}],"ec_funded":1,"date_updated":"2023-12-18T08:06:14Z","publication":"STAR Protocols","intvolume":"         5","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"volume":5,"oa":1,"author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-12-13T11:48:05Z","_id":"14683","citation":{"ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2023.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","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>","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>."},"year":"2023","article_number":"102771","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"}],"publication_status":"epub_ahead","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","oa_version":"Submitted Version","article_processing_charge":"No","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"doi":"10.1016/j.xpro.2023.102771","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.","publication_identifier":{"issn":["2666-1667"]},"article_type":"review","month":"12","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"type":"journal_article","date_published":"2023-12-08T00:00:00Z","external_id":{"pmid":["38070137"]},"pmid":1,"publisher":"Elsevier","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}],"quality_controlled":"1","day":"08"},{"_id":"14742","date_created":"2024-01-08T12:43:48Z","abstract":[{"lang":"eng","text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life."}],"article_number":"a041447","year":"2023","citation":{"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>","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).","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447."},"article_processing_charge":"No","oa_version":"Published Version","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","publication_status":"published","article_type":"original","publication_identifier":{"issn":["1943-0264"]},"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":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"doi":"10.1101/cshperspect.a041447","scopus_import":"1","publication":"Cold Spring Harbor Perspectives in Biology","date_updated":"2024-01-08T12:52:29Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"intvolume":"        15","oa":1,"volume":15,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"full_name":"Giménez, Mabel D.","first_name":"Mabel D.","last_name":"Giménez"},{"full_name":"Joron, Mathieu","first_name":"Mathieu","last_name":"Joron"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"last_name":"Walden","first_name":"Nora","full_name":"Walden, Nora"},{"first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"issue":"11","quality_controlled":"1","day":"01","status":"public","month":"11","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"date_published":"2023-11-01T00:00:00Z","external_id":{"pmid":["37604585"]},"type":"journal_article","publisher":"Cold Spring Harbor Laboratory","pmid":1},{"intvolume":"        20","publication":"Nature Methods","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","last_name":"Velicky","first_name":"Philipp"}],"related_material":{"record":[{"id":"13267","relation":"extended_version","status":"public"}]},"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"}],"year":"2023","citation":{"ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","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>.","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>"},"_id":"14770","date_created":"2024-01-10T08:07:15Z","article_type":"letter_note","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"doi":"10.1038/s41592-023-01937-5","scopus_import":"1","oa_version":"None","article_processing_charge":"No","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","publication_status":"published","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"language":[{"iso":"eng"}],"status":"public","month":"08","isi":1,"publisher":"Springer Nature","date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["001025621500002"]},"type":"journal_article","issue":"8","day":"01","page":"1141-1142","quality_controlled":"1"},{"external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"date_published":"2023-10-01T00:00:00Z","type":"journal_article","publisher":"The Company of Biologists","pmid":1,"month":"10","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Developmental Biology","Molecular Biology"],"quality_controlled":"1","day":"01","issue":"19","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","oa":1,"volume":150,"author":[{"first_name":"Rohit K","last_name":"Harish","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","full_name":"Harish, Rohit K"},{"last_name":"Gupta","first_name":"Mansi","full_name":"Gupta, Mansi"},{"first_name":"Daniela","last_name":"Zöller","full_name":"Zöller, Daniela"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"first_name":"Ali","last_name":"Gheisari","full_name":"Gheisari, Ali"},{"last_name":"Machate","first_name":"Anja","full_name":"Machate, Anja"},{"full_name":"Hans, Stefan","last_name":"Hans","first_name":"Stefan"},{"last_name":"Brand","first_name":"Michael","full_name":"Brand, Michael"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnKi"}],"publication":"Development","date_updated":"2024-01-10T12:45:25Z","intvolume":"       150","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","publication_status":"published","file_date_updated":"2024-01-10T12:41:13Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","doi":"10.1242/dev.201559","article_type":"original","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.","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"_id":"14774","date_created":"2024-01-10T09:18:54Z","file":[{"file_id":"14790","creator":"dernst","content_type":"application/pdf","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","access_level":"open_access","success":1,"file_name":"2023_Development_Harish.pdf","file_size":12836306,"relation":"main_file","date_created":"2024-01-10T12:41:13Z","date_updated":"2024-01-10T12:41:13Z"}],"year":"2023","article_number":"dev201559","citation":{"ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","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.","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.","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>.","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>.","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>"},"abstract":[{"lang":"eng","text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential."}]},{"intvolume":"        24","department":[{"_id":"JiFr"}],"date_updated":"2024-01-10T13:41:10Z","publication":"International Journal of Molecular Sciences","author":[{"first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"last_name":"Pigidanov","first_name":"Artemii A.","full_name":"Pigidanov, Artemii A."},{"full_name":"Serebryakova, Marina V.","last_name":"Serebryakova","first_name":"Marina V."},{"first_name":"Sergei A.","last_name":"Golyshev","full_name":"Golyshev, Sergei A."},{"full_name":"Galiullina, Raisa A.","last_name":"Galiullina","first_name":"Raisa A."},{"first_name":"Nina V.","last_name":"Chichkova","full_name":"Chichkova, Nina V."},{"full_name":"Vartapetian, Andrey B.","first_name":"Andrey B.","last_name":"Vartapetian"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":24,"oa":1,"citation":{"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>.","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>.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527."},"year":"2023","article_number":"16527","abstract":[{"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.","lang":"eng"}],"date_created":"2024-01-10T09:24:35Z","file":[{"content_type":"application/pdf","file_id":"14791","creator":"dernst","checksum":"4df7d206ba022b7f54eff1f0aec1659a","success":1,"access_level":"open_access","file_name":"2023_IJMS_Teplova.pdf","file_size":2637784,"date_updated":"2024-01-10T13:39:42Z","date_created":"2024-01-10T13:39:42Z","relation":"main_file"}],"_id":"14776","doi":"10.3390/ijms242216527","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.","publication_identifier":{"issn":["1422-0067"]},"article_type":"original","publication_status":"published","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","article_processing_charge":"Yes","oa_version":"Published Version","file_date_updated":"2024-01-10T13:39:42Z","ddc":["580"],"language":[{"iso":"eng"}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"isi":1,"month":"11","status":"public","pmid":1,"publisher":"MDPI","type":"journal_article","external_id":{"pmid":["38003717"],"isi":["001113792600001"]},"date_published":"2023-11-01T00:00:00Z","issue":"22","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"01","quality_controlled":"1"},{"oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","publication_identifier":{"issn":["1534-5807"]},"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"doi":"10.1016/j.devcel.2023.06.009","date_created":"2024-01-10T09:41:21Z","_id":"14781","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"citation":{"ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","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>","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.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>."},"year":"2023","volume":58,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Westerich","first_name":"Kim Joana","full_name":"Westerich, Kim Joana"},{"full_name":"Tarbashevich, Katsiaryna","first_name":"Katsiaryna","last_name":"Tarbashevich"},{"first_name":"Jan","last_name":"Schick","full_name":"Schick, Jan"},{"full_name":"Gupta, Antra","first_name":"Antra","last_name":"Gupta"},{"full_name":"Zhu, Mingzhao","last_name":"Zhu","first_name":"Mingzhao"},{"last_name":"Hull","first_name":"Kenneth","full_name":"Hull, Kenneth"},{"full_name":"Romo, Daniel","last_name":"Romo","first_name":"Daniel"},{"last_name":"Zeuschner","first_name":"Dagmar","full_name":"Zeuschner, Dagmar"},{"full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad"},{"last_name":"Gross-Thebing","first_name":"Theresa","full_name":"Gross-Thebing, Theresa"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"date_updated":"2024-01-16T08:56:36Z","publication":"Developmental Cell","department":[{"_id":"Bio"}],"intvolume":"        58","quality_controlled":"1","day":"11","page":"1578-1592.e5","issue":"17","type":"journal_article","external_id":{"pmid":["37463577"]},"date_published":"2023-09-11T00:00:00Z","pmid":1,"publisher":"Elsevier","status":"public","month":"09","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"language":[{"iso":"eng"}]},{"publisher":"Public Library of Science","external_id":{"isi":["000924885500005"]},"date_published":"2022-10-17T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"month":"10","isi":1,"status":"public","day":"17","quality_controlled":"1","issue":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752"}],"author":[{"last_name":"Jiang","first_name":"Xiuyun","full_name":"Jiang, Xiuyun"},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","last_name":"Vanhille-Campos","first_name":"Christian Eduardo"},{"first_name":"Anna-Katharina","last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina"},{"full_name":"Lominadze, Elene","last_name":"Lominadze","first_name":"Elene"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"oa":1,"volume":18,"intvolume":"        18","department":[{"_id":"AnSa"}],"publication":"PLOS Computational Biology","date_updated":"2023-08-04T09:03:21Z","ec_funded":1,"doi":"10.1371/journal.pcbi.1010586","scopus_import":"1","article_type":"original","acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","file_date_updated":"2023-01-24T10:45:01Z","article_processing_charge":"No","oa_version":"Published Version","article_number":"e1010586","year":"2022","citation":{"mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>.","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586."},"abstract":[{"text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.","lang":"eng"}],"_id":"12152","file":[{"file_name":"2022_PLoSCompBio_Jiang.pdf","success":1,"access_level":"open_access","date_created":"2023-01-24T10:45:01Z","relation":"main_file","file_size":2641067,"date_updated":"2023-01-24T10:45:01Z","file_id":"12359","creator":"dernst","content_type":"application/pdf","checksum":"bada6a7865e470cf42bbdfa67dd471d2"}],"date_created":"2023-01-12T12:08:10Z"},{"scopus_import":"1","doi":"10.1016/j.coisb.2022.100435","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","publication_identifier":{"issn":["2452-3100"]},"article_type":"original","publication_status":"published","title":"Eukaryotic gene regulation at equilibrium, or non?","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","file_date_updated":"2023-01-24T12:14:10Z","citation":{"mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>"},"year":"2022","article_number":"100435","abstract":[{"lang":"eng","text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code."}],"file":[{"access_level":"open_access","success":1,"file_name":"2022_CurrentBiology_Zoller.pdf","date_updated":"2023-01-24T12:14:10Z","file_size":2214944,"date_created":"2023-01-24T12:14:10Z","relation":"main_file","creator":"dernst","file_id":"12362","content_type":"application/pdf","checksum":"97ef01e0cc60cdc84f45640a0f248fb0"}],"date_created":"2023-01-12T12:08:51Z","_id":"12156","author":[{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":31,"oa":1,"intvolume":"        31","department":[{"_id":"GaTk"}],"date_updated":"2023-02-13T09:20:34Z","publication":"Current Opinion in Systems Biology","day":"01","quality_controlled":"1","issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publisher":"Elsevier","type":"journal_article","date_published":"2022-09-01T00:00:00Z","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"month":"09","status":"public"},{"_id":"12157","date_created":"2023-01-12T12:09:00Z","file":[{"relation":"main_file","date_created":"2023-01-24T12:21:32Z","file_size":18935612,"date_updated":"2023-01-24T12:21:32Z","success":1,"access_level":"open_access","file_name":"2022_eLife_Hayward.pdf","checksum":"28de155b231ac1c8d4501c98b2fb359a","file_id":"12363","creator":"dernst","content_type":"application/pdf"}],"article_number":"66697","year":"2022","citation":{"ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"title":"Polygenic adaptation after a sudden change in environment","publication_status":"published","file_date_updated":"2023-01-24T12:21:32Z","oa_version":"Published Version","article_processing_charge":"No","doi":"10.7554/elife.66697","scopus_import":"1","article_type":"original","acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","publication_identifier":{"eissn":["2050-084X"]},"department":[{"_id":"NiBa"}],"publication":"eLife","date_updated":"2023-08-04T09:04:58Z","intvolume":"        11","oa":1,"volume":11,"author":[{"full_name":"Hayward, Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","last_name":"Hayward","first_name":"Laura"},{"last_name":"Sella","first_name":"Guy","full_name":"Sella, Guy"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"quality_controlled":"1","day":"26","month":"09","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"external_id":{"isi":["000890735600001"]},"date_published":"2022-09-26T00:00:00Z","type":"journal_article","publisher":"eLife Sciences Publications"},{"intvolume":"        13","department":[{"_id":"StFr"}],"date_updated":"2023-08-04T09:15:31Z","publication":"Nature Communications","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"von Mentlen, Jean-Marc","first_name":"Jean-Marc","last_name":"von Mentlen"},{"full_name":"Drvarič Talian, Sara","first_name":"Sara","last_name":"Drvarič Talian"},{"full_name":"Vizintin, Alen","last_name":"Vizintin","first_name":"Alen"},{"full_name":"Dominko, Robert","last_name":"Dominko","first_name":"Robert"},{"last_name":"Amenitsch","first_name":"Heinz","full_name":"Amenitsch, Heinz"},{"full_name":"Porcar, Lionel","last_name":"Porcar","first_name":"Lionel"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Wood","first_name":"Vanessa","full_name":"Wood, Vanessa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":13,"oa":1,"citation":{"short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).","apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>","chicago":"Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin, Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger, and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>.","mla":"Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>, vol. 13, 6326, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>.","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>","ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326.","ieee":"C. Prehal <i>et al.</i>, “On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"year":"2022","article_number":"6326","abstract":[{"text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells.","lang":"eng"}],"date_created":"2023-01-16T09:45:09Z","file":[{"file_id":"12411","creator":"dernst","content_type":"application/pdf","checksum":"5034336dbf0f860030ef745c08df9e0e","access_level":"open_access","success":1,"file_name":"2022_NatureCommunications_Prehal.pdf","file_size":4216931,"date_created":"2023-01-27T07:19:11Z","date_updated":"2023-01-27T07:19:11Z","relation":"main_file"}],"_id":"12208","scopus_import":"1","doi":"10.1038/s41467-022-33931-4","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for the access to the Austrian SAXS beamline and TU Graz for support through the Lead Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition, the authors acknowledge access to the D-22SANS beamline at the ILL neutron source. Electron microscopy measurements were performed at the Scientific Scenter for Optical and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P. and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F. is indebted to IST Austria for support. ","publication_identifier":{"issn":["2041-1723"]},"article_type":"original","publication_status":"published","title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2023-01-27T07:19:11Z","ddc":["540"],"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"isi":1,"month":"10","status":"public","pmid":1,"publisher":"Springer Nature","type":"journal_article","date_published":"2022-10-24T00:00:00Z","external_id":{"pmid":["36280671"],"isi":["000871563700006"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"24","quality_controlled":"1"}]