[{"isi":1,"OA_place":"publisher","publication_status":"published","corr_author":"1","external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"supplementarymaterial":"yes","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"intvolume":"        31","date_updated":"2026-10-02T11:21:19Z","OA_type":"hybrid","author":[{"first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler"},{"last_name":"Hansen","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","orcid":"0000-0001-7967-2085"},{"full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Thader"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"last_name":"Bauer","full_name":"Bauer, Lukas W","first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"}],"date_created":"2024-02-12T09:59:45Z","publisher":"Springer Nature","page":"1114-1123","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.","doi":"10.1038/s41594-023-01201-6","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","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."}],"volume":31,"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2024-07-22T11:27:22Z","date_created":"2024-07-22T11:27:22Z","success":1,"file_name":"2024_NatureStrucBio_Datler.pdf","relation":"main_file","creator":"dernst","file_id":"17307","file_size":17485494,"checksum":"bda7bf65d81455480efaed8ca293b0db"}],"project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"ddc":["570"],"related_material":{"record":[{"relation":"dissertation_contains","id":"18766","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","keyword":["Molecular Biology","Structural Biology"],"month":"07","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","das_tickbox":"1","researchdata_availability":"yes","file_date_updated":"2024-07-22T11:27:22Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"pmid":1,"language":[{"iso":"eng"}],"date_published":"2024-07-01T00:00:00Z","year":"2024","APC_amount":"11700 EUR","oa":1,"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","quality_controlled":"1","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>.","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>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","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;31:1114-1123. 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. 31, 1114–1123.","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>","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>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>."},"_id":"14979","dataavailabilitystatement":"The electron microscopy density maps of the A10 trimer and the hexameric flower-shaped pore, the subtomogram average of the palisade layer and representative tomograms for complete viruses as well as isolated cores have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410, EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB 8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1), orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1) were used for protein sequence alignment. Source data for MS experiments are provided as Supplementary Information accompanying this manuscript.","has_accepted_license":"1","publication":"Nature Structural & Molecular Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","article_type":"original"},{"APC_amount":"2792,52 EUR","oa":1,"pmid":1,"language":[{"iso":"eng"}],"year":"2024","date_published":"2024-02-21T00:00:00Z","file_date_updated":"2024-07-22T11:51:50Z","article_processing_charge":"Yes","oa_version":"Published Version","das_tickbox":"1","researchdata_availability":"yes (supplementary data)","day":"21","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","publication":"eLife","dataavailabilitystatement":"All data generated or analysed during this study are included in the manuscript and supporting files. No additional source files were provided.","has_accepted_license":"1","ec_funded":1,"status":"public","quality_controlled":"1","citation":{"short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>"},"_id":"15033","scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research Council Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","doi":"10.7554/elife.68993","department":[{"_id":"JiFr"}],"date_updated":"2026-10-15T08:07:21Z","intvolume":"        13","date_created":"2024-02-27T07:10:11Z","OA_type":"gold","author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publisher":"eLife Sciences Publications","corr_author":"1","external_id":{"isi":["001174278000001"],"pmid":["38381485"]},"supplementarymaterial":"no","isi":1,"OA_place":"publisher","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","month":"02","DOAJ_listed":"1","ddc":["580"],"file":[{"date_updated":"2024-07-22T11:51:50Z","content_type":"application/pdf","success":1,"date_created":"2024-07-22T11:51:50Z","access_level":"open_access","relation":"main_file","file_name":"2024_eLife_Adamowski.pdf","creator":"dernst","checksum":"b2b2d583b433823af731842f1420113e","file_id":"17310","file_size":15675744}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.68993","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"}],"volume":13},{"issue":"1","external_id":{"isi":["001152705700001"],"pmid":["38128538"]},"supplementarymaterial":"yes","isi":1,"publication_status":"published","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","doi":"10.1016/j.cell.2023.11.021","intvolume":"       187","date_updated":"2026-10-15T08:06:16Z","department":[{"_id":"JiFr"}],"author":[{"full_name":"Kuhn, Andre","first_name":"Andre","last_name":"Kuhn"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"last_name":"Mutte","full_name":"Mutte, Sumanth","first_name":"Sumanth"},{"full_name":"Dubey, Shiv Mani","first_name":"Shiv Mani","last_name":"Dubey"},{"full_name":"Carrillo Carrasco, Vanessa Polet","first_name":"Vanessa Polet","last_name":"Carrillo Carrasco"},{"first_name":"Sjef","full_name":"Boeren, Sjef","last_name":"Boeren"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"last_name":"Koehorst","full_name":"Koehorst, Jasper","first_name":"Jasper"},{"first_name":"Takayuki","full_name":"Kohchi, Takayuki","last_name":"Kohchi"},{"last_name":"Nishihama","full_name":"Nishihama, Ryuichi","first_name":"Ryuichi"},{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joris","full_name":"Sprakel, Joris","last_name":"Sprakel"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"date_created":"2024-01-17T12:45:40Z","publisher":"Elsevier","page":"130-148.e17","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","date_updated":"2024-01-22T13:41:41Z","date_created":"2024-01-22T13:41:41Z","success":1,"access_level":"open_access","relation":"main_file","file_name":"2024_Cell_Kuhn.pdf","creator":"dernst","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","file_size":13194060,"file_id":"14874"}],"fulldoi":"https://doi.org/10.1016/j.cell.2023.11.021","type":"journal_article","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."}],"volume":187,"related_material":{"record":[{"id":"19395","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","keyword":["General Biochemistry","Genetics and Molecular Biology"],"title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","month":"01","ddc":["580"],"file_date_updated":"2024-01-22T13:41:41Z","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","das_tickbox":"1","researchdata_availability":"yes","oa":1,"pmid":1,"language":[{"iso":"eng"}],"year":"2024","date_published":"2024-01-04T00:00:00Z","status":"public","quality_controlled":"1","citation":{"short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","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>.","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>","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.","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>"},"_id":"14826","scopus_import":"1","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"04","article_type":"original","publication":"Cell","dataavailabilitystatement":"Phosphoproteome data are available in the ProteomeXchange PRIDE database: PXD038369 and PXD038363. Transcriptome data are available in the NCBI Sequence Read Archive: PRJNA881051. Data underlying RAF-like kinase phylogeny is deposited at the iTOL: https://itol.embl.de/shared/dolfweijers. This paper analyzes existing, publicly available data phospho-proteome data. The accession number for the datasets are listed in the key resources table.\r\n\r\nCode for the AuxPhos app and for MATlab code for analysis of cytoplasmic streaming are available at Github: https://github.com/WeijersLab/AuxPhos and https://github.com/jorissprakel/RAF_track_analysis.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead author upon request.","has_accepted_license":"1","ec_funded":1},{"publication_status":"published","supplementarymaterial":"yes","corr_author":"1","external_id":{"pmid":["38441122"]},"publisher":"eLife Sciences Publications","date_updated":"2026-10-15T08:30:04Z","department":[{"_id":"JiFr"}],"intvolume":"        12","date_created":"2024-04-02T11:35:58Z","author":[{"last_name":"Kulich","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan"},{"last_name":"Schmid","id":"07cf4637-baaf-11ee-9227-e1de57d1d69b","first_name":"Julia","full_name":"Schmid, Julia"},{"first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia","last_name":"Teplova"},{"orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","last_name":"Qi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"doi":"10.7554/elife.91523","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F. This research was also supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria, namely Tereza Bělinová for her help with the imaging. JS was supported by FemTECH fellowship.","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.91523","volume":12,"abstract":[{"text":"Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.","lang":"eng"}],"file":[{"file_name":"2024_eLife_Kulich.pdf","relation":"main_file","access_level":"open_access","date_created":"2024-04-03T13:18:00Z","success":1,"date_updated":"2024-04-03T13:18:00Z","content_type":"application/pdf","file_id":"15288","file_size":11451904,"checksum":"a73a84d3bf97a6d09d24308ca6dd0a0c","creator":"dernst"}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"ddc":["580"],"DOAJ_listed":"1","title":"Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"month":"03","related_material":{"record":[{"relation":"dissertation_contains","id":"22984","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/beneath-the-surface/","description":"News on ISTA website","relation":"press_release"}]},"publication_identifier":{"issn":["2050-084X"]},"researchdata_availability":"yes (supplementary data)","article_processing_charge":"Yes","das_tickbox":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2024-04-03T13:18:00Z","language":[{"iso":"eng"}],"pmid":1,"year":"2024","date_published":"2024-03-05T00:00:00Z","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","citation":{"short":"I. Kulich, J. Schmid, A. Teplova, L. Qi, J. Friml, ELife 12 (2024).","ieee":"I. Kulich, J. Schmid, A. Teplova, L. Qi, and J. Friml, “Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","chicago":"Kulich, Ivan, Julia Schmid, Anastasiia Teplova, Linlin Qi, and Jiří Friml. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>.","mla":"Kulich, Ivan, et al. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>, vol. 12, 91523, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>.","ista":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. 2024. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife. 12, 91523.","apa":"Kulich, I., Schmid, J., Teplova, A., Qi, L., &#38; Friml, J. (2024). Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>","ama":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>"},"_id":"15257","status":"public","quality_controlled":"1","article_number":"91523","has_accepted_license":"1","ec_funded":1,"dataavailabilitystatement":"All data generated in this study are included as a manuscript supporting files.","article_type":"original","day":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"eLife"},{"quality_controlled":"1","status":"public","_id":"15045","citation":{"ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. 2024;65. doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>","apa":"Varshney, A., Ghazaryan, A., &#38; Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>, vol. 65, 12, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>.","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>.","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” <i>Few-Body Systems</i>, vol. 65. Springer Nature, 2024.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024)."},"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Few-Body Systems","day":"17","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","article_number":"12","file_date_updated":"2024-03-04T07:07:10Z","oa_version":"Published Version","das_tickbox":"0","article_processing_charge":"Yes (via OA deal)","researchdata_availability":"no","oa":1,"date_published":"2024-02-17T00:00:00Z","year":"2024","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2024-03-04T07:07:10Z","date_created":"2024-03-04T07:07:10Z","success":1,"access_level":"open_access","relation":"main_file","file_name":"2024_FewBodySys_Varshney.pdf","creator":"dernst","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_id":"15049","file_size":436712}],"volume":65,"abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"fulldoi":"https://doi.org/10.1007/s00601-024-01880-x","type":"journal_article","publication_identifier":{"issn":["1432-5411"]},"month":"02","keyword":["Atomic and Molecular Physics","and Optics"],"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","arxiv":1,"ddc":["530"],"external_id":{"arxiv":["2401.08454"],"isi":["001163768200001"]},"corr_author":"1","supplementarymaterial":"no","isi":1,"publication_status":"published","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s00601-024-01880-x","date_created":"2024-03-01T11:39:33Z","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney"},{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"intvolume":"        65","department":[{"_id":"MiLe"}],"date_updated":"2026-10-16T12:17:10Z","publisher":"Springer Nature"},{"day":"10","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Experimental Biology","dataavailabilitystatement":"Raw data for this paper are available from Zenodo (doi:10.5281/zenodo.10423540). All analysis code is available from GitHub (https://github.com/arka-pal/Cnemaspis-SexualSignaling)","article_number":"jeb246217","has_accepted_license":"1","quality_controlled":"1","status":"public","_id":"14850","citation":{"chicago":"Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal of Experimental Biology</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>.","ieee":"A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite levels using more signal modalities than females utilise,” <i>Journal of Experimental Biology</i>, vol. 227, no. 1. The Company of Biologists, 2024.","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","apa":"Pal, A., Joshi, M., &#38; Thaker, M. (2024). Too much information? Males convey parasite levels using more signal modalities than females utilise. <i>Journal of Experimental Biology</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jeb.246217\">https://doi.org/10.1242/jeb.246217</a>","ista":"Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite levels using more signal modalities than females utilise. Journal of Experimental Biology. 227(1), jeb246217.","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>","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>."},"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"date_published":"2024-01-10T00:00:00Z","year":"2024","language":[{"iso":"eng"}],"pmid":1,"file_date_updated":"2024-01-23T12:08:24Z","das_tickbox":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","researchdata_availability":"yes","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"related_material":{"record":[{"status":"public","id":"22868","relation":"research_data"}],"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"month":"01","title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"ddc":["570"],"file":[{"relation":"main_file","file_name":"2024_JourExperimBiology_Pal.pdf","success":1,"date_created":"2024-01-23T12:08:24Z","content_type":"application/pdf","date_updated":"2024-01-23T12:08:24Z","access_level":"open_access","checksum":"136325372f6f45abaa62a71e2d23bfb6","file_size":594128,"file_id":"14877","creator":"dernst"}],"volume":227,"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"}],"type":"journal_article","fulldoi":"https://doi.org/10.1242/jeb.246217","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.","doi":"10.1242/jeb.246217","author":[{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","last_name":"Pal"},{"first_name":"Mihir","full_name":"Joshi, Mihir","last_name":"Joshi"},{"last_name":"Thaker","first_name":"Maria","full_name":"Thaker, Maria"}],"date_created":"2024-01-22T08:14:49Z","date_updated":"2026-10-21T08:13:07Z","department":[{"_id":"NiBa"}],"intvolume":"       227","publisher":"The Company of Biologists","external_id":{"isi":["001214515700016"],"pmid":["38054353"]},"corr_author":"1","issue":"1","supplementarymaterial":"yes","isi":1,"publication_status":"published"},{"doi":"10.1364/optica.507451","acknowledgement":"We thank Rishabh Sahu and Sebastian Wald for technical contributions to the experiment. Funding by Institute of Science and Technology Austria.","publisher":"Optica Publishing Group","page":"26-31","intvolume":"        11","date_updated":"2026-10-21T08:26:22Z","department":[{"_id":"OnHo"}],"OA_type":"gold","author":[{"full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R","last_name":"Diorico"},{"last_name":"Zhutov","id":"0f02ed6a-b514-11ee-b891-8379c5f19cb7","first_name":"Artem","full_name":"Zhutov, Artem"},{"last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"}],"date_created":"2024-01-15T10:25:38Z","supplementarymaterial":"no","issue":"1","corr_author":"1","external_id":{"isi":["001202817000004"]},"publication_status":"published","isi":1,"OA_place":"publisher","keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"title":"Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth","month":"01","publication_identifier":{"issn":["2334-2536"]},"DOAJ_listed":"1","ddc":["530"],"file":[{"creator":"dernst","file_size":4558986,"file_id":"14824","checksum":"eb99ca7d0fe73e22f121875175546ed7","access_level":"open_access","date_updated":"2024-01-17T08:53:16Z","content_type":"application/pdf","date_created":"2024-01-17T08:53:16Z","success":1,"file_name":"2023_Optica_Diorico.pdf","relation":"main_file"}],"type":"journal_article","fulldoi":"https://doi.org/10.1364/optica.507451","abstract":[{"text":"Frequency-stable lasers form the back bone of precision measurements in science and technology. Such lasers typically attain their stability through frequency locking to reference cavities. State-of-the-art locking performances to date had been achieved using frequency modulation based methods, complemented with active drift cancellation systems. We demonstrate an all passive, modulation-free laser-cavity locking technique (squash locking) that utilizes changes in spatial beam ellipticity for error signal generation, and a coherent polarization post-selection for noise resilience. By comparing two identically built proof-of-principle systems, we show a frequency locking instability of 5×10<jats:sup>−7</jats:sup> relative to the cavity linewidth at 10 s averaging. The results surpass the demonstrated performances of methods engineered over the last five decades, potentially enabling an advancement in the precision control of lasers, while creating avenues for bridging the performance gaps between industrial grade lasers with scientific ones due to the afforded simplicity and scalability.","lang":"eng"}],"volume":11,"oa":1,"APC_amount":"3393,38 EUR","language":[{"iso":"eng"}],"date_published":"2024-01-20T00:00:00Z","year":"2024","file_date_updated":"2024-01-17T08:53:16Z","researchdata_availability":"upon request","article_processing_charge":"Yes","das_tickbox":"1","oa_version":"Published Version","day":"20","article_type":"original","publication":"Optica","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","citation":{"ama":"Diorico FR, Zhutov A, Hosten O. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. 2024;11(1):26-31. doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>","apa":"Diorico, F. R., Zhutov, A., &#38; Hosten, O. (2024). Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>","ista":"Diorico FR, Zhutov A, Hosten O. 2024. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. Optica. 11(1), 26–31.","mla":"Diorico, Fritz R., et al. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>, vol. 11, no. 1, Optica Publishing Group, 2024, pp. 26–31, doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>.","chicago":"Diorico, Fritz R, Artem Zhutov, and Onur Hosten. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>.","ieee":"F. R. Diorico, A. Zhutov, and O. Hosten, “Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth,” <i>Optica</i>, vol. 11, no. 1. Optica Publishing Group, pp. 26–31, 2024.","short":"F.R. Diorico, A. Zhutov, O. Hosten, Optica 11 (2024) 26–31."},"_id":"14802","status":"public","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"review","publication":"STAR Protocols","day":"15","dataavailabilitystatement":"No custom code or dataset was generated in this protocol.","ec_funded":1,"has_accepted_license":"1","article_number":"102771","quality_controlled":"1","status":"public","_id":"14683","citation":{"ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","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, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","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>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). 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>","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","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, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>."},"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"year":"2024","date_published":"2024-03-15T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"file_date_updated":"2024-07-16T11:50:03Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","das_tickbox":"1","article_processing_charge":"Yes (in subscription journal)","researchdata_availability":"not applicable","publication_identifier":{"issn":["2666-1667"]},"month":"03","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","ddc":["570"],"project":[{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"creator":"dernst","file_size":8871807,"file_id":"17260","checksum":"3f0ee62e04bf5a44b45b035662826e95","access_level":"open_access","date_updated":"2024-07-16T11:50:03Z","content_type":"application/pdf","success":1,"date_created":"2024-07-16T11:50:03Z","file_name":"2024_STARProtoc_Amberg.pdf","relation":"main_file"}],"volume":5,"abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.xpro.2023.102771","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","doi":"10.1016/j.xpro.2023.102771","date_created":"2023-12-13T11:48:05Z","author":[{"last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"date_updated":"2026-10-21T08:40:15Z","intvolume":"         5","department":[{"_id":"SiHi"}],"publisher":"Elsevier","external_id":{"pmid":["38070137"]},"corr_author":"1","issue":"1","supplementarymaterial":"no","publication_status":"published"},{"issue":"6","corr_author":"1","external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"publication_status":"published","isi":1,"doi":"10.1002/1873-3468.14540","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.","publisher":"Wiley","page":"762-777","intvolume":"       597","department":[{"_id":"MaLo"}],"date_updated":"2024-10-09T21:03:42Z","author":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"last_name":"Auer","orcid":"0000-0002-3580-2906","full_name":"Auer, Albert","first_name":"Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel","last_name":"Brognara"},{"full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","last_name":"Budiman"},{"id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","first_name":"Lukasz M","full_name":"Kowalski, Lukasz M","last_name":"Kowalski"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"}],"date_created":"2023-01-12T12:09:58Z","file":[{"file_name":"2023_FEBSLetters_Loose.pdf","relation":"main_file","access_level":"open_access","success":1,"date_created":"2023-08-16T08:31:04Z","content_type":"application/pdf","date_updated":"2023-08-16T08:31:04Z","file_id":"14063","file_size":3148143,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","creator":"dernst"}],"fulldoi":"https://doi.org/10.1002/1873-3468.14540","type":"journal_article","volume":597,"abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"title":"In vitro reconstitution of small GTPase regulation","month":"03","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"file_date_updated":"2023-08-16T08:31:04Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","oa":1,"pmid":1,"language":[{"iso":"eng"}],"year":"2023","date_published":"2023-03-01T00:00:00Z","citation":{"ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","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>","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>.","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>.","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.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"_id":"12163","status":"public","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"scopus_import":"1","day":"01","publication":"FEBS Letters","article_type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1"},{"oa":1,"language":[{"iso":"eng"}],"date_published":"2023-04-14T00:00:00Z","year":"2023","file_date_updated":"2023-07-31T09:02:27Z","article_processing_charge":"No","oa_version":"Published Version","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication":"SciPost Physics Core","article_number":"029","has_accepted_license":"1","ec_funded":1,"citation":{"short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” <i>SciPost Physics Core</i>, vol. 6, no. 2. SciPost Foundation, 2023.","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>.","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. 2023;6(2). doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>","apa":"Tucci, G., De Nicola, S., Wald, S., &#38; Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029."},"_id":"13277","status":"public","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","doi":"10.21468/scipostphyscore.6.2.029","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"date_updated":"2025-04-14T07:43:56Z","intvolume":"         6","date_created":"2023-07-24T10:47:46Z","author":[{"first_name":"Gennaro","full_name":"Tucci, Gennaro","last_name":"Tucci"},{"first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola"},{"full_name":"Wald, Sascha","first_name":"Sascha","last_name":"Wald"},{"first_name":"Andrea","full_name":"Gambassi, Andrea","last_name":"Gambassi"}],"issue":"2","corr_author":"1","external_id":{"arxiv":["2211.01923"]},"publication_status":"published","title":"Stochastic representation of the quantum quartic oscillator","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"month":"04","publication_identifier":{"issn":["2666-9366"]},"ddc":["530"],"arxiv":1,"file":[{"success":1,"date_created":"2023-07-31T09:02:27Z","date_updated":"2023-07-31T09:02:27Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2023_SciPostPhysCore_Tucci.pdf","creator":"dernst","checksum":"b472bc82108747eda5d52adf9e2ac7f3","file_size":523236,"file_id":"13329"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.21468/scipostphyscore.6.2.029","type":"journal_article","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}],"volume":6},{"doi":"10.1038/s41467-023-38540-3","main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"publisher":"Springer Nature","author":[{"last_name":"Hales","first_name":"Jordyn","full_name":"Hales, Jordyn"},{"first_name":"Utkarsh","full_name":"Bajpai, Utkarsh","last_name":"Bajpai"},{"last_name":"Liu","first_name":"Tongtong","full_name":"Liu, Tongtong"},{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"last_name":"Li","first_name":"Mingda","full_name":"Li, Mingda"},{"first_name":"Matteo","full_name":"Mitrano, Matteo","last_name":"Mitrano"},{"last_name":"Wang","full_name":"Wang, Yao","first_name":"Yao"}],"date_created":"2023-08-09T13:06:59Z","date_updated":"2023-08-22T06:50:04Z","intvolume":"        14","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"publication_status":"published","month":"06","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publication_identifier":{"eissn":["2041-1723"]},"extern":"1","arxiv":1,"abstract":[{"text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.","lang":"eng"}],"volume":14,"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41467-023-38540-3","oa":1,"year":"2023","date_published":"2023-06-14T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"oa_version":"Published Version","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","publication":"Nature Communications","article_type":"original","article_number":"3512","_id":"13989","citation":{"short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","ieee":"J. Hales <i>et al.</i>, “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>.","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>.","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>","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.","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>"},"quality_controlled":"1","status":"public","scopus_import":"1"},{"oa":1,"date_published":"2023-08-01T00:00:00Z","year":"2023","pmid":1,"language":[{"iso":"eng"}],"file_date_updated":"2023-11-07T09:00:19Z","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"G3: Genes, Genomes, Genetics","day":"01","article_type":"original","ec_funded":1,"has_accepted_license":"1","quality_controlled":"1","status":"public","_id":"14077","citation":{"short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","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>"},"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","doi":"10.1093/g3journal/jkad121","author":[{"last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-08-18T06:52:14Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2026-04-07T13:25:34Z","intvolume":"        13","publisher":"Oxford University Press","corr_author":"1","external_id":{"pmid":["37259621"],"isi":["001002997200001"]},"issue":"8","isi":1,"publication_status":"published","publication_identifier":{"issn":["2160-1836"]},"related_material":{"record":[{"status":"public","id":"12933","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"month":"08","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","ddc":["570"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"file":[{"content_type":"application/pdf","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z","success":1,"access_level":"open_access","relation":"main_file","file_name":"2023_G3_Puixeu.pdf","creator":"dernst","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","file_size":845642}],"abstract":[{"lang":"eng","text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns."}],"volume":13,"fulldoi":"https://doi.org/10.1093/g3journal/jkad121","type":"journal_article"},{"file":[{"file_id":"14640","file_size":14791081,"checksum":"279efd212005549aba817a487d56d363","creator":"dernst","file_name":"2023_GenomeMed_Lin.pdf","relation":"main_file","access_level":"open_access","success":1,"date_created":"2023-12-04T08:15:43Z","date_updated":"2023-12-04T08:15:43Z","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"volume":15,"type":"journal_article","fulldoi":"https://doi.org/10.1186/s13073-023-01258-4","month":"11","title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"publication_identifier":{"issn":["1756-994X"]},"extern":"1","ddc":["570"],"publication_status":"published","doi":"10.1186/s13073-023-01258-4","publisher":"Springer Nature","date_created":"2023-12-04T08:10:55Z","author":[{"first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia","last_name":"Lin"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"full_name":"Lau, Tracy","first_name":"Tracy","last_name":"Lau"},{"last_name":"Huang","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin"},{"first_name":"Maha S.","full_name":"Zaki, Maha S.","last_name":"Zaki"},{"first_name":"Huda Shujaa","full_name":"Aldeen, Huda Shujaa","last_name":"Aldeen"},{"first_name":"Ehsan Ghayoor","full_name":"Karimiani, Ehsan Ghayoor","last_name":"Karimiani"},{"first_name":"Clarissa","full_name":"Rocca, Clarissa","last_name":"Rocca"},{"full_name":"Noureldeen, Mahmoud M.","first_name":"Mahmoud M.","last_name":"Noureldeen"},{"last_name":"Saad","full_name":"Saad, Ahmed K.","first_name":"Ahmed K."},{"last_name":"Petree","first_name":"Cassidy","full_name":"Petree, Cassidy"},{"last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias","first_name":"Tobias"},{"full_name":"Abou Jamra, Rami","first_name":"Rami","last_name":"Abou Jamra"},{"last_name":"Zifarelli","first_name":"Giovanni","full_name":"Zifarelli, Giovanni"},{"last_name":"Gotkhindikar","first_name":"Aditi","full_name":"Gotkhindikar, Aditi"},{"last_name":"Wentzensen","first_name":"Ingrid M.","full_name":"Wentzensen, Ingrid M."},{"last_name":"Liao","full_name":"Liao, Mingjuan","first_name":"Mingjuan"},{"last_name":"Cork","full_name":"Cork, Emalyn Elise","first_name":"Emalyn Elise"},{"first_name":"Pratishtha","full_name":"Varshney, Pratishtha","last_name":"Varshney"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan","last_name":"Mohammadi"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"first_name":"Juanita","full_name":"Neira, Juanita","last_name":"Neira"},{"last_name":"Toosi","first_name":"Mehran Beiraghi","full_name":"Toosi, Mehran Beiraghi"},{"last_name":"Knopp","full_name":"Knopp, Cordula","first_name":"Cordula"},{"last_name":"Kurth","full_name":"Kurth, Ingo","first_name":"Ingo"},{"full_name":"Challman, Thomas D.","first_name":"Thomas D.","last_name":"Challman"},{"last_name":"Smith","first_name":"Rebecca","full_name":"Smith, Rebecca"},{"last_name":"Abdalla","full_name":"Abdalla, Asmahan","first_name":"Asmahan"},{"first_name":"Thomas","full_name":"Haaf, Thomas","last_name":"Haaf"},{"last_name":"Suri","full_name":"Suri, Mohnish","first_name":"Mohnish"},{"full_name":"Joshi, Manali","first_name":"Manali","last_name":"Joshi"},{"full_name":"Chung, Wendy K.","first_name":"Wendy K.","last_name":"Chung"},{"last_name":"Moreno-De-Luca","first_name":"Andres","full_name":"Moreno-De-Luca, Andres"},{"first_name":"Henry","full_name":"Houlden, Henry","last_name":"Houlden"},{"last_name":"Maroofian","first_name":"Reza","full_name":"Maroofian, Reza"},{"last_name":"Varshney","first_name":"Gaurav K.","full_name":"Varshney, Gaurav K."}],"intvolume":"        15","date_updated":"2023-12-04T08:17:22Z","_id":"14639","citation":{"chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","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).","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.","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>","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>","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>."},"quality_controlled":"1","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Genome Medicine","day":"23","has_accepted_license":"1","article_number":"102","file_date_updated":"2023-12-04T08:15:43Z","oa_version":"Published Version","article_processing_charge":"Yes","oa":1,"year":"2023","date_published":"2023-11-23T00:00:00Z","language":[{"iso":"eng"}]},{"article_number":"a041447","publication":"Cold Spring Harbor Perspectives in Biology","article_type":"original","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","citation":{"short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory Press, 2023.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory Press, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>"},"_id":"14742","status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"year":"2023","date_published":"2023-11-01T00:00:00Z","oa":1,"article_processing_charge":"No","oa_version":"Published Version","ddc":["570"],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","month":"11","publication_identifier":{"issn":["1943-0264"]},"type":"journal_article","fulldoi":"https://doi.org/10.1101/cshperspect.a041447","abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"volume":15,"publisher":"Cold Spring Harbor Laboratory Press","intvolume":"        15","date_updated":"2026-06-18T17:37:44Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"last_name":"Giménez","full_name":"Giménez, Mabel D.","first_name":"Mabel D."},{"last_name":"Joron","full_name":"Joron, Mathieu","first_name":"Mathieu"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"last_name":"Searle","first_name":"Jeremy B.","full_name":"Searle, Jeremy B."},{"last_name":"Walden","first_name":"Nora","full_name":"Walden, Nora"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"date_created":"2024-01-08T12:43:48Z","doi":"10.1101/cshperspect.a041447","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","publication_status":"published","isi":1,"issue":"11","external_id":{"pmid":["37604585"],"isi":["001096272600001"]}},{"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41592-023-01937-5","abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"volume":20,"related_material":{"record":[{"status":"public","id":"13267","relation":"extended_version"}]},"publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","month":"08","isi":1,"publication_status":"published","issue":"8","external_id":{"isi":["001025621500002"]},"corr_author":"1","department":[{"_id":"JoDa"}],"date_updated":"2026-04-14T08:34:34Z","intvolume":"        20","author":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky"}],"date_created":"2024-01-10T08:07:15Z","publisher":"Springer Nature","page":"1141-1142","doi":"10.1038/s41592-023-01937-5","scopus_import":"1","status":"public","quality_controlled":"1","citation":{"mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","apa":"Danzl, J. G., &#38; Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023."},"_id":"14770","publication":"Nature Methods","article_type":"letter_note","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"None","language":[{"iso":"eng"}],"year":"2023","date_published":"2023-08-01T00:00:00Z"},{"oa":1,"year":"2023","date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"file_date_updated":"2024-01-10T13:39:42Z","oa_version":"Published Version","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication":"International Journal of Molecular Sciences","day":"01","has_accepted_license":"1","article_number":"16527","quality_controlled":"1","status":"public","_id":"14776","citation":{"chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>.","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22, 16527, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","doi":"10.3390/ijms242216527","date_created":"2024-01-10T09:24:35Z","author":[{"last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"last_name":"Pigidanov","full_name":"Pigidanov, Artemii A.","first_name":"Artemii A."},{"last_name":"Serebryakova","full_name":"Serebryakova, Marina V.","first_name":"Marina V."},{"full_name":"Golyshev, Sergei A.","first_name":"Sergei A.","last_name":"Golyshev"},{"last_name":"Galiullina","first_name":"Raisa A.","full_name":"Galiullina, Raisa A."},{"last_name":"Chichkova","full_name":"Chichkova, Nina V.","first_name":"Nina V."},{"last_name":"Vartapetian","full_name":"Vartapetian, Andrey B.","first_name":"Andrey B."}],"department":[{"_id":"JiFr"}],"intvolume":"        24","date_updated":"2024-10-09T21:07:49Z","publisher":"MDPI","corr_author":"1","external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"issue":"22","isi":1,"publication_status":"published","publication_identifier":{"issn":["1422-0067"]},"month":"11","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"ddc":["580"],"file":[{"date_created":"2024-01-10T13:39:42Z","success":1,"content_type":"application/pdf","date_updated":"2024-01-10T13:39:42Z","access_level":"open_access","relation":"main_file","file_name":"2023_IJMS_Teplova.pdf","creator":"dernst","checksum":"4df7d206ba022b7f54eff1f0aec1659a","file_id":"14791","file_size":2637784}],"volume":24,"abstract":[{"text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.3390/ijms242216527"},{"issue":"17","external_id":{"pmid":["37463577"]},"publication_status":"published","doi":"10.1016/j.devcel.2023.06.009","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"publisher":"Elsevier","page":"1578-1592.e5","date_updated":"2024-01-16T08:56:36Z","department":[{"_id":"Bio"}],"intvolume":"        58","author":[{"full_name":"Westerich, Kim Joana","first_name":"Kim Joana","last_name":"Westerich"},{"last_name":"Tarbashevich","first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna"},{"first_name":"Jan","full_name":"Schick, Jan","last_name":"Schick"},{"first_name":"Antra","full_name":"Gupta, Antra","last_name":"Gupta"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"first_name":"Kenneth","full_name":"Hull, Kenneth","last_name":"Hull"},{"last_name":"Romo","full_name":"Romo, Daniel","first_name":"Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross-Thebing","full_name":"Gross-Thebing, Theresa","first_name":"Theresa"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"date_created":"2024-01-10T09:41:21Z","type":"journal_article","fulldoi":"https://doi.org/10.1016/j.devcel.2023.06.009","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"volume":58,"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"month":"09","publication_identifier":{"issn":["1534-5807"]},"article_processing_charge":"No","oa_version":"Preprint","oa":1,"language":[{"iso":"eng"}],"pmid":1,"year":"2023","date_published":"2023-09-11T00:00:00Z","citation":{"short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>.","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>.","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5."},"_id":"14781","status":"public","quality_controlled":"1","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication":"Developmental Cell"},{"month":"03","title":"Structural snapshots of R-loop formation by a type I-C CRISPR Cascade","keyword":["Cell Biology","Molecular Biology"],"extern":"1","publication_identifier":{"issn":["1097-2765"]},"volume":83,"abstract":[{"lang":"eng","text":"Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the “belly” subunits, securing the NTS in place. This “molecular seatbelt” mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity."}],"fulldoi":"https://doi.org/10.1016/j.molcel.2023.01.024","type":"journal_article","page":"746-758.e5","publisher":"Elsevier","date_created":"2024-03-20T10:40:56Z","author":[{"last_name":"O’Brien","full_name":"O’Brien, Roisin E.","first_name":"Roisin E."},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo"},{"first_name":"Delisa","full_name":"Ramos, Delisa","last_name":"Ramos"},{"last_name":"Hibshman","full_name":"Hibshman, Grace N.","first_name":"Grace N."},{"full_name":"Wright, Jacquelyn T.","first_name":"Jacquelyn T.","last_name":"Wright"},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."}],"intvolume":"        83","date_updated":"2024-06-04T06:33:54Z","doi":"10.1016/j.molcel.2023.01.024","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2023.01.024"}],"publication_status":"published","external_id":{"pmid":["36805026"]},"issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Molecular Cell","day":"02","article_type":"original","scopus_import":"1","_id":"15129","citation":{"short":"R.E. O’Brien, J.P.K. Bravo, D. Ramos, G.N. Hibshman, J.T. Wright, D.W. Taylor, Molecular Cell 83 (2023) 746–758.e5.","ieee":"R. E. O’Brien, J. P. K. Bravo, D. Ramos, G. N. Hibshman, J. T. Wright, and D. W. Taylor, “Structural snapshots of R-loop formation by a type I-C CRISPR Cascade,” <i>Molecular Cell</i>, vol. 83, no. 5. Elsevier, p. 746–758.e5, 2023.","chicago":"O’Brien, Roisin E., Jack Peter Kelly Bravo, Delisa Ramos, Grace N. Hibshman, Jacquelyn T. Wright, and David W. Taylor. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” <i>Molecular Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">https://doi.org/10.1016/j.molcel.2023.01.024</a>.","mla":"O’Brien, Roisin E., et al. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” <i>Molecular Cell</i>, vol. 83, no. 5, Elsevier, 2023, p. 746–758.e5, doi:<a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">10.1016/j.molcel.2023.01.024</a>.","ama":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. <i>Molecular Cell</i>. 2023;83(5):746-758.e5. doi:<a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">10.1016/j.molcel.2023.01.024</a>","ista":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. 2023. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell. 83(5), 746–758.e5.","apa":"O’Brien, R. E., Bravo, J. P. K., Ramos, D., Hibshman, G. N., Wright, J. T., &#38; Taylor, D. W. (2023). Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">https://doi.org/10.1016/j.molcel.2023.01.024</a>"},"quality_controlled":"1","status":"public","date_published":"2023-03-02T00:00:00Z","year":"2023","language":[{"iso":"eng"}],"pmid":1,"oa":1,"oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)"},{"_id":"15149","citation":{"chicago":"Isbel, Luke, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S. Grand, Eric Hietter-Pfeiffer, Zuzanna Kozicka, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41594-023-01021-8\">https://doi.org/10.1038/s41594-023-01021-8</a>.","ieee":"L. Isbel <i>et al.</i>, “Readout of histone methylation by Trim24 locally restricts chromatin opening by p53,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 30, no. 7. Springer Nature, pp. 948–957, 2023.","short":"L. Isbel, M. Iskar, S. Durdu, J. Weiss, R.S. Grand, E. Hietter-Pfeiffer, Z. Kozicka, A.K. Michael, L. Burger, N.H. Thomä, D. Schübeler, Nature Structural &#38; Molecular Biology 30 (2023) 948–957.","apa":"Isbel, L., Iskar, M., Durdu, S., Weiss, J., Grand, R. S., Hietter-Pfeiffer, E., … Schübeler, D. (2023). Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01021-8\">https://doi.org/10.1038/s41594-023-01021-8</a>","ista":"Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D. 2023. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural &#38; Molecular Biology. 30(7), 948–957.","ama":"Isbel L, Iskar M, Durdu S, et al. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. <i>Nature Structural &#38; Molecular Biology</i>. 2023;30(7):948-957. doi:<a href=\"https://doi.org/10.1038/s41594-023-01021-8\">10.1038/s41594-023-01021-8</a>","mla":"Isbel, Luke, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 30, no. 7, Springer Nature, 2023, pp. 948–57, doi:<a href=\"https://doi.org/10.1038/s41594-023-01021-8\">10.1038/s41594-023-01021-8</a>."},"quality_controlled":"1","status":"public","scopus_import":"1","article_type":"original","publication":"Nature Structural & Molecular Biology","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"No","oa":1,"date_published":"2023-06-29T00:00:00Z","year":"2023","pmid":1,"language":[{"iso":"eng"}],"abstract":[{"text":"The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.","lang":"eng"}],"volume":30,"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41594-023-01021-8","month":"06","title":"Readout of histone methylation by Trim24 locally restricts chromatin opening by p53","keyword":["Molecular Biology","Structural Biology"],"extern":"1","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"external_id":{"pmid":["37386214"]},"issue":"7","publication_status":"published","doi":"10.1038/s41594-023-01021-8","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01021-8","open_access":"1"}],"page":"948-957","publisher":"Springer Nature","date_created":"2024-03-21T07:53:24Z","author":[{"full_name":"Isbel, Luke","first_name":"Luke","last_name":"Isbel"},{"first_name":"Murat","full_name":"Iskar, Murat","last_name":"Iskar"},{"last_name":"Durdu","full_name":"Durdu, Sevi","first_name":"Sevi"},{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"full_name":"Hietter-Pfeiffer, Eric","first_name":"Eric","last_name":"Hietter-Pfeiffer"},{"last_name":"Kozicka","first_name":"Zuzanna","full_name":"Kozicka, Zuzanna"},{"full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","last_name":"Michael"},{"last_name":"Burger","full_name":"Burger, Lukas","first_name":"Lukas"},{"last_name":"Thomä","full_name":"Thomä, Nicolas H.","first_name":"Nicolas H."},{"full_name":"Schübeler, Dirk","first_name":"Dirk","last_name":"Schübeler"}],"date_updated":"2024-03-25T12:37:20Z","intvolume":"        30"},{"publication_identifier":{"eissn":["1539-4794"],"issn":["0146-9592"]},"month":"07","title":"Monitoring and active stabilization of laser injection locking using beam ellipticity","keyword":["Atomic and Molecular Physics","and Optics"],"arxiv":1,"volume":48,"abstract":[{"text":"We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry.","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.1364/ol.495553","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.01266","open_access":"1"}],"doi":"10.1364/ol.495553","date_created":"2024-01-08T13:01:46Z","author":[{"first_name":"Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","full_name":"Mishra, Umang","last_name":"Mishra"},{"last_name":"Li","full_name":"Li, Vyacheslav","first_name":"Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian","orcid":"0000-0002-5869-1604","last_name":"Wald"},{"full_name":"Agafonova, Sofya","orcid":"0000-0003-0582-2946","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","last_name":"Agafonova"},{"last_name":"Diorico","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten"}],"intvolume":"        48","date_updated":"2026-07-08T08:41:47Z","department":[{"_id":"OnHo"}],"page":"3973-3976","publisher":"Optica Publishing Group","external_id":{"arxiv":["2212.01266"],"isi":["001051044600008"]},"corr_author":"1","issue":"15","supplementarymaterial":"no","isi":1,"publication_status":"published","publication":"Optics Letters","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","day":"21","article_type":"original","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","quality_controlled":"1","status":"public","_id":"14749","citation":{"ama":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. <i>Optics Letters</i>. 2023;48(15):3973-3976. doi:<a href=\"https://doi.org/10.1364/ol.495553\">10.1364/ol.495553</a>","ista":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976.","apa":"Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., &#38; Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ol.495553\">https://doi.org/10.1364/ol.495553</a>","mla":"Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” <i>Optics Letters</i>, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:<a href=\"https://doi.org/10.1364/ol.495553\">10.1364/ol.495553</a>.","ieee":"U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” <i>Optics Letters</i>, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023.","chicago":"Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofia Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” <i>Optics Letters</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ol.495553\">https://doi.org/10.1364/ol.495553</a>.","short":"U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976."},"scopus_import":"1","oa":1,"date_published":"2023-07-21T00:00:00Z","year":"2023","language":[{"iso":"eng"}],"oa_version":"Preprint","das_tickbox":"1","article_processing_charge":"No","researchdata_availability":"upon request"}]