[{"article_type":"original","issue":"8018","das_tickbox":"1","supplementarymaterial":"yes","citation":{"chicago":"Bravo, Jack Peter Kelly, Delisa A. Ramos, Rodrigo Fregoso Ocampo, Caiden Ingram, and David W. Taylor. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07515-9\">https://doi.org/10.1038/s41586-024-07515-9</a>.","short":"J.P.K. Bravo, D.A. Ramos, R. Fregoso Ocampo, C. Ingram, D.W. Taylor, Nature 630 (2024) 961–967.","ista":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. 2024. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 630(8018), 961–967.","ama":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. <i>Nature</i>. 2024;630(8018):961-967. doi:<a href=\"https://doi.org/10.1038/s41586-024-07515-9\">10.1038/s41586-024-07515-9</a>","apa":"Bravo, J. P. K., Ramos, D. A., Fregoso Ocampo, R., Ingram, C., &#38; Taylor, D. W. (2024). Plasmid targeting and destruction by the DdmDE bacterial defence system. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07515-9\">https://doi.org/10.1038/s41586-024-07515-9</a>","mla":"Bravo, Jack Peter Kelly, et al. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” <i>Nature</i>, vol. 630, no. 8018, Springer Nature, 2024, pp. 961–67, doi:<a href=\"https://doi.org/10.1038/s41586-024-07515-9\">10.1038/s41586-024-07515-9</a>.","ieee":"J. P. K. Bravo, D. A. Ramos, R. Fregoso Ocampo, C. Ingram, and D. W. Taylor, “Plasmid targeting and destruction by the DdmDE bacterial defence system,” <i>Nature</i>, vol. 630, no. 8018. Springer Nature, pp. 961–967, 2024."},"researchdata_availability":"yes","oa":1,"fulldoi":"https://doi.org/10.1038/s41586-024-07515-9","acknowledgement":"We thank K. Kiernan, G. Hibshman and I. Strohkendl for insightful discussions and comments on the manuscript, and R. Lin for assistance with the ATPase assay. Data were collected at the Sauer Structural Biology Laboratory at the University of Texas at Austin. This work was supported in part by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) R35GM138348 (to D.W.T.) and Welch Foundation research grant F-1938 (to D.W.T.).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-08-19T09:41:18Z","publisher":"Springer Nature","date_updated":"2026-10-02T11:59:25Z","day":"27","article_processing_charge":"No","publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"17442","year":"2024","page":"961-967","abstract":[{"lang":"eng","text":"Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE–guide–target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.\r\n\r\n"}],"title":"Plasmid targeting and destruction by the DdmDE bacterial defence system","publication":"Nature","author":[{"first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly"},{"first_name":"Delisa A.","last_name":"Ramos","full_name":"Ramos, Delisa A."},{"first_name":"Rodrigo","full_name":"Fregoso Ocampo, Rodrigo","last_name":"Fregoso Ocampo"},{"first_name":"Caiden","last_name":"Ingram","full_name":"Ingram, Caiden"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"language":[{"iso":"eng"}],"volume":630,"external_id":{"pmid":["38740055"]},"oa_version":"Submitted Version","type":"journal_article","date_published":"2024-06-27T00:00:00Z","intvolume":"       630","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11649018/"}],"quality_controlled":"1","dataavailabilitystatement":"Structures of the DdmE in complex with guide and target, the DdmD monomer in complex with ssDNA, the DdmDE handover complex, the DdmD dimer and the DdmD dimer in complex with ssDNA have been deposited in the Electron Microscopy Data Bank with the accession codes EMD-41781, EMD-41790, EMD-41865, EMD-44825 and EMD-41785, respectively. Associated atomic coordinates have been deposited in the Protein Data Bank with the accession codes 8U0J, 8U0W, 8U3K, 9BVQ and 8U0U, respectively. Source data are provided with this paper.","month":"06","doi":"10.1038/s41586-024-07515-9","scopus_import":"1","pmid":1,"corr_author":"1","status":"public","department":[{"_id":"JaBr"}],"OA_place":"repository"},{"doi":"10.1038/s41586-023-05991-z","pmid":1,"scopus_import":"1","department":[{"_id":"PaSc"}],"has_accepted_license":"1","status":"public","external_id":{"isi":["000991386800011"],"pmid":["37198476"]},"volume":618,"language":[{"iso":"eng"}],"intvolume":"       618","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"type":"journal_article","date_published":"2023-06-29T00:00:00Z","oa_version":"Published Version","quality_controlled":"1","ddc":["570"],"file":[{"date_updated":"2023-11-14T11:48:18Z","file_name":"2023_Nature_Degen.pdf","content_type":"application/pdf","checksum":"0fab69252453bff1de7f0e2eceb76d34","creator":"dernst","file_size":12292188,"relation":"main_file","success":1,"file_id":"14533","access_level":"open_access","date_created":"2023-11-14T11:48:18Z"}],"month":"06","date_updated":"2025-04-23T08:57:12Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","day":"29","year":"2023","_id":"13096","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","author":[{"full_name":"Degen, Morris","last_name":"Degen","first_name":"Morris"},{"full_name":"Santos, José Carlos","last_name":"Santos","first_name":"José Carlos"},{"first_name":"Kristyna","full_name":"Pluhackova, Kristyna","last_name":"Pluhackova"},{"first_name":"Gonzalo","last_name":"Cebrero","full_name":"Cebrero, Gonzalo"},{"full_name":"Ramos, Saray","last_name":"Ramos","first_name":"Saray"},{"first_name":"Gytis","last_name":"Jankevicius","full_name":"Jankevicius, Gytis"},{"first_name":"Ella","last_name":"Hartenian","full_name":"Hartenian, Ella"},{"full_name":"Guillerm, Undina","last_name":"Guillerm","first_name":"Undina","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183"},{"full_name":"Mari, Stefania A.","last_name":"Mari","first_name":"Stefania A."},{"last_name":"Kohl","full_name":"Kohl, Bastian","first_name":"Bastian"},{"last_name":"Müller","full_name":"Müller, Daniel J.","first_name":"Daniel J."},{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"full_name":"Maier, Timm","last_name":"Maier","first_name":"Timm"},{"first_name":"Camilo","full_name":"Perez, Camilo","last_name":"Perez"},{"last_name":"Sieben","full_name":"Sieben, Christian","first_name":"Christian"},{"first_name":"Petr","last_name":"Broz","full_name":"Broz, Petr"},{"last_name":"Hiller","full_name":"Hiller, Sebastian","first_name":"Sebastian"}],"publication":"Nature","abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"page":"1065-1071","article_type":"original","oa":1,"citation":{"ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. 2023;618:1065-1071. doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","ieee":"M. Degen <i>et al.</i>, “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” <i>Nature</i>, vol. 618. Springer Nature, pp. 1065–1071, 2023.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>."},"file_date_updated":"2023-11-14T11:48:18Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","fulldoi":"https://doi.org/10.1038/s41586-023-05991-z","publisher":"Springer Nature","isi":1,"date_created":"2023-05-28T22:01:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"original","citation":{"ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720.","ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. 2023;618:716-720. doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 716–20, doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>.","ieee":"V. Helson <i>et al.</i>, “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” <i>Nature</i>, vol. 618. Springer Nature, pp. 716–720, 2023.","chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>.","short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720."},"file_date_updated":"2023-11-14T13:00:19Z","oa":1,"acknowledgement":"Open access funding provided by EPFL Lausanne.We acknowledge discussions with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","fulldoi":"https://doi.org/10.1038/s41586-023-06018-3","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","isi":1,"date_created":"2023-06-04T22:01:03Z","date_updated":"2025-04-23T08:58:21Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","day":"22","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"13119","year":"2023","abstract":[{"text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.","lang":"eng"}],"page":"716-720","title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions","author":[{"first_name":"Victor","last_name":"Helson","full_name":"Helson, Victor"},{"first_name":"Timo","last_name":"Zwettler","full_name":"Zwettler, Timo"},{"last_name":"Mivehvar","full_name":"Mivehvar, Farokh","first_name":"Farokh"},{"full_name":"Colella, Elvia","last_name":"Colella","first_name":"Elvia"},{"last_name":"Roux","full_name":"Roux, Kevin Etienne Robert","first_name":"Kevin Etienne Robert","id":"53f93ea2-803f-11ed-ab7e-b283135794ef"},{"first_name":"Hideki","last_name":"Konishi","full_name":"Konishi, Hideki"},{"first_name":"Helmut","last_name":"Ritsch","full_name":"Ritsch, Helmut"},{"first_name":"Jean Philippe","full_name":"Brantut, Jean Philippe","last_name":"Brantut"}],"publication":"Nature","volume":618,"external_id":{"pmid":["37225993"],"isi":["001001139300008"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"       618","type":"journal_article","date_published":"2023-06-22T00:00:00Z","ddc":["530"],"file":[{"file_name":"2023_Nature_Helson.pdf","date_updated":"2023-11-14T13:00:19Z","checksum":"4887a296e3b6f54e8c0b946cbfd24f49","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":8156497,"date_created":"2023-11-14T13:00:19Z","success":1,"file_id":"14534","access_level":"open_access"}],"quality_controlled":"1","month":"06","doi":"10.1038/s41586-023-06018-3","scopus_import":"1","pmid":1,"has_accepted_license":"1","status":"public","department":[{"_id":"GeKa"}]},{"fulldoi":"https://doi.org/10.1038/s41586-022-05387-5","publisher":"Springer Nature","date_created":"2026-03-30T12:22:47Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","oa":1,"citation":{"short":"Y. Yang, C. Roques-Carmes, S.E. Kooi, H. Tang, J. Beroz, E. Mazur, I. Kaminer, J.D. Joannopoulos, M. Soljačić, Nature 613 (2023) 42–47.","chicago":"Yang, Yi, Charles Roques-Carmes, Steven E. Kooi, Haoning Tang, Justin Beroz, Eric Mazur, Ido Kaminer, John D. Joannopoulos, and Marin Soljačić. “Photonic Flatband Resonances for Free-Electron Radiation.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-022-05387-5\">https://doi.org/10.1038/s41586-022-05387-5</a>.","ieee":"Y. Yang <i>et al.</i>, “Photonic flatband resonances for free-electron radiation,” <i>Nature</i>, vol. 613. Springer Nature, pp. 42–47, 2023.","ama":"Yang Y, Roques-Carmes C, Kooi SE, et al. Photonic flatband resonances for free-electron radiation. <i>Nature</i>. 2023;613:42-47. doi:<a href=\"https://doi.org/10.1038/s41586-022-05387-5\">10.1038/s41586-022-05387-5</a>","apa":"Yang, Y., Roques-Carmes, C., Kooi, S. E., Tang, H., Beroz, J., Mazur, E., … Soljačić, M. (2023). Photonic flatband resonances for free-electron radiation. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05387-5\">https://doi.org/10.1038/s41586-022-05387-5</a>","mla":"Yang, Yi, et al. “Photonic Flatband Resonances for Free-Electron Radiation.” <i>Nature</i>, vol. 613, Springer Nature, 2023, pp. 42–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-05387-5\">10.1038/s41586-022-05387-5</a>.","ista":"Yang Y, Roques-Carmes C, Kooi SE, Tang H, Beroz J, Mazur E, Kaminer I, Joannopoulos JD, Soljačić M. 2023. Photonic flatband resonances for free-electron radiation. Nature. 613, 42–47."},"year":"2023","_id":"21547","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"title":"Photonic flatband resonances for free-electron radiation","publication":"Nature","author":[{"first_name":"Yi","full_name":"Yang, Yi","last_name":"Yang"},{"last_name":"Roques-Carmes","full_name":"Roques-Carmes, Charles","first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"first_name":"Steven E.","last_name":"Kooi","full_name":"Kooi, Steven E."},{"full_name":"Tang, Haoning","last_name":"Tang","first_name":"Haoning"},{"last_name":"Beroz","full_name":"Beroz, Justin","first_name":"Justin"},{"last_name":"Mazur","full_name":"Mazur, Eric","first_name":"Eric"},{"last_name":"Kaminer","full_name":"Kaminer, Ido","first_name":"Ido"},{"full_name":"Joannopoulos, John D.","last_name":"Joannopoulos","first_name":"John D."},{"first_name":"Marin","full_name":"Soljačić, Marin","last_name":"Soljačić"}],"abstract":[{"lang":"eng","text":"Flatbands have become a cornerstone of contemporary condensed-matter physics\r\nand photonics. In electronics, flatbands entail comparable energy bandwidth and\r\nCoulomb interaction, leading to correlated phenomena such as the fractional\r\nquantum Hall effect and recently those in magic-angle systems. In photonics, they\r\nenable properties including slow light1 and lasing2. Notably, flatbands support\r\nsupercollimation—diffractionless wavepacket propagation—in both systems3,4.\r\nDespite these intense parallel efforts, flatbands have never been shown to affect the\r\ncore interaction between free electrons and photons. Their interaction, pivotal for\r\nfree-electron lasers5, microscopy and spectroscopy6,7, and particle accelerators8,9,\r\nis, in fact, limited by a dimensionality mismatch between localized electrons and\r\nextended photons. Here we reveal theoretically that photonic flatbands can overcome\r\nthis mismatch and thus remarkably boost their interaction. We design flatband\r\nresonances in a silicon-on-insulator photonic crystal slab to control and enhance the\r\nassociated free-electron radiation by tuning their trajectory and velocity. We observe\r\nsignatures of flatband enhancement, recording a two-order increase from the\r\nconventional diffraction-enabled Smith–Purcell radiation. The enhancement enables\r\npolarization shaping of free-electron radiation and characterization of photonic\r\nbands through electron-beam measurements. Our results support the use of\r\nflatbands as test beds for strong light–electron interaction, particularly relevant for\r\nefficient and compact free-electron light sources and accelerators."}],"page":"42-47","date_updated":"2026-04-27T09:10:26Z","arxiv":1,"publication_status":"published","day":"04","article_processing_charge":"No","extern":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2110.03550","open_access":"1"}],"ddc":["530"],"OA_type":"green","month":"01","volume":613,"external_id":{"pmid":["36600060"],"arxiv":["2110.03550"]},"language":[{"iso":"eng"}],"intvolume":"       613","type":"journal_article","date_published":"2023-01-04T00:00:00Z","oa_version":"Preprint","OA_place":"repository","status":"public","doi":"10.1038/s41586-022-05387-5","pmid":1,"scopus_import":"1"},{"article_processing_charge":"No","day":"07","publication_status":"published","date_updated":"2025-09-09T12:59:04Z","page":"71-74","abstract":[{"lang":"eng","text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines."}],"title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","author":[{"last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","last_name":"Varshney"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"}],"publication":"Nature","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2023","_id":"14341","file_date_updated":"2024-06-04T09:24:34Z","citation":{"apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., &#38; Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. 2023;621(7977):71-74. doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>.","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” <i>Nature</i>, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74."},"oa":1,"article_type":"original","issue":"7977","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-09-17T22:01:09Z","isi":1,"publisher":"Springer Nature","acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","fulldoi":"https://doi.org/10.1038/s41586-023-06399-5","scopus_import":"1","pmid":1,"related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/"}]},"doi":"10.1038/s41586-023-06399-5","status":"public","has_accepted_license":"1","department":[{"_id":"BjHo"}],"project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"},{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","name":"Instabilities in pulsating pipe flow in complex fluids","call_identifier":"FWF"}],"corr_author":"1","oa_version":"Submitted Version","date_published":"2023-09-07T00:00:00Z","type":"journal_article","intvolume":"       621","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001168947700009"],"pmid":["37673988"]},"volume":621,"month":"09","file":[{"file_size":3247252,"relation":"main_file","file_id":"17118","success":1,"access_level":"open_access","date_created":"2024-06-04T09:24:34Z","date_updated":"2024-06-04T09:24:34Z","file_name":"2023_submittedversion.pdf","content_type":"application/pdf","checksum":"9c9f172ba0a9a301d76fff4229812464","creator":"dernst"}],"ddc":["530"],"quality_controlled":"1"},{"author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"last_name":"Mangiarotti","full_name":"Mangiarotti, Agustín","first_name":"Agustín"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo"},{"first_name":"Beren","full_name":"Aylan, Beren","last_name":"Aylan"},{"full_name":"Pellegrino, Enrica","last_name":"Pellegrino","first_name":"Enrica"},{"last_name":"Athanasiadi","full_name":"Athanasiadi, Natalia","first_name":"Natalia"},{"first_name":"Antony","full_name":"Fearns, Antony","last_name":"Fearns"},{"first_name":"Angela","last_name":"Rodgers","full_name":"Rodgers, Angela"},{"full_name":"Franzmann, Titus M.","last_name":"Franzmann","first_name":"Titus M."},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Dimova","full_name":"Dimova, Rumiana","first_name":"Rumiana"},{"first_name":"Maximiliano G.","last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G."}],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","publication":"Nature","page":"1062-1069","abstract":[{"text":"Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.","lang":"eng"}],"year":"2023","_id":"14610","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"day":"30","article_processing_charge":"Yes (via OA deal)","publication_status":"published","date_updated":"2025-09-09T13:30:34Z","date_created":"2023-11-27T07:56:37Z","publisher":"Springer Nature","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1038/s41586-023-06726-w","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","oa":1,"file_date_updated":"2024-07-16T07:41:39Z","citation":{"chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature 623 (2023) 1062–1069.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>, vol. 623. Springer Nature, pp. 1062–1069, 2023.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 623, 1062–1069.","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023;623:1062-1069. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>."},"article_type":"original","department":[{"_id":"AnSa"}],"has_accepted_license":"1","status":"public","pmid":1,"scopus_import":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"id":"14472","relation":"research_data","status":"public"}]},"doi":"10.1038/s41586-023-06726-w","month":"11","quality_controlled":"1","file":[{"date_updated":"2024-07-16T07:41:39Z","file_name":"2023_Nature_Bussi.pdf","content_type":"application/pdf","creator":"dernst","checksum":"b939a19e4c228fbf3beca298ac2ac014","file_size":17047711,"relation":"main_file","access_level":"open_access","success":1,"file_id":"17248","date_created":"2024-07-16T07:41:39Z"}],"ddc":["570"],"type":"journal_article","date_published":"2023-11-30T00:00:00Z","intvolume":"       623","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["37968398"],"isi":["001105882300018"]},"volume":623},{"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41586-022-05560-w","open_access":"1"}],"month":"01","external_id":{"pmid":["36599980"]},"volume":613,"language":[{"iso":"eng"}],"intvolume":"       613","date_published":"2023-01-04T00:00:00Z","type":"journal_article","oa_version":"Published Version","status":"public","doi":"10.1038/s41586-022-05560-w","pmid":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41586-022-05560-w","publisher":"Springer Nature","date_created":"2024-03-20T10:41:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7944","article_type":"original","oa":1,"citation":{"short":"J.P.K. Bravo, T. Hallmark, B. Naegle, C.L. Beisel, R.N. Jackson, D.W. Taylor, Nature 613 (2023) 582–587.","chicago":"Bravo, Jack Peter Kelly, Thomson Hallmark, Bronson Naegle, Chase L. Beisel, Ryan N. Jackson, and David W. Taylor. “RNA Targeting Unleashes Indiscriminate Nuclease Activity of CRISPR–Cas12a2.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-022-05560-w\">https://doi.org/10.1038/s41586-022-05560-w</a>.","ieee":"J. P. K. Bravo, T. Hallmark, B. Naegle, C. L. Beisel, R. N. Jackson, and D. W. Taylor, “RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2,” <i>Nature</i>, vol. 613, no. 7944. Springer Nature, pp. 582–587, 2023.","ama":"Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW. RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2. <i>Nature</i>. 2023;613(7944):582-587. doi:<a href=\"https://doi.org/10.1038/s41586-022-05560-w\">10.1038/s41586-022-05560-w</a>","apa":"Bravo, J. P. K., Hallmark, T., Naegle, B., Beisel, C. L., Jackson, R. N., &#38; Taylor, D. W. (2023). RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05560-w\">https://doi.org/10.1038/s41586-022-05560-w</a>","mla":"Bravo, Jack Peter Kelly, et al. “RNA Targeting Unleashes Indiscriminate Nuclease Activity of CRISPR–Cas12a2.” <i>Nature</i>, vol. 613, no. 7944, Springer Nature, 2023, pp. 582–87, doi:<a href=\"https://doi.org/10.1038/s41586-022-05560-w\">10.1038/s41586-022-05560-w</a>.","ista":"Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW. 2023. RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2. Nature. 613(7944), 582–587."},"_id":"15130","year":"2023","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication":"Nature","title":"RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2","author":[{"full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"first_name":"Thomson","full_name":"Hallmark, Thomson","last_name":"Hallmark"},{"last_name":"Naegle","full_name":"Naegle, Bronson","first_name":"Bronson"},{"first_name":"Chase L.","full_name":"Beisel, Chase L.","last_name":"Beisel"},{"first_name":"Ryan N.","full_name":"Jackson, Ryan N.","last_name":"Jackson"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"abstract":[{"text":"Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided, sequence-nonspecific degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA following recognition of a complementary RNA target, culminating in abortive infection<jats:sup>1</jats:sup>. Here we report structures of Cas12a2 in binary, ternary and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of ‘aromatic clamp’ residues that are crucial for double-stranded DNA degradation and in vivo immune system function. Our work provides a structural basis for this mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.","lang":"eng"}],"page":"582-587","date_updated":"2024-06-04T06:30:59Z","publication_status":"published","day":"04","article_processing_charge":"Yes (in subscription journal)","extern":"1"},{"date_updated":"2024-03-25T12:42:29Z","publication_status":"published","day":"05","article_processing_charge":"No","extern":"1","year":"2023","_id":"15148","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication":"Nature","title":"Cooperation between bHLH transcription factors and histones for DNA access","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","last_name":"Michael"},{"last_name":"Stoos","full_name":"Stoos, Lisa","first_name":"Lisa"},{"full_name":"Crosby, Priya","last_name":"Crosby","first_name":"Priya"},{"last_name":"Eggers","full_name":"Eggers, Nikolas","first_name":"Nikolas"},{"first_name":"Xinyu Y.","last_name":"Nie","full_name":"Nie, Xinyu Y."},{"last_name":"Makasheva","full_name":"Makasheva, Kristina","first_name":"Kristina"},{"first_name":"Martina","last_name":"Minnich","full_name":"Minnich, Martina"},{"full_name":"Healy, Kelly L.","last_name":"Healy","first_name":"Kelly L."},{"first_name":"Joscha","full_name":"Weiss, Joscha","last_name":"Weiss"},{"first_name":"Georg","full_name":"Kempf, Georg","last_name":"Kempf"},{"full_name":"Cavadini, Simone","last_name":"Cavadini","first_name":"Simone"},{"full_name":"Kater, Lukas","last_name":"Kater","first_name":"Lukas"},{"first_name":"Jan","last_name":"Seebacher","full_name":"Seebacher, Jan"},{"first_name":"Luca","full_name":"Vecchia, Luca","last_name":"Vecchia"},{"first_name":"Deyasini","last_name":"Chakraborty","full_name":"Chakraborty, Deyasini"},{"last_name":"Isbel","full_name":"Isbel, Luke","first_name":"Luke"},{"full_name":"Grand, Ralph S.","last_name":"Grand","first_name":"Ralph S."},{"full_name":"Andersch, Florian","last_name":"Andersch","first_name":"Florian"},{"full_name":"Fribourgh, Jennifer L.","last_name":"Fribourgh","first_name":"Jennifer L."},{"last_name":"Schübeler","full_name":"Schübeler, Dirk","first_name":"Dirk"},{"first_name":"Johannes","full_name":"Zuber, Johannes","last_name":"Zuber"},{"first_name":"Andrew C.","full_name":"Liu, Andrew C.","last_name":"Liu"},{"first_name":"Peter B.","full_name":"Becker, Peter B.","last_name":"Becker"},{"full_name":"Fierz, Beat","last_name":"Fierz","first_name":"Beat"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"},{"last_name":"Menet","full_name":"Menet, Jerome S.","first_name":"Jerome S."},{"first_name":"Nicolas H.","last_name":"Thomä","full_name":"Thomä, Nicolas H."}],"abstract":[{"text":"The basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members<jats:sup>1</jats:sup>. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. <jats:sup>2,3</jats:sup>). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry–exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A–H2B acidic patch<jats:sup>4</jats:sup>, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes<jats:sup>5–7</jats:sup> at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.","lang":"eng"}],"page":"385-393","issue":"7969","article_type":"original","oa":1,"citation":{"chicago":"Michael, Alicia K., Lisa Stoos, Priya Crosby, Nikolas Eggers, Xinyu Y. Nie, Kristina Makasheva, Martina Minnich, et al. “Cooperation between BHLH Transcription Factors and Histones for DNA Access.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06282-3\">https://doi.org/10.1038/s41586-023-06282-3</a>.","short":"A.K. Michael, L. Stoos, P. Crosby, N. Eggers, X.Y. Nie, K. Makasheva, M. Minnich, K.L. Healy, J. Weiss, G. Kempf, S. Cavadini, L. Kater, J. Seebacher, L. Vecchia, D. Chakraborty, L. Isbel, R.S. Grand, F. Andersch, J.L. Fribourgh, D. Schübeler, J. Zuber, A.C. Liu, P.B. Becker, B. Fierz, C.L. Partch, J.S. Menet, N.H. Thomä, Nature 619 (2023) 385–393.","ieee":"A. K. Michael <i>et al.</i>, “Cooperation between bHLH transcription factors and histones for DNA access,” <i>Nature</i>, vol. 619, no. 7969. Springer Nature, pp. 385–393, 2023.","ista":"Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH. 2023. Cooperation between bHLH transcription factors and histones for DNA access. Nature. 619(7969), 385–393.","apa":"Michael, A. K., Stoos, L., Crosby, P., Eggers, N., Nie, X. Y., Makasheva, K., … Thomä, N. H. (2023). Cooperation between bHLH transcription factors and histones for DNA access. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06282-3\">https://doi.org/10.1038/s41586-023-06282-3</a>","mla":"Michael, Alicia K., et al. “Cooperation between BHLH Transcription Factors and Histones for DNA Access.” <i>Nature</i>, vol. 619, no. 7969, Springer Nature, 2023, pp. 385–93, doi:<a href=\"https://doi.org/10.1038/s41586-023-06282-3\">10.1038/s41586-023-06282-3</a>.","ama":"Michael AK, Stoos L, Crosby P, et al. Cooperation between bHLH transcription factors and histones for DNA access. <i>Nature</i>. 2023;619(7969):385-393. doi:<a href=\"https://doi.org/10.1038/s41586-023-06282-3\">10.1038/s41586-023-06282-3</a>"},"fulldoi":"https://doi.org/10.1038/s41586-023-06282-3","publisher":"Springer Nature","date_created":"2024-03-21T07:52:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41586-023-06282-3","scopus_import":"1","status":"public","volume":619,"language":[{"iso":"eng"}],"intvolume":"       619","type":"journal_article","date_published":"2023-07-05T00:00:00Z","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06282-3","open_access":"1"}],"month":"07"},{"extern":"1","day":"19","article_processing_charge":"No","publication_status":"published","arxiv":1,"date_updated":"2024-10-14T12:32:28Z","page":"61-66","abstract":[{"lang":"eng","text":"White dwarfs, the extremely dense remnants left behind by most stars after their death, are characterized by a mass comparable to that of the Sun compressed into the size of an Earth-like planet. In the resulting strong gravity, heavy elements sink towards the centre and the upper layer of the atmosphere contains only the lightest element present, usually hydrogen or helium1,2. Several mechanisms compete with gravitational settling to change a white dwarf’s surface composition as it cools3, and the fraction of white dwarfs with helium atmospheres is known to increase by a factor of about 2.5 below a temperature of about 30,000 kelvin4,5,6,7,8; therefore, some white dwarfs that appear to have hydrogen-dominated atmospheres above 30,000 kelvin are bound to transition to be helium-dominated as they cool below it. Here we report observations of ZTF J203349.8+322901.1, a transitioning white dwarf with two faces: one side of its atmosphere is dominated by hydrogen and the other one by helium. This peculiar nature is probably caused by the presence of a small magnetic field, which creates an inhomogeneity in temperature, pressure or mixing strength over the surface9,10,11. ZTF J203349.8+322901.1 might be the most extreme member of a class of magnetic, transitioning white dwarfs—together with GD 323 (ref. 12), a white dwarf that shows similar but much more subtle variations. This class of white dwarfs could help shed light on the physical mechanisms behind the spectral evolution of white dwarfs."}],"title":"A rotating white dwarf shows different compositions on its opposite faces","author":[{"orcid":"0000-0002-4770-5388","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","first_name":"Ilaria","last_name":"Caiazzo","full_name":"Caiazzo, Ilaria"},{"full_name":"Burdge, Kevin B.","last_name":"Burdge","first_name":"Kevin B."},{"first_name":"Pier-Emmanuel","full_name":"Tremblay, Pier-Emmanuel","last_name":"Tremblay"},{"full_name":"Fuller, James","last_name":"Fuller","first_name":"James"},{"first_name":"Lilia","last_name":"Ferrario","full_name":"Ferrario, Lilia"},{"last_name":"Gänsicke","full_name":"Gänsicke, Boris T.","first_name":"Boris T."},{"full_name":"Hermes, J. J.","last_name":"Hermes","first_name":"J. J."},{"full_name":"Heyl, Jeremy","last_name":"Heyl","first_name":"Jeremy"},{"last_name":"Kawka","full_name":"Kawka, Adela","first_name":"Adela"},{"first_name":"S. R.","last_name":"Kulkarni","full_name":"Kulkarni, S. R."},{"first_name":"Thomas R.","last_name":"Marsh","full_name":"Marsh, Thomas R."},{"first_name":"Przemek","full_name":"Mróz, Przemek","last_name":"Mróz"},{"first_name":"Thomas A.","last_name":"Prince","full_name":"Prince, Thomas A."},{"full_name":"Richer, Harvey B.","last_name":"Richer","first_name":"Harvey B."},{"full_name":"Rodriguez, Antonio C.","last_name":"Rodriguez","first_name":"Antonio C."},{"first_name":"Jan","last_name":"van Roestel","full_name":"van Roestel, Jan"},{"last_name":"Vanderbosch","full_name":"Vanderbosch, Zachary P.","first_name":"Zachary P."},{"first_name":"Stéphane","full_name":"Vennes, Stéphane","last_name":"Vennes"},{"last_name":"Wickramasinghe","full_name":"Wickramasinghe, Dayal","first_name":"Dayal"},{"full_name":"Dhillon, Vikram S.","last_name":"Dhillon","first_name":"Vikram S."},{"first_name":"Stuart P.","full_name":"Littlefair, Stuart P.","last_name":"Littlefair"},{"full_name":"Munday, James","last_name":"Munday","first_name":"James"},{"full_name":"Pelisoli, Ingrid","last_name":"Pelisoli","first_name":"Ingrid"},{"last_name":"Perley","full_name":"Perley, Daniel","first_name":"Daniel"},{"first_name":"Eric C.","last_name":"Bellm","full_name":"Bellm, Eric C."},{"last_name":"Breedt","full_name":"Breedt, Elmé","first_name":"Elmé"},{"full_name":"Brown, Alex J.","last_name":"Brown","first_name":"Alex J."},{"first_name":"Richard","last_name":"Dekany","full_name":"Dekany, Richard"},{"first_name":"Andrew","last_name":"Drake","full_name":"Drake, Andrew"},{"full_name":"Dyer, Martin J.","last_name":"Dyer","first_name":"Martin J."},{"first_name":"Matthew J.","full_name":"Graham, Matthew J.","last_name":"Graham"},{"first_name":"Matthew J.","last_name":"Green","full_name":"Green, Matthew J."},{"full_name":"Laher, Russ R.","last_name":"Laher","first_name":"Russ R."},{"first_name":"Paul","full_name":"Kerry, Paul","last_name":"Kerry"},{"first_name":"Steven G.","last_name":"Parsons","full_name":"Parsons, Steven G."},{"last_name":"Riddle","full_name":"Riddle, Reed L.","first_name":"Reed L."},{"first_name":"Ben","last_name":"Rusholme","full_name":"Rusholme, Ben"},{"first_name":"Dave I.","full_name":"Sahman, Dave I.","last_name":"Sahman"}],"publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"15195","year":"2023","citation":{"chicago":"Caiazzo, Ilaria, Kevin B. Burdge, Pier-Emmanuel Tremblay, James Fuller, Lilia Ferrario, Boris T. Gänsicke, J. J. Hermes, et al. “A Rotating White Dwarf Shows Different Compositions on Its Opposite Faces.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06171-9\">https://doi.org/10.1038/s41586-023-06171-9</a>.","short":"I. Caiazzo, K.B. Burdge, P.-E. Tremblay, J. Fuller, L. Ferrario, B.T. Gänsicke, J.J. Hermes, J. Heyl, A. Kawka, S.R. Kulkarni, T.R. Marsh, P. Mróz, T.A. Prince, H.B. Richer, A.C. Rodriguez, J. van Roestel, Z.P. Vanderbosch, S. Vennes, D. Wickramasinghe, V.S. Dhillon, S.P. Littlefair, J. Munday, I. Pelisoli, D. Perley, E.C. Bellm, E. Breedt, A.J. Brown, R. Dekany, A. Drake, M.J. Dyer, M.J. Graham, M.J. Green, R.R. Laher, P. Kerry, S.G. Parsons, R.L. Riddle, B. Rusholme, D.I. Sahman, Nature 620 (2023) 61–66.","ieee":"I. Caiazzo <i>et al.</i>, “A rotating white dwarf shows different compositions on its opposite faces,” <i>Nature</i>, vol. 620, no. 7972. Springer Nature, pp. 61–66, 2023.","ista":"Caiazzo I, Burdge KB, Tremblay P-E, Fuller J, Ferrario L, Gänsicke BT, Hermes JJ, Heyl J, Kawka A, Kulkarni SR, Marsh TR, Mróz P, Prince TA, Richer HB, Rodriguez AC, van Roestel J, Vanderbosch ZP, Vennes S, Wickramasinghe D, Dhillon VS, Littlefair SP, Munday J, Pelisoli I, Perley D, Bellm EC, Breedt E, Brown AJ, Dekany R, Drake A, Dyer MJ, Graham MJ, Green MJ, Laher RR, Kerry P, Parsons SG, Riddle RL, Rusholme B, Sahman DI. 2023. A rotating white dwarf shows different compositions on its opposite faces. Nature. 620(7972), 61–66.","mla":"Caiazzo, Ilaria, et al. “A Rotating White Dwarf Shows Different Compositions on Its Opposite Faces.” <i>Nature</i>, vol. 620, no. 7972, Springer Nature, 2023, pp. 61–66, doi:<a href=\"https://doi.org/10.1038/s41586-023-06171-9\">10.1038/s41586-023-06171-9</a>.","ama":"Caiazzo I, Burdge KB, Tremblay P-E, et al. A rotating white dwarf shows different compositions on its opposite faces. <i>Nature</i>. 2023;620(7972):61-66. doi:<a href=\"https://doi.org/10.1038/s41586-023-06171-9\">10.1038/s41586-023-06171-9</a>","apa":"Caiazzo, I., Burdge, K. B., Tremblay, P.-E., Fuller, J., Ferrario, L., Gänsicke, B. T., … Sahman, D. I. (2023). A rotating white dwarf shows different compositions on its opposite faces. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06171-9\">https://doi.org/10.1038/s41586-023-06171-9</a>"},"oa":1,"article_type":"original","issue":"7972","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-03-26T09:46:57Z","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41586-023-06171-9","scopus_import":"1","doi":"10.1038/s41586-023-06171-9","status":"public","oa_version":"Preprint","date_published":"2023-07-19T00:00:00Z","type":"journal_article","intvolume":"       620","language":[{"iso":"eng"}],"volume":620,"external_id":{"arxiv":["2308.07430"]},"month":"07","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2308.07430"}]},{"abstract":[{"lang":"eng","text":"Fasting initiates a multitude of adaptations to allow survival. Activation of the hypothalamic–pituitary–adrenal (HPA) axis and subsequent release of glucocorticoid hormones is a key response that mobilizes fuel stores to meet energy demands1,2,3,4,5. Despite the importance of the HPA axis response, the neural mechanisms that drive its activation during energy deficit are unknown. Here, we show that fasting-activated hypothalamic agouti-related peptide (AgRP)-expressing neurons trigger and are essential for fasting-induced HPA axis activation. AgRP neurons do so through projections to the paraventricular hypothalamus (PVH), where, in a mechanism not previously described for AgRP neurons, they presynaptically inhibit the terminals of tonically active GABAergic afferents from the bed nucleus of the stria terminalis (BNST) that otherwise restrain activity of corticotrophin-releasing hormone (CRH)-expressing neurons. This disinhibition of PVHCrh neurons requires γ-aminobutyric acid (GABA)/GABA-B receptor signalling and potently activates the HPA axis. Notably, stimulation of the HPA axis by AgRP neurons is independent of their induction of hunger, showing that these canonical ‘hunger neurons’ drive many distinctly different adaptations to the fasted state. Together, our findings identify the neural basis for fasting-induced HPA axis activation and uncover a unique means by which AgRP neurons activate downstream neurons: through presynaptic inhibition of GABAergic afferents. Given the potency of this disinhibition of tonically active BNST afferents, other activators of the HPA axis, such as psychological stress, may also work by reducing BNST inhibitory tone onto PVHCrh neurons."}],"page":"154-162","title":"Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis","publication":"Nature","author":[{"full_name":"Douglass, Amelia May Barnett","last_name":"Douglass","orcid":"0000-0001-5398-6473","first_name":"Amelia May Barnett","id":"de5f6fda-80fb-11ef-996f-a8c4ecd8e289"},{"last_name":"Resch","full_name":"Resch, Jon M.","first_name":"Jon M."},{"last_name":"Madara","full_name":"Madara, Joseph C.","first_name":"Joseph C."},{"first_name":"Hakan","last_name":"Kucukdereli","full_name":"Kucukdereli, Hakan"},{"first_name":"Ofer","last_name":"Yizhar","full_name":"Yizhar, Ofer"},{"first_name":"Abhinav","last_name":"Grama","full_name":"Grama, Abhinav"},{"full_name":"Yamagata, Masahito","last_name":"Yamagata","first_name":"Masahito"},{"first_name":"Zongfang","last_name":"Yang","full_name":"Yang, Zongfang"},{"last_name":"Lowell","full_name":"Lowell, Bradford B.","first_name":"Bradford B."}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"19471","year":"2023","extern":"1","publication_status":"published","day":"03","article_processing_charge":"No","date_updated":"2025-07-10T11:51:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2025-04-03T12:28:51Z","fulldoi":"https://doi.org/10.1038/s41586-023-06358-0","citation":{"ieee":"A. M. Douglass <i>et al.</i>, “Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis,” <i>Nature</i>, vol. 620, no. 7972. Springer Nature, pp. 154–162, 2023.","ista":"Douglass AM, Resch JM, Madara JC, Kucukdereli H, Yizhar O, Grama A, Yamagata M, Yang Z, Lowell BB. 2023. Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis. Nature. 620(7972), 154–162.","ama":"Douglass AM, Resch JM, Madara JC, et al. Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis. <i>Nature</i>. 2023;620(7972):154-162. doi:<a href=\"https://doi.org/10.1038/s41586-023-06358-0\">10.1038/s41586-023-06358-0</a>","mla":"Douglass, Amelia M., et al. “Neural Basis for Fasting Activation of the Hypothalamic–Pituitary–Adrenal Axis.” <i>Nature</i>, vol. 620, no. 7972, Springer Nature, 2023, pp. 154–62, doi:<a href=\"https://doi.org/10.1038/s41586-023-06358-0\">10.1038/s41586-023-06358-0</a>.","apa":"Douglass, A. M., Resch, J. M., Madara, J. C., Kucukdereli, H., Yizhar, O., Grama, A., … Lowell, B. B. (2023). Neural basis for fasting activation of the hypothalamic–pituitary–adrenal axis. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06358-0\">https://doi.org/10.1038/s41586-023-06358-0</a>","chicago":"Douglass, Amelia M., Jon M. Resch, Joseph C. Madara, Hakan Kucukdereli, Ofer Yizhar, Abhinav Grama, Masahito Yamagata, Zongfang Yang, and Bradford B. Lowell. “Neural Basis for Fasting Activation of the Hypothalamic–Pituitary–Adrenal Axis.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06358-0\">https://doi.org/10.1038/s41586-023-06358-0</a>.","short":"A.M. Douglass, J.M. Resch, J.C. Madara, H. Kucukdereli, O. Yizhar, A. Grama, M. Yamagata, Z. Yang, B.B. Lowell, Nature 620 (2023) 154–162."},"oa":1,"issue":"7972","article_type":"original","status":"public","OA_place":"repository","scopus_import":"1","pmid":1,"doi":"10.1038/s41586-023-06358-0","month":"08","OA_type":"green","quality_controlled":"1","main_file_link":[{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11168300/","open_access":"1"}],"oa_version":"Submitted Version","intvolume":"       620","type":"journal_article","date_published":"2023-08-03T00:00:00Z","external_id":{"pmid":["37495689 "]},"volume":620,"language":[{"iso":"eng"}]},{"month":"06","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.10919"}],"oa_version":"Preprint","intvolume":"       619","date_published":"2023-06-21T00:00:00Z","type":"journal_article","external_id":{"arxiv":["2210.10919"],"pmid":["37344594 "]},"volume":619,"language":[{"iso":"eng"}],"status":"public","scopus_import":"1","pmid":1,"doi":"10.1038/s41586-023-06122-4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2024-10-07T11:46:13Z","fulldoi":"https://doi.org/10.1038/s41586-023-06122-4","citation":{"ieee":"J. Leonard <i>et al.</i>, “Realization of a fractional quantum Hall state with ultracold atoms,” <i>Nature</i>, vol. 619, no. 7970. Springer Nature, pp. 495–499, 2023.","ista":"Leonard J, Kim S, Kwan J, Segura P, Grusdt F, Repellin C, Goldman N, Greiner M. 2023. Realization of a fractional quantum Hall state with ultracold atoms. Nature. 619(7970), 495–499.","mla":"Leonard, Julian, et al. “Realization of a Fractional Quantum Hall State with Ultracold Atoms.” <i>Nature</i>, vol. 619, no. 7970, Springer Nature, 2023, pp. 495–99, doi:<a href=\"https://doi.org/10.1038/s41586-023-06122-4\">10.1038/s41586-023-06122-4</a>.","apa":"Leonard, J., Kim, S., Kwan, J., Segura, P., Grusdt, F., Repellin, C., … Greiner, M. (2023). Realization of a fractional quantum Hall state with ultracold atoms. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06122-4\">https://doi.org/10.1038/s41586-023-06122-4</a>","ama":"Leonard J, Kim S, Kwan J, et al. Realization of a fractional quantum Hall state with ultracold atoms. <i>Nature</i>. 2023;619(7970):495-499. doi:<a href=\"https://doi.org/10.1038/s41586-023-06122-4\">10.1038/s41586-023-06122-4</a>","chicago":"Leonard, Julian, Sooshin Kim, Joyce Kwan, Perrin Segura, Fabian Grusdt, Cécile Repellin, Nathan Goldman, and Markus Greiner. “Realization of a Fractional Quantum Hall State with Ultracold Atoms.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06122-4\">https://doi.org/10.1038/s41586-023-06122-4</a>.","short":"J. Leonard, S. Kim, J. Kwan, P. Segura, F. Grusdt, C. Repellin, N. Goldman, M. Greiner, Nature 619 (2023) 495–499."},"oa":1,"issue":"7970","article_type":"original","abstract":[{"text":"Strongly interacting topological matter1 exhibits fundamentally new phenomena with potential applications in quantum information technology2,3. Emblematic instances are fractional quantum Hall (FQH) states4, in which the interplay of a magnetic field and strong interactions gives rise to fractionally charged quasi-particles, long-ranged entanglement and anyonic exchange statistics. Progress in engineering synthetic magnetic fields5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21 has raised the hope to create these exotic states in controlled quantum systems. However, except for a recent Laughlin state of light22, preparing FQH states in engineered systems remains elusive. Here we realize a FQH state with ultracold atoms in an optical lattice. The state is a lattice version of a bosonic ν = 1/2 Laughlin state4,23 with two particles on 16 sites. This minimal system already captures many hallmark features of Laughlin-type FQH states24,25,26,27,28: we observe a suppression of two-body interactions, we find a distinctive vortex structure in the density correlations and we measure a fractional Hall conductivity of σH/σ0 = 0.6(2) by means of the bulk response to a magnetic perturbation. Furthermore, by tuning the magnetic field, we map out the transition point between the normal and the FQH regime through a spectroscopic investigation of the many-body gap. Our work provides a starting point for exploring highly entangled topological matter with ultracold atoms29,30,31,32,33.","lang":"eng"}],"page":"495-499","author":[{"first_name":"Julian","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","last_name":"Leonard","full_name":"Leonard, Julian"},{"last_name":"Kim","full_name":"Kim, Sooshin","first_name":"Sooshin"},{"last_name":"Kwan","full_name":"Kwan, Joyce","first_name":"Joyce"},{"first_name":"Perrin","full_name":"Segura, Perrin","last_name":"Segura"},{"first_name":"Fabian","last_name":"Grusdt","full_name":"Grusdt, Fabian"},{"full_name":"Repellin, Cécile","last_name":"Repellin","first_name":"Cécile"},{"last_name":"Goldman","full_name":"Goldman, Nathan","first_name":"Nathan"},{"first_name":"Markus","full_name":"Greiner, Markus","last_name":"Greiner"}],"publication":"Nature","title":"Realization of a fractional quantum Hall state with ultracold atoms","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"18189","year":"2023","extern":"1","publication_status":"published","article_processing_charge":"No","day":"21","date_updated":"2024-10-08T11:09:24Z","arxiv":1},{"quality_controlled":"1","file":[{"relation":"main_file","file_size":25360311,"date_created":"2022-08-05T06:08:24Z","success":1,"file_id":"11727","access_level":"open_access","file_name":"2022_Nature_Lukacisin.pdf","date_updated":"2022-08-05T06:08:24Z","checksum":"d68cd1596bb9fd819b750fe47c8a138a","creator":"dernst","content_type":"application/pdf"}],"ddc":["570"],"month":"05","language":[{"iso":"eng"}],"volume":605,"external_id":{"isi":["000784934100003"],"pmid":["35444278"]},"type":"journal_article","date_published":"2022-05-05T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"intvolume":"       605","oa_version":"Published Version","project":[{"call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"}],"status":"public","has_accepted_license":"1","doi":"10.1038/s41586-022-04633-0","pmid":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the IST Austria Life Science Facility, the Miba Machine Shop and M. Lukačišinová for support with the liquid handling robot; the Bioimaging Facility at IST Austria, J. Power and B. Meier at the University of Cologne, and C. Göttlinger at the FACS Analysis Facility at the Institute for Genetics, University of Cologne, for support with flow cytometry experiments; L. Horst for the development of the automated experimental methods in Cologne; J. Parenteau, S. Abou Elela, G. Stormo, M. Springer and M. Schuldiner for providing us with yeast strains; B. Fernando, T. Fink, G. Ansmann and G. Chevreau for technical support; H. Köver, G. Tkačik, N. Barton, A. Angermayr and B. Kavčič for support during laboratory relocation; D. Siekhaus, M. Springer and all the members of the Bollenbach group for support and discussions; and K. Mitosch, M. Lukačišinová, G. Liti and A. de Luna for critical reading of our manuscript. This work was supported in part by an Austrian Science Fund (FWF) standalone grant P 27201-B22 (to T.B.), HFSP program Grant RGP0042/2013 (to T.B.), EU Marie Curie Career Integration Grant No. 303507, and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). A.E.-C. was supported by a Georg Forster fellowship from the Alexander von Humboldt Foundation.","fulldoi":"https://doi.org/10.1038/s41586-022-04633-0","date_created":"2022-05-01T22:01:42Z","publisher":"Springer Nature","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"file_date_updated":"2022-08-05T06:08:24Z","citation":{"ieee":"M. Lukacisin, A. Espinosa-Cantú, and M. T. Bollenbach, “Intron-mediated induction of phenotypic heterogeneity,” <i>Nature</i>, vol. 605. Springer Nature, pp. 113–118, 2022.","ista":"Lukacisin M, Espinosa-Cantú A, Bollenbach MT. 2022. Intron-mediated induction of phenotypic heterogeneity. Nature. 605, 113–118.","ama":"Lukacisin M, Espinosa-Cantú A, Bollenbach MT. Intron-mediated induction of phenotypic heterogeneity. <i>Nature</i>. 2022;605:113-118. doi:<a href=\"https://doi.org/10.1038/s41586-022-04633-0\">10.1038/s41586-022-04633-0</a>","apa":"Lukacisin, M., Espinosa-Cantú, A., &#38; Bollenbach, M. T. (2022). Intron-mediated induction of phenotypic heterogeneity. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-04633-0\">https://doi.org/10.1038/s41586-022-04633-0</a>","mla":"Lukacisin, Martin, et al. “Intron-Mediated Induction of Phenotypic Heterogeneity.” <i>Nature</i>, vol. 605, Springer Nature, 2022, pp. 113–18, doi:<a href=\"https://doi.org/10.1038/s41586-022-04633-0\">10.1038/s41586-022-04633-0</a>.","short":"M. Lukacisin, A. Espinosa-Cantú, M.T. Bollenbach, Nature 605 (2022) 113–118.","chicago":"Lukacisin, Martin, Adriana Espinosa-Cantú, and Mark Tobias Bollenbach. “Intron-Mediated Induction of Phenotypic Heterogeneity.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-04633-0\">https://doi.org/10.1038/s41586-022-04633-0</a>."},"_id":"11341","year":"2022","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication":"Nature","title":"Intron-mediated induction of phenotypic heterogeneity","author":[{"last_name":"Lukacisin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Adriana","last_name":"Espinosa-Cantú","full_name":"Espinosa-Cantú, Adriana"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"page":"113-118","abstract":[{"text":"Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.","lang":"eng"}],"date_updated":"2025-04-14T09:40:45Z","article_processing_charge":"No","day":"05","publication_status":"published","ec_funded":1},{"date_updated":"2023-08-03T13:41:44Z","publication_status":"published","article_processing_charge":"No","day":"02","_id":"12054","year":"2022","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","author":[{"first_name":"Z","full_name":"Yang, Z","last_name":"Yang"},{"last_name":"Xia","full_name":"Xia, J","first_name":"J"},{"last_name":"Hong","full_name":"Hong, J","first_name":"J"},{"first_name":"C","full_name":"Zhang, C","last_name":"Zhang"},{"last_name":"Wei","full_name":"Wei, H","first_name":"H"},{"first_name":"W","full_name":"Ying, W","last_name":"Ying"},{"full_name":"Sun, C","last_name":"Sun","first_name":"C"},{"last_name":"Sun","full_name":"Sun, L","first_name":"L"},{"first_name":"Y","full_name":"Mao, Y","last_name":"Mao"},{"full_name":"Gao, Y","last_name":"Gao","first_name":"Y"},{"first_name":"S","last_name":"Tan","full_name":"Tan, S"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"D","full_name":"Li, D","last_name":"Li"},{"first_name":"X","full_name":"Liu, X","last_name":"Liu"},{"full_name":"Sun, L","last_name":"Sun","first_name":"L"}],"publication":"Nature","abstract":[{"text":"Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.","lang":"eng"}],"page":"611-615","issue":"7927","article_type":"original","oa":1,"citation":{"short":"Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.","chicago":"Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>.","ieee":"Z. Yang <i>et al.</i>, “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","ama":"Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. 2022;609(7927):611-615. doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>","mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>.","apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>","ista":"Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615."},"file_date_updated":"2022-09-08T08:02:54Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","fulldoi":"https://doi.org/10.1038/s41586-022-05143-9","publisher":"Springer Nature","isi":1,"date_created":"2022-09-07T14:19:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41586-022-05143-9","pmid":1,"scopus_import":"1","department":[{"_id":"JiFr"}],"has_accepted_license":"1","status":"public","external_id":{"isi":["000848082900002"],"pmid":["35917925"]},"volume":609,"language":[{"iso":"eng"}],"intvolume":"       609","type":"journal_article","date_published":"2022-08-02T00:00:00Z","oa_version":"Published Version","quality_controlled":"1","ddc":["580"],"file":[{"relation":"main_file","file_size":32344580,"date_created":"2022-09-08T08:02:54Z","file_id":"12064","success":1,"access_level":"open_access","file_name":"2022_Nature_Yang.pdf","date_updated":"2022-09-08T08:02:54Z","checksum":"3136a585f8e1c7e73b5e1418b3d01898","creator":"dernst","content_type":"application/pdf"}],"month":"08"},{"_id":"12118","year":"2022","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","full_name":"Valentini, Marco"},{"id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim","full_name":"Borovkov, Maksim","last_name":"Borovkov"},{"last_name":"Prada","full_name":"Prada, Elsa","first_name":"Elsa"},{"full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez","first_name":"Sara"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Ramón","full_name":"Aguado, Ramón","last_name":"Aguado"},{"first_name":"Pablo","full_name":"San-Jose, Pablo","last_name":"San-Jose"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X"}],"title":"Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks","page":"442-447","abstract":[{"lang":"eng","text":"Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes."}],"date_updated":"2026-04-07T13:27:22Z","arxiv":1,"day":"15","article_processing_charge":"No","publication_status":"published","ec_funded":1,"acknowledgement":"We thank P. Krogstrup for providing us with the NW materials. We thank A. Higginbotham, E. J. H. Lee, C. Marcus and S. Vaitiekėnas for helpful discussions and G. Steffensen for his input on the diffusive Little-Parks theory. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation; the CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). A.H. acknowledges support from H2020-MSCA-IF-2018/844511. ICN2 also acknowledges funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa Program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. Authors acknowledge the use of instrumentation as well as the technical advice provided by the National Facility ELECMI ICTS, node ‘Laboratorio de Microscopías Avanzadas’ at University of Zaragoza. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 823717-ESTEEM3. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. This research is part of the CSIC programme for the Spanish Recovery, Transformation and Resilience Plan funded by the Recovery and Resilience Facility of the European Union, established by the Regulation (EU) 2020/2094. We thank support from Grant PGC2018-097018-BI00, project FlagERA TOPOGRAPH (PCI2018-093026) and project NANOGEN (PID2020-116093RB-C43), funded by MCIN/AEI/10.13039/501100011033/ and by ‘ERDF A way of making Europe’, by the European Union. M. Botifoll acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund (project ref. 2020 FI 00103).","fulldoi":"https://doi.org/10.1038/s41586-022-05382-w","date_created":"2023-01-12T11:56:45Z","isi":1,"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","issue":"7940","oa":1,"citation":{"chicago":"Valentini, Marco, Maksim Borovkov, Elsa Prada, Sara Martí-Sánchez, Marc Botifoll, Andrea C Hofmann, Jordi Arbiol, Ramón Aguado, Pablo San-Jose, and Georgios Katsaros. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>.","short":"M. Valentini, M. Borovkov, E. Prada, S. Martí-Sánchez, M. Botifoll, A.C. Hofmann, J. Arbiol, R. Aguado, P. San-Jose, G. Katsaros, Nature 612 (2022) 442–447.","ista":"Valentini M, Borovkov M, Prada E, Martí-Sánchez S, Botifoll M, Hofmann AC, Arbiol J, Aguado R, San-Jose P, Katsaros G. 2022. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. Nature. 612(7940), 442–447.","mla":"Valentini, Marco, et al. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>, vol. 612, no. 7940, Springer Nature, 2022, pp. 442–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>.","apa":"Valentini, M., Borovkov, M., Prada, E., Martí-Sánchez, S., Botifoll, M., Hofmann, A. C., … Katsaros, G. (2022). Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>","ama":"Valentini M, Borovkov M, Prada E, et al. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. 2022;612(7940):442-447. doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>","ieee":"M. Valentini <i>et al.</i>, “Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks,” <i>Nature</i>, vol. 612, no. 7940. Springer Nature, pp. 442–447, 2022."},"corr_author":"1","department":[{"_id":"GeKa"}],"project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"status":"public","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/imposter-particles-revealed-and-explained/","relation":"press_release"}],"record":[{"relation":"research_data","id":"12522","status":"public"},{"status":"public","relation":"dissertation_contains","id":"13286"}]},"doi":"10.1038/s41586-022-05382-w","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2203.07829"}],"quality_controlled":"1","month":"12","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"volume":612,"external_id":{"isi":["000899725400001"],"pmid":["36517713"],"arxiv":["2203.07829"]},"type":"journal_article","date_published":"2022-12-15T00:00:00Z","intvolume":"       612","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Preprint"},{"oa":1,"citation":{"short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.","chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>.","ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. 2022;611(7934):133-138. doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>","ieee":"L. Qi <i>et al.</i>, “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” <i>Nature</i>, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022."},"issue":"7934","article_type":"original","publisher":"Springer Nature","isi":1,"date_created":"2023-01-12T12:06:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s41586-022-05369-7","acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","publication_status":"published","day":"03","article_processing_charge":"No","ec_funded":1,"date_updated":"2025-04-14T07:45:02Z","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","publication":"Nature","author":[{"orcid":"0000-0001-5187-8401","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","full_name":"Qi, Linlin"},{"full_name":"Kwiatkowski, Mateusz","last_name":"Kwiatkowski","first_name":"Mateusz"},{"last_name":"Chen","full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang"},{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair","full_name":"Sinclair, Scott A"},{"full_name":"Zou, Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia"},{"last_name":"del Genio","full_name":"del Genio, Charo I.","first_name":"Charo I."},{"first_name":"Martin F.","last_name":"Kubeš","full_name":"Kubeš, Martin F."},{"full_name":"Napier, Richard","last_name":"Napier","first_name":"Richard"},{"full_name":"Jaworski, Krzysztof","last_name":"Jaworski","first_name":"Krzysztof"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"abstract":[{"lang":"eng","text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants."}],"page":"133-138","year":"2022","_id":"12144","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"intvolume":"       611","type":"journal_article","date_published":"2022-11-03T00:00:00Z","oa_version":"Submitted Version","external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"volume":611,"language":[{"iso":"eng"}],"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf"}],"pmid":1,"scopus_import":"1","doi":"10.1038/s41586-022-05369-7","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"JiFr"}],"status":"public","corr_author":"1"},{"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"external_id":{"isi":["000824430000004"],"pmid":["35831497"]},"volume":607,"type":"journal_article","date_published":"2022-07-13T00:00:00Z","intvolume":"       607","oa_version":"Submitted Version","quality_controlled":"1","main_file_link":[{"url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780","open_access":"1"}],"month":"07","related_material":{"link":[{"relation":"software","url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022"}]},"doi":"10.1038/s41586-022-04962-0","pmid":1,"scopus_import":"1","corr_author":"1","department":[{"_id":"EdHa"}],"project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"status":"public","article_type":"original","issue":"7919","oa":1,"citation":{"ieee":"M. Azkanaz <i>et al.</i>, “Retrograde movements determine effective stem cell numbers in the intestine,” <i>Nature</i>, vol. 607, no. 7919. Springer Nature, pp. 548–554, 2022.","ista":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P, Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.","ama":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements determine effective stem cell numbers in the intestine. <i>Nature</i>. 2022;607(7919):548-554. doi:<a href=\"https://doi.org/10.1038/s41586-022-04962-0\">10.1038/s41586-022-04962-0</a>","mla":"Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” <i>Nature</i>, vol. 607, no. 7919, Springer Nature, 2022, pp. 548–54, doi:<a href=\"https://doi.org/10.1038/s41586-022-04962-0\">10.1038/s41586-022-04962-0</a>.","apa":"Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb, A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine effective stem cell numbers in the intestine. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-04962-0\">https://doi.org/10.1038/s41586-022-04962-0</a>","short":"M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb, D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal, D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom, H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen, Nature 607 (2022) 548–554.","chicago":"Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-04962-0\">https://doi.org/10.1038/s41586-022-04962-0</a>."},"fulldoi":"https://doi.org/10.1038/s41586-022-04962-0","acknowledgement":"We thank the members of the van Rheenen laboratory for reading the manuscript, and the members of the bioimaging, FACS and animal facility of the NKI for experimental support. We acknowledge the staff at the MedH Flow Cytometry core facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska Institutet. This work was financially supported by the Netherlands Organization of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004 to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research) program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges funding from the Royal Society E.P. Abraham Research Professorship (RP\\R1\\180165) and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the support of the field of excellence ‘Complexity of life in basic research and innovation’ of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom laboratory (A21139). P.K. and their laboratory are supported by grants from the Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation. P.L. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617). E.H. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).","date_created":"2023-01-16T10:01:29Z","publisher":"Springer Nature","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-14T07:52:27Z","day":"13","article_processing_charge":"No","publication_status":"published","ec_funded":1,"_id":"12274","year":"2022","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"author":[{"last_name":"Azkanaz","full_name":"Azkanaz, Maria","first_name":"Maria"},{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"},{"last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I. J.","first_name":"Saskia I. J."},{"last_name":"Bruens","full_name":"Bruens, Lotte","first_name":"Lotte"},{"first_name":"Anna T.","last_name":"Webb","full_name":"Webb, Anna T."},{"full_name":"Laskaris, Dimitrios","last_name":"Laskaris","first_name":"Dimitrios"},{"first_name":"Koen C.","full_name":"Oost, Koen C.","last_name":"Oost"},{"last_name":"Lafirenze","full_name":"Lafirenze, Simona J. A.","first_name":"Simona J. A."},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"last_name":"Messal","full_name":"Messal, Hendrik A.","first_name":"Hendrik A."},{"first_name":"Sharif","last_name":"Iqbal","full_name":"Iqbal, Sharif"},{"last_name":"Flanagan","full_name":"Flanagan, Dustin J.","first_name":"Dustin J."},{"last_name":"Huels","full_name":"Huels, David J.","first_name":"David J."},{"full_name":"Rojas-Rodríguez, Felipe","last_name":"Rojas-Rodríguez","first_name":"Felipe"},{"first_name":"Miguel","full_name":"Vizoso, Miguel","last_name":"Vizoso"},{"full_name":"Kasper, Maria","last_name":"Kasper","first_name":"Maria"},{"full_name":"Sansom, Owen J.","last_name":"Sansom","first_name":"Owen J."},{"last_name":"Snippert","full_name":"Snippert, Hugo J.","first_name":"Hugo J."},{"full_name":"Liberali, Prisca","last_name":"Liberali","first_name":"Prisca"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Pekka","last_name":"Katajisto","full_name":"Katajisto, Pekka"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Jacco","full_name":"van Rheenen, Jacco","last_name":"van Rheenen"}],"title":"Retrograde movements determine effective stem cell numbers in the intestine","publication":"Nature","page":"548-554","abstract":[{"lang":"eng","text":"The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated."}]},{"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-022-05386-6"}],"quality_controlled":"1","oa_version":"Published Version","intvolume":"       611","date_published":"2022-11-17T00:00:00Z","type":"journal_article","external_id":{"pmid":["36323776"]},"volume":611,"language":[{"iso":"eng"}],"status":"public","department":[{"_id":"XiFe"}],"scopus_import":"1","pmid":1,"doi":"10.1038/s41586-022-05386-6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2023-02-23T09:17:05Z","fulldoi":"https://doi.org/10.1038/s41586-022-05386-6","citation":{"chicago":"Buttress, Toby, Shengbo He, Liang Wang, Shaoli Zhou, Gerhard Saalbach, Martin Vickers, Guohong Li, Pilong Li, and Xiaoqi Feng. “Histone H2B.8 Compacts Flowering Plant Sperm through Chromatin Phase Separation.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05386-6\">https://doi.org/10.1038/s41586-022-05386-6</a>.","short":"T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P. Li, X. Feng, Nature 611 (2022) 614–622.","ieee":"T. Buttress <i>et al.</i>, “Histone H2B.8 compacts flowering plant sperm through chromatin phase separation,” <i>Nature</i>, vol. 611, no. 7936. Springer Nature, pp. 614–622, 2022.","ista":"Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng X. 2022. Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. Nature. 611(7936), 614–622.","apa":"Buttress, T., He, S., Wang, L., Zhou, S., Saalbach, G., Vickers, M., … Feng, X. (2022). Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05386-6\">https://doi.org/10.1038/s41586-022-05386-6</a>","mla":"Buttress, Toby, et al. “Histone H2B.8 Compacts Flowering Plant Sperm through Chromatin Phase Separation.” <i>Nature</i>, vol. 611, no. 7936, Springer Nature, 2022, pp. 614–22, doi:<a href=\"https://doi.org/10.1038/s41586-022-05386-6\">10.1038/s41586-022-05386-6</a>.","ama":"Buttress T, He S, Wang L, et al. Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. <i>Nature</i>. 2022;611(7936):614-622. doi:<a href=\"https://doi.org/10.1038/s41586-022-05386-6\">10.1038/s41586-022-05386-6</a>"},"oa":1,"issue":"7936","article_type":"original","abstract":[{"lang":"eng","text":"Sperm chromatin is typically transformed by protamines into a compact and transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines, yet they have small, transcriptionally active nuclei with chromatin condensed through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8 causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression in somatic cells produces smaller nuclei with aggregated chromatin. This result demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates transcriptionally inactive AT-rich chromatin into phase-separated condensates, which facilitates nuclear compaction without reducing transcription. Reciprocal crosses show that mutation of h2b.8 reduces male transmission, which suggests that H2B.8-mediated sperm compaction is important for fertility. Altogether, our results reveal a new mechanism of nuclear compaction through global aggregation of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation of flowering plants that achieves nuclear condensation compatible with active transcription."}],"page":"614-622","title":"Histone H2B.8 compacts flowering plant sperm through chromatin phase separation","publication":"Nature","author":[{"first_name":"Toby","full_name":"Buttress, Toby","last_name":"Buttress"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Liang","last_name":"Wang","full_name":"Wang, Liang"},{"full_name":"Zhou, Shaoli","last_name":"Zhou","first_name":"Shaoli"},{"full_name":"Saalbach, Gerhard","last_name":"Saalbach","first_name":"Gerhard"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"full_name":"Li, Guohong","last_name":"Li","first_name":"Guohong"},{"first_name":"Pilong","last_name":"Li","full_name":"Li, Pilong"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2022","_id":"12671","extern":"1","publication_status":"published","article_processing_charge":"No","day":"17","date_updated":"2024-10-14T12:03:36Z"},{"month":"12","quality_controlled":"1","oa_version":"None","intvolume":"       612","date_published":"2022-12-21T00:00:00Z","type":"journal_article","volume":612,"external_id":{"pmid":["36543947"],"isi":["000934065100010"]},"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"status":"public","department":[{"_id":"MaIb"}],"corr_author":"1","scopus_import":"1","pmid":1,"doi":"10.1038/d41586-022-04447-0","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publisher":"Springer Nature","date_created":"2023-10-17T11:14:43Z","fulldoi":"https://doi.org/10.1038/d41586-022-04447-0","citation":{"short":"H. Utzat, M. Ibáñez, Nature 612 (2022) 638–639.","chicago":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>.","ieee":"H. Utzat and M. Ibáñez, “Molecular engineering enables bright blue LEDs,” <i>Nature</i>, vol. 612, no. 7941. Springer Nature, pp. 638–639, 2022.","apa":"Utzat, H., &#38; Ibáñez, M. (2022). Molecular engineering enables bright blue LEDs. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>","mla":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>, vol. 612, no. 7941, Springer Nature, 2022, pp. 638–39, doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>.","ama":"Utzat H, Ibáñez M. Molecular engineering enables bright blue LEDs. <i>Nature</i>. 2022;612(7941):638-639. doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>","ista":"Utzat H, Ibáñez M. 2022. Molecular engineering enables bright blue LEDs. Nature. 612(7941), 638–639."},"issue":"7941","article_type":"letter_note","abstract":[{"text":"Future LEDs could be based on lead halide perovskites. A breakthrough in preparing device-compatible solids composed of nanoscale perovskite crystals overcomes a long-standing hurdle in making blue perovskite LEDs.","lang":"eng"}],"page":"638-639","author":[{"first_name":"Hendrik","last_name":"Utzat","full_name":"Utzat, Hendrik"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature","title":"Molecular engineering enables bright blue LEDs","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"_id":"14437","year":"2022","publication_status":"published","day":"21","article_processing_charge":"No","date_updated":"2025-09-10T09:55:51Z"},{"main_file_link":[{"url":"https://doi.org/10.1038/s41586-022-04470-1","open_access":"1"}],"quality_controlled":"1","month":"03","language":[{"iso":"eng"}],"volume":603,"external_id":{"pmid":["35236982"]},"oa_version":"Published Version","type":"journal_article","date_published":"2022-03-02T00:00:00Z","intvolume":"       603","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-022-04655-8","relation":"erratum"}]},"doi":"10.1038/s41586-022-04470-1","scopus_import":"1","pmid":1,"fulldoi":"https://doi.org/10.1038/s41586-022-04470-1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-03-20T10:42:21Z","publisher":"Springer Nature","article_type":"original","issue":"7900","citation":{"short":"J.P.K. Bravo, M.-S. Liu, G.N. Hibshman, T.L. Dangerfield, K. Jung, R.S. McCool, K.A. Johnson, D.W. Taylor, Nature 603 (2022) 343–347.","chicago":"Bravo, Jack Peter Kelly, Mu-Sen Liu, Grace N. Hibshman, Tyler L. Dangerfield, Kyungseok Jung, Ryan S. McCool, Kenneth A. Johnson, and David W. Taylor. “Structural Basis for Mismatch Surveillance by CRISPR–Cas9.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-04470-1\">https://doi.org/10.1038/s41586-022-04470-1</a>.","ama":"Bravo JPK, Liu M-S, Hibshman GN, et al. Structural basis for mismatch surveillance by CRISPR–Cas9. <i>Nature</i>. 2022;603(7900):343-347. doi:<a href=\"https://doi.org/10.1038/s41586-022-04470-1\">10.1038/s41586-022-04470-1</a>","apa":"Bravo, J. P. K., Liu, M.-S., Hibshman, G. N., Dangerfield, T. L., Jung, K., McCool, R. S., … Taylor, D. W. (2022). Structural basis for mismatch surveillance by CRISPR–Cas9. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-04470-1\">https://doi.org/10.1038/s41586-022-04470-1</a>","mla":"Bravo, Jack Peter Kelly, et al. “Structural Basis for Mismatch Surveillance by CRISPR–Cas9.” <i>Nature</i>, vol. 603, no. 7900, Springer Nature, 2022, pp. 343–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-04470-1\">10.1038/s41586-022-04470-1</a>.","ista":"Bravo JPK, Liu M-S, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW. 2022. Structural basis for mismatch surveillance by CRISPR–Cas9. Nature. 603(7900), 343–347.","ieee":"J. P. K. Bravo <i>et al.</i>, “Structural basis for mismatch surveillance by CRISPR–Cas9,” <i>Nature</i>, vol. 603, no. 7900. Springer Nature, pp. 343–347, 2022."},"oa":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"15136","year":"2022","page":"343-347","abstract":[{"text":"CRISPR–Cas9 as a programmable genome editing tool is hindered by off-target DNA cleavage1,2,3,4, and the underlying mechanisms by which Cas9 recognizes mismatches are poorly understood5,6,7. Although Cas9 variants with greater discrimination against mismatches have been designed8,9,10, these suffer from substantially reduced rates of on-target DNA cleavage5,11. Here we used kinetics-guided cryo-electron microscopy to determine the structure of Cas9 at different stages of mismatch cleavage. We observed a distinct, linear conformation of the guide RNA–DNA duplex formed in the presence of mismatches, which prevents Cas9 activation. Although the canonical kinked guide RNA–DNA duplex conformation facilitates DNA cleavage, we observe that substrates that contain mismatches distal to the protospacer adjacent motif are stabilized by reorganization of a loop in the RuvC domain. Mutagenesis of mismatch-stabilizing residues reduces off-target DNA cleavage but maintains rapid on-target DNA cleavage. By targeting regions that are exclusively involved in mismatch tolerance, we provide a proof of concept for the design of next-generation high-fidelity Cas9 variants.","lang":"eng"}],"title":"Structural basis for mismatch surveillance by CRISPR–Cas9","author":[{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo"},{"first_name":"Mu-Sen","full_name":"Liu, Mu-Sen","last_name":"Liu"},{"first_name":"Grace N.","full_name":"Hibshman, Grace N.","last_name":"Hibshman"},{"last_name":"Dangerfield","full_name":"Dangerfield, Tyler L.","first_name":"Tyler L."},{"last_name":"Jung","full_name":"Jung, Kyungseok","first_name":"Kyungseok"},{"first_name":"Ryan S.","last_name":"McCool","full_name":"McCool, Ryan S."},{"first_name":"Kenneth A.","full_name":"Johnson, Kenneth A.","last_name":"Johnson"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"publication":"Nature","date_updated":"2024-06-04T06:36:59Z","extern":"1","article_processing_charge":"Yes (in subscription journal)","day":"02","publication_status":"published"},{"day":"05","article_processing_charge":"No","publication_status":"published","extern":"1","arxiv":1,"date_updated":"2024-04-02T07:18:43Z","title":"A dense 0.1-solar-mass star in a 51-minute-orbital-period eclipsing binary","author":[{"full_name":"Burdge, Kevin B.","last_name":"Burdge","first_name":"Kevin B."},{"first_name":"Kareem","full_name":"El-Badry, Kareem","last_name":"El-Badry"},{"full_name":"Marsh, Thomas R.","last_name":"Marsh","first_name":"Thomas R."},{"first_name":"Saul","last_name":"Rappaport","full_name":"Rappaport, Saul"},{"first_name":"Warren R.","last_name":"Brown","full_name":"Brown, Warren R."},{"orcid":"0000-0002-4770-5388","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","first_name":"Ilaria","full_name":"Caiazzo, Ilaria","last_name":"Caiazzo"},{"full_name":"Chakrabarty, Deepto","last_name":"Chakrabarty","first_name":"Deepto"},{"full_name":"Dhillon, V. S.","last_name":"Dhillon","first_name":"V. S."},{"full_name":"Fuller, Jim","last_name":"Fuller","first_name":"Jim"},{"first_name":"Boris T.","last_name":"Gänsicke","full_name":"Gänsicke, Boris T."},{"first_name":"Matthew J.","full_name":"Graham, Matthew J.","last_name":"Graham"},{"full_name":"Kara, Erin","last_name":"Kara","first_name":"Erin"},{"first_name":"S. R.","last_name":"Kulkarni","full_name":"Kulkarni, S. R."},{"full_name":"Littlefair, S. P.","last_name":"Littlefair","first_name":"S. P."},{"first_name":"Przemek","full_name":"Mróz, Przemek","last_name":"Mróz"},{"last_name":"Rodríguez-Gil","full_name":"Rodríguez-Gil, Pablo","first_name":"Pablo"},{"full_name":"Roestel, Jan van","last_name":"Roestel","first_name":"Jan van"},{"first_name":"Robert A.","full_name":"Simcoe, Robert A.","last_name":"Simcoe"},{"first_name":"Eric C.","full_name":"Bellm, Eric C.","last_name":"Bellm"},{"first_name":"Andrew J.","full_name":"Drake, Andrew J.","last_name":"Drake"},{"first_name":"Richard G.","full_name":"Dekany, Richard G.","last_name":"Dekany"},{"first_name":"Steven L.","last_name":"Groom","full_name":"Groom, Steven L."},{"full_name":"Laher, Russ R.","last_name":"Laher","first_name":"Russ R."},{"full_name":"Masci, Frank J.","last_name":"Masci","first_name":"Frank J."},{"first_name":"Reed","full_name":"Riddle, Reed","last_name":"Riddle"},{"full_name":"Smith, Roger M.","last_name":"Smith","first_name":"Roger M."},{"full_name":"Prince, Thomas A.","last_name":"Prince","first_name":"Thomas A."}],"publication":"Nature","page":"467-471","abstract":[{"text":"Of more than a thousand known cataclysmic variables (CVs), where a white dwarf is accreting from a hydrogen-rich star, only a dozen have orbital periods below 75 minutes1,2,3,4,5,6,7,8,9. One way to achieve these short periods requires the donor star to have undergone substantial nuclear evolution before interacting with the white dwarf10,11,12,13,14, and it is expected that these objects will transition to helium accretion. These transitional CVs have been proposed as progenitors of helium CVs13,14,15,16,17,18. However, no known transitional CV is expected to reach an orbital period short enough to account for most of the helium CV population, leaving the role of this evolutionary pathway unclear. Here we report observations of ZTF J1813+4251, a 51-minute-orbital-period, fully eclipsing binary system consisting of a star with a temperature comparable to that of the Sun but a density 100 times greater owing to its helium-rich composition, accreting onto a white dwarf. Phase-resolved spectra, multi-band light curves and the broadband spectral energy distribution allow us to obtain precise and robust constraints on the masses, radii and temperatures of both components. Evolutionary modelling shows that ZTF J1813+4251 is destined to become a helium CV binary, reaching an orbital period under 20 minutes, rendering ZTF J1813+4251 a previously missing link between helium CV binaries and hydrogen-rich CVs.","lang":"eng"}],"_id":"15207","year":"2022","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"citation":{"short":"K.B. Burdge, K. El-Badry, T.R. Marsh, S. Rappaport, W.R. Brown, I. Caiazzo, D. Chakrabarty, V.S. Dhillon, J. Fuller, B.T. Gänsicke, M.J. Graham, E. Kara, S.R. Kulkarni, S.P. Littlefair, P. Mróz, P. Rodríguez-Gil, J. van Roestel, R.A. Simcoe, E.C. Bellm, A.J. Drake, R.G. Dekany, S.L. Groom, R.R. Laher, F.J. Masci, R. Riddle, R.M. Smith, T.A. Prince, Nature 610 (2022) 467–471.","chicago":"Burdge, Kevin B., Kareem El-Badry, Thomas R. Marsh, Saul Rappaport, Warren R. Brown, Ilaria Caiazzo, Deepto Chakrabarty, et al. “A Dense 0.1-Solar-Mass Star in a 51-Minute-Orbital-Period Eclipsing Binary.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05195-x\">https://doi.org/10.1038/s41586-022-05195-x</a>.","ista":"Burdge KB, El-Badry K, Marsh TR, Rappaport S, Brown WR, Caiazzo I, Chakrabarty D, Dhillon VS, Fuller J, Gänsicke BT, Graham MJ, Kara E, Kulkarni SR, Littlefair SP, Mróz P, Rodríguez-Gil P, Roestel J van, Simcoe RA, Bellm EC, Drake AJ, Dekany RG, Groom SL, Laher RR, Masci FJ, Riddle R, Smith RM, Prince TA. 2022. A dense 0.1-solar-mass star in a 51-minute-orbital-period eclipsing binary. Nature. 610(7932), 467–471.","mla":"Burdge, Kevin B., et al. “A Dense 0.1-Solar-Mass Star in a 51-Minute-Orbital-Period Eclipsing Binary.” <i>Nature</i>, vol. 610, no. 7932, Springer Nature, 2022, pp. 467–71, doi:<a href=\"https://doi.org/10.1038/s41586-022-05195-x\">10.1038/s41586-022-05195-x</a>.","ama":"Burdge KB, El-Badry K, Marsh TR, et al. A dense 0.1-solar-mass star in a 51-minute-orbital-period eclipsing binary. <i>Nature</i>. 2022;610(7932):467-471. doi:<a href=\"https://doi.org/10.1038/s41586-022-05195-x\">10.1038/s41586-022-05195-x</a>","apa":"Burdge, K. B., El-Badry, K., Marsh, T. R., Rappaport, S., Brown, W. R., Caiazzo, I., … Prince, T. A. (2022). A dense 0.1-solar-mass star in a 51-minute-orbital-period eclipsing binary. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05195-x\">https://doi.org/10.1038/s41586-022-05195-x</a>","ieee":"K. B. Burdge <i>et al.</i>, “A dense 0.1-solar-mass star in a 51-minute-orbital-period eclipsing binary,” <i>Nature</i>, vol. 610, no. 7932. Springer Nature, pp. 467–471, 2022."},"article_type":"original","issue":"7932","date_created":"2024-03-26T09:52:17Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1038/s41586-022-05195-x","pmid":1,"scopus_import":"1","doi":"10.1038/s41586-022-05195-x","status":"public","type":"journal_article","date_published":"2022-10-05T00:00:00Z","intvolume":"       610","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":610,"external_id":{"pmid":["36198793"],"arxiv":["2210.01809"]},"month":"10","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2210.01809","open_access":"1"}]}]