[{"file_date_updated":"2024-01-22T13:41:41Z","article_type":"original","_id":"14826","doi":"10.1016/j.cell.2023.11.021","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.","year":"2024","date_created":"2024-01-17T12:45:40Z","citation":{"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.","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.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","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>."},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"ec_funded":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"}],"publisher":"Elsevier","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_published":"2024-01-04T00:00:00Z","department":[{"_id":"JiFr"}],"page":"130-148.e17","quality_controlled":"1","volume":187,"publication_status":"published","ddc":["580"],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"external_id":{"pmid":["38128538"]},"abstract":[{"lang":"eng","text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage."}],"language":[{"iso":"eng"}],"publication":"Cell","date_updated":"2024-01-22T13:43:40Z","oa":1,"issue":"1","article_processing_charge":"Yes (in subscription journal)","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","intvolume":"       187","has_accepted_license":"1","scopus_import":"1","pmid":1,"status":"public","type":"journal_article","author":[{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"first_name":"Sumanth","full_name":"Mutte, Sumanth","last_name":"Mutte"},{"first_name":"Shiv Mani","full_name":"Dubey, Shiv Mani","last_name":"Dubey"},{"first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet","last_name":"Carrillo Carrasco"},{"full_name":"Boeren, Sjef","first_name":"Sjef","last_name":"Boeren"},{"last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","first_name":"Aline"},{"first_name":"Jasper","full_name":"Koehorst, Jasper","last_name":"Koehorst"},{"last_name":"Kohchi","first_name":"Takayuki","full_name":"Kohchi, Takayuki"},{"last_name":"Nishihama","full_name":"Nishihama, Ryuichi","first_name":"Ryuichi"},{"first_name":"Matyas","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"first_name":"Joris","full_name":"Sprakel, Joris","last_name":"Sprakel"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"}],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"month":"01","oa_version":"Published Version","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"06fd236a9ee0b46ccb05f44695bfc34b","file_name":"2024_Cell_Kuhn.pdf","file_id":"14874","success":1,"date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-22T13:41:41Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":13194060}]},{"project":[{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"department":[{"_id":"MaLo"}],"volume":103,"quality_controlled":"1","publisher":"Elsevier","date_published":"2024-01-12T00:00:00Z","publication_status":"epub_ahead","external_id":{"pmid":["38218128"]},"abstract":[{"lang":"eng","text":"Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today."}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"review","_id":"14834","doi":"10.1016/j.ejcb.2023.151380","date_created":"2024-01-18T08:16:43Z","citation":{"apa":"Radler, P., &#38; Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>","ieee":"P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” <i>European Journal of Cell Biology</i>, vol. 103, no. 1. Elsevier, 2024.","ama":"Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. <i>European Journal of Cell Biology</i>. 2024;103(1). doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>","short":"P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).","ista":"Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380.","chicago":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">https://doi.org/10.1016/j.ejcb.2023.151380</a>.","mla":"Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” <i>European Journal of Cell Biology</i>, vol. 103, no. 1, 151380, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2023.151380\">10.1016/j.ejcb.2023.151380</a>."},"keyword":["Cell Biology","General Medicine","Histology","Pathology and Forensic Medicine"],"acknowledgement":"We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L.","year":"2024","article_number":"151380","pmid":1,"status":"public","type":"journal_article","author":[{"first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","orcid":"0000-0001-9198-2182 "},{"full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"day":"12","main_file_link":[{"url":"https://doi.org/10.1016/j.ejcb.2023.151380","open_access":"1"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0171-9335"]},"month":"01","language":[{"iso":"eng"}],"publication":"European Journal of Cell Biology","title":"A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches","date_updated":"2024-01-23T08:37:13Z","oa":1,"issue":"1","article_processing_charge":"Yes","has_accepted_license":"1","intvolume":"       103","scopus_import":"1"},{"volume":227,"quality_controlled":"1","department":[{"_id":"NiBa"}],"date_published":"2024-01-10T00:00:00Z","publisher":"The Company of Biologists","abstract":[{"text":"Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals.</jats:p>","lang":"eng"}],"external_id":{"pmid":["38054353"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","doi":"10.1242/jeb.246217","article_type":"original","_id":"14850","file_date_updated":"2024-01-23T12:08:24Z","related_material":{"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"article_number":"jeb246217","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"citation":{"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>","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>.","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","mla":"Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>, vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jeb.246217\">10.1242/jeb.246217</a>.","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>"},"date_created":"2024-01-22T08:14:49Z","year":"2024","acknowledgement":"We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions, and help with sampling and colour analyses. We thank Muralidhar and the central LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch funding was provided by the Department of Science and Technology Fund for Improvement of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute of Science (DBT-IISc) partnership program and a Science and Engineering Research Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian Institute of Science. Deposited in PMC for immediate release.","status":"public","type":"journal_article","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2024-01-23T12:08:24Z","date_updated":"2024-01-23T12:08:24Z","success":1,"file_id":"14877","checksum":"136325372f6f45abaa62a71e2d23bfb6","file_name":"2024_JourExperimBiology_Pal.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":594128,"creator":"dernst"}],"day":"10","oa_version":"Published Version","month":"01","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"author":[{"full_name":"Pal, Arka","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","orcid":"0000-0002-4530-8469"},{"last_name":"Joshi","full_name":"Joshi, Mihir","first_name":"Mihir"},{"last_name":"Thaker","full_name":"Thaker, Maria","first_name":"Maria"}],"publication":"Journal of Experimental Biology","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"       227","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","issue":"1","article_processing_charge":"Yes (via OA deal)","date_updated":"2024-01-23T12:13:08Z","oa":1},{"date_published":"2024-02-05T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"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."}],"external_id":{"pmid":["38316877"]},"publication_status":"epub_ahead","doi":"10.1038/s41594-023-01201-6","article_type":"original","_id":"14979","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website"}]},"year":"2024","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","keyword":["Molecular Biology","Structural Biology"],"date_created":"2024-02-12T09:59:45Z","citation":{"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>.","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>.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","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.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology (2024).","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>"},"status":"public","type":"journal_article","pmid":1,"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"day":"05","author":[{"orcid":"0000-0002-3616-8580","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","first_name":"Julia"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse","full_name":"Hansen, Jesse"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","first_name":"Andreas","full_name":"Thader, Andreas"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"first_name":"Lukas W","full_name":"Bauer, Lukas W","last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature Structural & Molecular Biology","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","oa":1,"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"},{"doi":"10.15479/at:ista:15020","_id":"15020","file_date_updated":"2024-02-23T14:20:16Z","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7553","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7606"},{"id":"12081","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"year":"2024","keyword":["Theoretical biology","Optimality","Evolution","Information"],"citation":{"apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>."},"date_created":"2024-02-23T14:02:04Z","date_published":"2024-02-23T00:00:00Z","supervisor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"publisher":"Institute of Science and Technology Austria","page":"158","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"ddc":["576","519"],"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","date_updated":"2025-06-30T13:21:09Z","oa":1,"title":"Genetic information and biological optimization","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663 - 337X"]},"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"mhledik","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":7102089,"success":1,"file_name":"hledik thesis pdfa 2b.pdf","checksum":"b2d3da47c98d481577a4baf68944fe41","file_id":"15021","date_created":"2024-02-23T13:50:53Z","date_updated":"2024-02-23T13:50:53Z"},{"creator":"mhledik","file_size":14014790,"relation":"source_file","content_type":"application/zip","access_level":"closed","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z"}],"day":"23","oa_version":"Published Version","author":[{"full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}]},{"publication":"eLife","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"        13","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","date_updated":"2024-02-28T12:29:43Z","oa":1,"article_processing_charge":"Yes","status":"public","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"day":"21","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2050-084X"]},"month":"02","author":[{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","first_name":"Maciek"},{"full_name":"Matijevic, Ivana","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"}],"doi":"10.7554/elife.68993","article_type":"original","_id":"15033","ec_funded":1,"citation":{"apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","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>.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","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>"},"date_created":"2024-02-27T07:10:11Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","year":"2024","department":[{"_id":"JiFr"}],"quality_controlled":"1","volume":13,"publisher":"eLife Sciences Publications","date_published":"2024-02-21T00:00:00Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"ddc":["580"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"epub_ahead"},{"pmid":1,"type":"journal_article","status":"public","author":[{"first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"}],"month":"12","publication_identifier":{"issn":["1084-9521"]},"oa_version":"Published Version","day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_size":1343750,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_created":"2024-01-08T10:16:04Z","date_updated":"2024-01-08T10:16:04Z","success":1,"checksum":"c619887cf130f4649bf3035417186004","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","file_id":"14741"}],"language":[{"iso":"eng"}],"publication":"Seminars in Cell & Developmental Biology","oa":1,"date_updated":"2024-01-16T13:22:32Z","article_processing_charge":"Yes (via OA deal)","title":"Modelling the dynamics of mammalian gut homeostasis","isi":1,"scopus_import":"1","has_accepted_license":"1","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"publisher":"Elsevier","date_published":"2023-12-02T00:00:00Z","page":"58-65","department":[{"_id":"EdHa"}],"volume":"150-151","quality_controlled":"1","publication_status":"published","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001053522200001"],"pmid":["36470715"]},"abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"file_date_updated":"2024-01-08T10:16:04Z","_id":"12162","article_type":"review","doi":"10.1016/j.semcdb.2022.11.005","acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","year":"2023","citation":{"ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell &#38; Developmental Biology. 150–151, 58–65.","chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. 2023;150-151:58-65. doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151. Elsevier, pp. 58–65, 2023.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell &#38; Developmental Biology 150–151 (2023) 58–65.","apa":"Corominas-Murtra, B., &#38; Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>"},"date_created":"2023-01-12T12:09:47Z","keyword":["Cell Biology","Developmental Biology"],"ec_funded":1},{"status":"public","type":"journal_article","pmid":1,"author":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"last_name":"Auer","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3580-2906","first_name":"Albert","full_name":"Auer, Albert"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel"},{"last_name":"Budiman","id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R"},{"id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","last_name":"Kowalski","full_name":"Kowalski, Lukasz M","first_name":"Lukasz M"},{"full_name":"Matijevic, Ivana","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_size":3148143,"content_type":"application/pdf","relation":"main_file","creator":"dernst","date_updated":"2023-08-16T08:31:04Z","date_created":"2023-08-16T08:31:04Z","file_id":"14063","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","file_name":"2023_FEBSLetters_Loose.pdf","success":1}],"day":"01","oa_version":"Published Version","month":"03","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"language":[{"iso":"eng"}],"publication":"FEBS Letters","title":"In vitro reconstitution of small GTPase regulation","issue":"6","article_processing_charge":"Yes (via OA deal)","oa":1,"date_updated":"2023-08-16T08:32:29Z","intvolume":"       597","has_accepted_license":"1","scopus_import":"1","isi":1,"volume":597,"quality_controlled":"1","department":[{"_id":"MaLo"}],"page":"762-777","date_published":"2023-03-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Wiley","publication_status":"published","abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"_id":"12163","article_type":"review","file_date_updated":"2023-08-16T08:31:04Z","doi":"10.1002/1873-3468.14540","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"date_created":"2023-01-12T12:09:58Z","citation":{"apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","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.","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>","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>."},"year":"2023","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."},{"language":[{"iso":"eng"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","oa":1,"date_updated":"2024-02-08T23:30:05Z","article_processing_charge":"No","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","author":[{"last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","full_name":"Zens, Bettina"}],"day":"02","oa_version":"Published Version","file":[{"date_created":"2023-02-07T13:07:38Z","date_updated":"2024-02-08T23:30:04Z","embargo":"2024-02-07","file_id":"12527","checksum":"069d87f025e0799bf9e3c375664264f2","file_name":"PhDThesis_BettinaZens_2023_final.pdf","file_size":23082464,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"bzens"},{"checksum":"8c66ed203495d6e078ed1002a866520c","file_name":"PhDThesis_BettinaZens_2023_final.docx","file_id":"12528","date_created":"2023-02-07T13:09:05Z","date_updated":"2024-02-08T23:30:04Z","creator":"bzens","embargo_to":"open_access","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":106169509}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2024-02-08T23:30:04Z","_id":"12491","doi":"10.15479/at:ista:12491","citation":{"ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>"},"date_created":"2023-02-02T14:50:20Z","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"year":"2023","related_material":{"record":[{"relation":"part_of_dissertation","id":"8586","status":"public"}]},"degree_awarded":"PhD","project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"page":"187","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078"}],"date_published":"2023-02-02T00:00:00Z","publication_status":"published","abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"ddc":["570"]},{"publication":"The Plant Cell","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"        35","title":"Beyond transcription: compelling open questions in plant RNA biology","oa":1,"date_updated":"2023-10-04T09:48:43Z","article_processing_charge":"No","issue":"6","pmid":1,"status":"public","type":"journal_article","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1093/plcell/koac346","open_access":"1"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"author":[{"first_name":"Pablo A","full_name":"Manavella, Pablo A","last_name":"Manavella"},{"first_name":"Micaela A","full_name":"Godoy Herz, Micaela A","last_name":"Godoy Herz"},{"last_name":"Kornblihtt","first_name":"Alberto R","full_name":"Kornblihtt, Alberto R"},{"last_name":"Sorenson","full_name":"Sorenson, Reed","first_name":"Reed"},{"full_name":"Sieburth, Leslie E","first_name":"Leslie E","last_name":"Sieburth"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"first_name":"Yiliang","full_name":"Ding, Yiliang","last_name":"Ding"},{"last_name":"Sun","first_name":"Qianwen","full_name":"Sun, Qianwen"},{"first_name":"Hunseung","full_name":"Kang, Hunseung","last_name":"Kang"},{"last_name":"Ariel","first_name":"Federico D","full_name":"Ariel, Federico D"},{"last_name":"Crespi","full_name":"Crespi, Martin","first_name":"Martin"},{"first_name":"Axel J","full_name":"Giudicatti, Axel J","last_name":"Giudicatti"},{"last_name":"Cai","full_name":"Cai, Qiang","first_name":"Qiang"},{"full_name":"Jin, Hailing","first_name":"Hailing","last_name":"Jin"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"last_name":"Qi","first_name":"Yijun","full_name":"Qi, Yijun"},{"first_name":"Craig S","full_name":"Pikaard, Craig S","last_name":"Pikaard"}],"doi":"10.1093/plcell/koac346","article_type":"original","_id":"12669","article_number":"koac346","citation":{"short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. 2023;35(6). doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>","ieee":"P. A. Manavella <i>et al.</i>, “Beyond transcription: compelling open questions in plant RNA biology,” <i>The Plant Cell</i>, vol. 35, no. 6. Oxford University Press, 2023.","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>.","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>"},"date_created":"2023-02-23T09:14:59Z","keyword":["Cell Biology","Plant Science"],"year":"2023","extern":"1","department":[{"_id":"XiFe"}],"volume":35,"quality_controlled":"1","publisher":"Oxford University Press","date_published":"2023-06-01T00:00:00Z","external_id":{"pmid":["36477566"]},"abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"publication_status":"published"},{"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_identifier":{"issn":["2522-5812"]},"author":[{"first_name":"Domagoj","full_name":"Cikes, Domagoj","last_name":"Cikes"},{"last_name":"Elsayad","full_name":"Elsayad, Kareem","first_name":"Kareem"},{"last_name":"Sezgin","full_name":"Sezgin, Erdinc","first_name":"Erdinc"},{"full_name":"Koitai, Erika","first_name":"Erika","last_name":"Koitai"},{"last_name":"Ferenc","full_name":"Ferenc, Torma","first_name":"Torma"},{"first_name":"Michael","full_name":"Orthofer, Michael","last_name":"Orthofer"},{"last_name":"Yarwood","first_name":"Rebecca","full_name":"Yarwood, Rebecca"},{"first_name":"Leonhard X.","full_name":"Heinz, Leonhard X.","last_name":"Heinz"},{"first_name":"Vitaly","full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov"},{"orcid":"0000-0002-8821-8236","last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser","first_name":"Nasser"},{"first_name":"Adrian","full_name":"Taylor, Adrian","last_name":"Taylor"},{"last_name":"Grapentine","full_name":"Grapentine, Sophie","first_name":"Sophie"},{"first_name":"Fathiya","full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi"},{"last_name":"Abot","first_name":"Anne","full_name":"Abot, Anne"},{"last_name":"Weidinger","full_name":"Weidinger, Adelheid","first_name":"Adelheid"},{"full_name":"Kutchukian, Candice","first_name":"Candice","last_name":"Kutchukian"},{"last_name":"Sanchez","full_name":"Sanchez, Colline","first_name":"Colline"},{"first_name":"Shane J. F.","full_name":"Cronin, Shane J. F.","last_name":"Cronin"},{"full_name":"Novatchkova, Maria","first_name":"Maria","last_name":"Novatchkova"},{"last_name":"Kavirayani","full_name":"Kavirayani, Anoop","first_name":"Anoop"},{"last_name":"Schuetz","first_name":"Thomas","full_name":"Schuetz, Thomas"},{"last_name":"Haubner","full_name":"Haubner, Bernhard","first_name":"Bernhard"},{"full_name":"Haas, Lisa","first_name":"Lisa","last_name":"Haas"},{"full_name":"Hagelkruys, Astrid","first_name":"Astrid","last_name":"Hagelkruys"},{"last_name":"Jackowski","full_name":"Jackowski, Suzanne","first_name":"Suzanne"},{"full_name":"Kozlov, Andrey","first_name":"Andrey","last_name":"Kozlov"},{"last_name":"Jacquemond","first_name":"Vincent","full_name":"Jacquemond, Vincent"},{"last_name":"Knauf","first_name":"Claude","full_name":"Knauf, Claude"},{"full_name":"Superti-Furga, Giulio","first_name":"Giulio","last_name":"Superti-Furga"},{"first_name":"Eric","full_name":"Rullman, Eric","last_name":"Rullman"},{"first_name":"Thomas","full_name":"Gustafsson, Thomas","last_name":"Gustafsson"},{"first_name":"John","full_name":"McDermot, John","last_name":"McDermot"},{"last_name":"Lowe","first_name":"Martin","full_name":"Lowe, Martin"},{"last_name":"Radak","first_name":"Zsolt","full_name":"Radak, Zsolt"},{"last_name":"Chamberlain","first_name":"Jeffrey S.","full_name":"Chamberlain, Jeffrey S."},{"last_name":"Bakovic","first_name":"Marica","full_name":"Bakovic, Marica"},{"full_name":"Banka, Siddharth","first_name":"Siddharth","last_name":"Banka"},{"full_name":"Penninger, Josef M.","first_name":"Josef M.","last_name":"Penninger"}],"pmid":1,"type":"journal_article","status":"public","intvolume":"         5","scopus_import":"1","isi":1,"title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","date_updated":"2023-11-28T07:31:33Z","oa":1,"article_processing_charge":"No","publication":"Nature Metabolism","language":[{"iso":"eng"}],"external_id":{"pmid":["36941451"],"isi":["000992064000002"]},"abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}],"publication_status":"published","department":[{"_id":"Bio"}],"page":"495-515","quality_controlled":"1","volume":5,"publisher":"Springer Nature","date_published":"2023-03-20T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"citation":{"apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>.","ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023.","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>"},"date_created":"2023-03-23T12:58:43Z","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","year":"2023","doi":"10.1038/s42255-023-00766-2","article_type":"original","_id":"12747"},{"isi":1,"intvolume":"       186","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","issue":"9","date_updated":"2024-02-07T08:03:32Z","oa":1,"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","publication":"Cell","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0092-8674"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":15712841,"file_id":"12889","checksum":"47e94fbe19e86505b429cb7a5b503ce6","file_name":"2023_Cell_Knaus.pdf","success":1,"date_updated":"2023-05-02T09:26:21Z","date_created":"2023-05-02T09:26:21Z"}],"oa_version":"Published Version","day":"27","author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa"},{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette"},{"last_name":"Malzl","full_name":"Malzl, Daniel","first_name":"Daniel"},{"first_name":"Maria","full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova"},{"last_name":"Smogavec","first_name":"Mateja","full_name":"Smogavec, Mateja"},{"full_name":"Schwarz, Lena A.","first_name":"Lena A.","last_name":"Schwarz"},{"full_name":"Gorkiewicz, Sarah","first_name":"Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Knittl-Frank, Christian","last_name":"Knittl-Frank"},{"last_name":"Tassinari","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","full_name":"Tassinari, Marianna","first_name":"Marianna"},{"first_name":"Nuno","full_name":"Maulide, Nuno","last_name":"Maulide"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","status":"public","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","description":"News on ISTA Website"}],"record":[{"relation":"dissertation_contains","id":"13107","status":"public"}]},"ec_funded":1,"year":"2023","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_created":"2023-04-05T08:15:40Z","citation":{"ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","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.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","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>"},"doi":"10.1016/j.cell.2023.02.037","_id":"12802","article_type":"original","file_date_updated":"2023-05-02T09:26:21Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"external_id":{"isi":["000991468700001"]},"publication_status":"published","date_published":"2023-04-27T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":186,"page":"1950-1967.e25","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"project":[{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"}]},{"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","date_updated":"2024-01-16T10:17:05Z","oa":1,"article_processing_charge":"No","issue":"3","has_accepted_license":"1","intvolume":"       222","isi":1,"language":[{"iso":"eng"}],"publication":"Journal of Cell Biology","author":[{"first_name":"Markus","full_name":"Mund, Markus","last_name":"Mund"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"full_name":"Wu, Yu-Le","first_name":"Yu-Le","last_name":"Wu"},{"orcid":"0000-0001-8501-6017","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","first_name":"Felix F"},{"full_name":"Mehl, Johanna L.","first_name":"Johanna L.","last_name":"Mehl"},{"first_name":"Marko","full_name":"Kaksonen, Marko","last_name":"Kaksonen"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."},{"last_name":"Ries","first_name":"Jonas","full_name":"Ries, Jonas"}],"day":"03","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":5678069,"creator":"dernst","date_updated":"2024-01-16T10:15:09Z","date_created":"2024-01-16T10:15:09Z","checksum":"505d5cac36c14b073b68c7fed1a92bd3","file_name":"2023_JCB_Mund.pdf","file_id":"14811","success":1}],"month":"02","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"pmid":1,"status":"public","type":"journal_article","date_created":"2024-01-10T10:45:55Z","citation":{"apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023."},"keyword":["Cell Biology"],"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","year":"2023","article_number":"e202206038","file_date_updated":"2024-01-16T10:15:09Z","article_type":"original","_id":"14788","doi":"10.1083/jcb.202206038","publication_status":"published","external_id":{"pmid":["36734980"],"isi":["000978065000001"]},"abstract":[{"text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.","lang":"eng"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"AnSa"}],"quality_controlled":"1","volume":222,"publisher":"Rockefeller University Press","date_published":"2023-02-03T00:00:00Z"},{"month":"12","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"day":"27","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Cornelia","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","first_name":"David"}],"pmid":1,"type":"journal_article","status":"public","scopus_import":"1","intvolume":"       136","date_updated":"2024-01-22T13:35:48Z","issue":"24","article_processing_charge":"No","title":"Connecting theory and experiment in cell and tissue mechanics","publication":"Journal of Cell Science","language":[{"iso":"eng"}],"external_id":{"pmid":["38149871"]},"abstract":[{"text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.","lang":"eng"}],"publication_status":"published","publisher":"The Company of Biologists","date_published":"2023-12-27T00:00:00Z","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"volume":136,"quality_controlled":"1","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"article_number":"jcs.261515","acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","year":"2023","citation":{"ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>.","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>"},"date_created":"2024-01-17T12:46:55Z","keyword":["Cell Biology"],"doi":"10.1242/jcs.261515","_id":"14827","article_type":"original"},{"status":"public","type":"journal_article","pmid":1,"arxiv":1,"author":[{"last_name":"Hales","full_name":"Hales, Jordyn","first_name":"Jordyn"},{"last_name":"Bajpai","first_name":"Utkarsh","full_name":"Bajpai, Utkarsh"},{"last_name":"Liu","full_name":"Liu, Tongtong","first_name":"Tongtong"},{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"full_name":"Li, Mingda","first_name":"Mingda","last_name":"Li"},{"full_name":"Mitrano, Matteo","first_name":"Matteo","last_name":"Mitrano"},{"first_name":"Yao","full_name":"Wang, Yao","last_name":"Wang"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","article_processing_charge":"No","oa":1,"date_updated":"2023-08-22T06:50:04Z","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","intvolume":"        14","scopus_import":"1","date_published":"2023-06-14T00:00:00Z","publisher":"Springer Nature","volume":14,"quality_controlled":"1","extern":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements."}],"external_id":{"pmid":["37316515"],"arxiv":["2209.02283"]},"_id":"13989","article_type":"original","doi":"10.1038/s41467-023-38540-3","year":"2023","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &#38; Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>.","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","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."},"date_created":"2023-08-09T13:06:59Z","article_number":"3512"},{"publication":"G3: Genes, Genomes, Genetics","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","intvolume":"        13","isi":1,"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","issue":"8","article_processing_charge":"Yes","date_updated":"2023-12-13T12:15:37Z","oa":1,"type":"journal_article","status":"public","file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_size":845642,"relation":"main_file","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","file_name":"2023_G3_Puixeu.pdf","date_created":"2023-11-07T09:00:19Z","date_updated":"2023-11-07T09:00:19Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"01","publication_identifier":{"issn":["2160-1836"]},"month":"08","author":[{"last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","first_name":"Gemma"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"doi":"10.1093/g3journal/jkad121","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","_id":"14077","file_date_updated":"2023-11-07T09:00:19Z","related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"citation":{"apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","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>.","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)."},"date_created":"2023-08-18T06:52:14Z","year":"2023","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).","quality_controlled":"1","volume":13,"department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"date_published":"2023-08-01T00:00:00Z","publisher":"Oxford University Press","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"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"}],"external_id":{"isi":["001002997200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published"},{"author":[{"first_name":"Clementine","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A"},{"full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297"},{"full_name":"Macon, Ariana","first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"month":"12","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"file":[{"date_updated":"2024-01-02T11:39:38Z","date_created":"2024-01-02T11:39:38Z","file_id":"14727","file_name":"2023_MolecularBioEvo_Lasne.pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","success":1,"file_size":8623505,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","status":"public","type":"journal_article","pmid":1,"article_processing_charge":"Yes (via OA deal)","issue":"12","oa":1,"date_updated":"2024-02-21T12:18:35Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","has_accepted_license":"1","scopus_import":"1","intvolume":"        40","language":[{"iso":"eng"}],"publication":"Molecular Biology and Evolution","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"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."}],"external_id":{"pmid":["37988296"]},"project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"date_published":"2023-12-01T00:00:00Z","publisher":"Oxford University Press","volume":40,"quality_controlled":"1","department":[{"_id":"BeVi"}],"year":"2023","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).","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"citation":{"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>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","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.","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>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023)."},"date_created":"2023-11-27T16:14:37Z","article_number":"msad245","related_material":{"record":[{"status":"public","id":"14614","relation":"research_data"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}]},"article_type":"original","_id":"14613","file_date_updated":"2024-01-02T11:39:38Z","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/molbev/msad245"},{"type":"journal_article","status":"public","author":[{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"last_name":"Vona","first_name":"Barbara","full_name":"Vona, Barbara"},{"last_name":"Lau","full_name":"Lau, Tracy","first_name":"Tracy"},{"full_name":"Huang, Kevin","first_name":"Kevin","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang"},{"first_name":"Maha S.","full_name":"Zaki, Maha S.","last_name":"Zaki"},{"last_name":"Aldeen","full_name":"Aldeen, Huda Shujaa","first_name":"Huda Shujaa"},{"first_name":"Ehsan Ghayoor","full_name":"Karimiani, Ehsan Ghayoor","last_name":"Karimiani"},{"first_name":"Clarissa","full_name":"Rocca, Clarissa","last_name":"Rocca"},{"last_name":"Noureldeen","full_name":"Noureldeen, Mahmoud M.","first_name":"Mahmoud M."},{"last_name":"Saad","first_name":"Ahmed K.","full_name":"Saad, Ahmed K."},{"first_name":"Cassidy","full_name":"Petree, Cassidy","last_name":"Petree"},{"last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias","first_name":"Tobias"},{"last_name":"Abou Jamra","first_name":"Rami","full_name":"Abou Jamra, Rami"},{"full_name":"Zifarelli, Giovanni","first_name":"Giovanni","last_name":"Zifarelli"},{"first_name":"Aditi","full_name":"Gotkhindikar, Aditi","last_name":"Gotkhindikar"},{"last_name":"Wentzensen","first_name":"Ingrid M.","full_name":"Wentzensen, Ingrid M."},{"full_name":"Liao, Mingjuan","first_name":"Mingjuan","last_name":"Liao"},{"last_name":"Cork","first_name":"Emalyn Elise","full_name":"Cork, Emalyn Elise"},{"last_name":"Varshney","full_name":"Varshney, Pratishtha","first_name":"Pratishtha"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"first_name":"Mohammad Hasan","full_name":"Mohammadi, Mohammad Hasan","last_name":"Mohammadi"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"full_name":"Neira, Juanita","first_name":"Juanita","last_name":"Neira"},{"full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi","last_name":"Toosi"},{"last_name":"Knopp","full_name":"Knopp, Cordula","first_name":"Cordula"},{"last_name":"Kurth","first_name":"Ingo","full_name":"Kurth, Ingo"},{"full_name":"Challman, Thomas D.","first_name":"Thomas D.","last_name":"Challman"},{"first_name":"Rebecca","full_name":"Smith, Rebecca","last_name":"Smith"},{"first_name":"Asmahan","full_name":"Abdalla, Asmahan","last_name":"Abdalla"},{"last_name":"Haaf","first_name":"Thomas","full_name":"Haaf, Thomas"},{"last_name":"Suri","full_name":"Suri, Mohnish","first_name":"Mohnish"},{"first_name":"Manali","full_name":"Joshi, Manali","last_name":"Joshi"},{"last_name":"Chung","full_name":"Chung, Wendy K.","first_name":"Wendy K."},{"first_name":"Andres","full_name":"Moreno-De-Luca, Andres","last_name":"Moreno-De-Luca"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"last_name":"Maroofian","full_name":"Maroofian, Reza","first_name":"Reza"},{"full_name":"Varshney, Gaurav K.","first_name":"Gaurav K.","last_name":"Varshney"}],"month":"11","publication_identifier":{"issn":["1756-994X"]},"file":[{"date_created":"2023-12-04T08:15:43Z","date_updated":"2023-12-04T08:15:43Z","success":1,"file_id":"14640","checksum":"279efd212005549aba817a487d56d363","file_name":"2023_GenomeMed_Lin.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":14791081,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"23","language":[{"iso":"eng"}],"publication":"Genome Medicine","article_processing_charge":"Yes","date_updated":"2023-12-04T08:17:22Z","oa":1,"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","intvolume":"        15","has_accepted_license":"1","date_published":"2023-11-23T00:00:00Z","publisher":"Springer Nature","volume":15,"quality_controlled":"1","extern":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.","lang":"eng"}],"_id":"14639","article_type":"original","file_date_updated":"2023-12-04T08:15:43Z","doi":"10.1186/s13073-023-01258-4","year":"2023","keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"citation":{"ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>, vol. 15, 102, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>.","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).","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>","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.","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>"},"date_created":"2023-12-04T08:10:55Z","article_number":"102"},{"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["38070137"]},"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"publication_status":"epub_ahead","publisher":"Elsevier","date_published":"2023-12-08T00:00:00Z","department":[{"_id":"SiHi"}],"volume":5,"quality_controlled":"1","project":[{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"ec_funded":1,"article_number":"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.","year":"2023","citation":{"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>","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","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."},"date_created":"2023-12-13T11:48:05Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"doi":"10.1016/j.xpro.2023.102771","article_type":"review","_id":"14683","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2666-1667"]},"month":"12","oa_version":"Submitted Version","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole"},{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"status":"public","type":"journal_article","scopus_import":"1","intvolume":"         5","date_updated":"2023-12-18T08:06:14Z","oa":1,"issue":"1","article_processing_charge":"No","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","publication":"STAR Protocols","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"month":"12","day":"23","main_file_link":[{"url":"https://doi.org/10.1093/plcell/koad324","open_access":"1"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Zhou","first_name":"Liang-Zi","full_name":"Zhou, Liang-Zi"},{"first_name":"Lele","full_name":"Wang, Lele","last_name":"Wang"},{"last_name":"Chen","full_name":"Chen, Xia","first_name":"Xia"},{"full_name":"Ge, Zengxiang","first_name":"Zengxiang","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge"},{"last_name":"Mergner","first_name":"Julia","full_name":"Mergner, Julia"},{"full_name":"Li, Xingli","first_name":"Xingli","last_name":"Li"},{"last_name":"Küster","full_name":"Küster, Bernhard","first_name":"Bernhard"},{"full_name":"Längst, Gernot","first_name":"Gernot","last_name":"Längst"},{"full_name":"Qu, Li-Jia","first_name":"Li-Jia","last_name":"Qu"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"}],"status":"public","type":"journal_article","has_accepted_license":"1","date_updated":"2024-01-03T12:43:41Z","oa":1,"article_processing_charge":"No","title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","publication":"The Plant Cell","language":[{"iso":"eng"}],"ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"abstract":[{"text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.","lang":"eng"}],"publication_status":"epub_ahead","publisher":"Oxford University Press","date_published":"2023-12-23T00:00:00Z","extern":"1","quality_controlled":"1","article_number":"koad324","year":"2023","citation":{"apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>","short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023).","ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. 2023. doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>","ieee":"L.-Z. Zhou <i>et al.</i>, “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” <i>The Plant Cell</i>. Oxford University Press, 2023.","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>, koad324, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>.","chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>.","ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324."},"date_created":"2024-01-02T11:19:37Z","keyword":["Cell Biology","Plant Science"],"doi":"10.1093/plcell/koad324","_id":"14726","article_type":"original"}]