[{"oa_version":"Published Version","article_type":"original","date_created":"2022-08-24T08:25:50Z","publisher":"Springer Nature","publication":"Nature Communications","language":[{"iso":"eng"}],"status":"public","isi":1,"file":[{"file_size":5910357,"content_type":"application/pdf","success":1,"date_updated":"2022-08-26T11:51:40Z","creator":"dernst","relation":"main_file","file_id":"11990","file_name":"2022_NatureCommunications_BenSimon.pdf","checksum":"405936d9e4d33625d80c093c9713a91f","date_created":"2022-08-26T11:51:40Z","access_level":"open_access"}],"oa":1,"author":[{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon"},{"last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","full_name":"Käfer, Karola"},{"first_name":"Philipp","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M"}],"date_updated":"2025-06-12T06:10:44Z","intvolume":"        13","quality_controlled":"1","corr_author":"1","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"}],"date_published":"2022-08-16T00:00:00Z","citation":{"ama":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>","ista":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. 2022. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. Nature Communications. 13, 4826.","mla":"Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>, vol. 13, 4826, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>.","short":"Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas, Nature Communications 13 (2022).","chicago":"Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>.","apa":"Ben Simon, Y., Käfer, K., Velicky, P., Csicsvari, J. L., Danzl, J. G., &#38; Jonas, P. M. (2022). A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>","ieee":"Y. Ben Simon, K. Käfer, P. Velicky, J. L. Csicsvari, J. G. Danzl, and P. M. Jonas, “A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"article_processing_charge":"No","ddc":["570"],"publication_status":"published","day":"16","volume":13,"has_accepted_license":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-32559-8","scopus_import":"1","ec_funded":1,"file_date_updated":"2022-08-26T11:51:40Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"_id":"11951","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"month":"08","type":"journal_article","external_id":{"isi":["000841396400008"],"pmid":["35974109"]},"year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","abstract":[{"text":"The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.","lang":"eng"}],"pmid":1,"acknowledgement":"We thank F. Marr and A. Schlögl for technical assistance, E. Kralli-Beller for manuscript editing, as well as C. Sommer and the Imaging and Optics Facility of the Institute of Science and Technology Austria (ISTA) for image analysis scripts and microscopy support. We extend our gratitude to J. Wallenschus and D. Rangel Guerrero for technical assistance acquiring single-unit data and I. Gridchyn for help with single-unit clustering. Finally, we also thank B. Suter for discussions, A. Saunders, M. Jösch, and H. Monyer for critically reading earlier versions of the manuscript, C. Petersen for sharing clearing protocols, and the Scientific Service Units of ISTA for efficient support. This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award for P.J. and I3600-B27 for J.G.D. and P.V.).","article_number":"4826"},{"publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-30673-1","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"_id":"15133","month":"05","type":"journal_article","external_id":{"pmid":["35624106"]},"extern":"1","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structural basis for broad anti-phage immunity by DISARM","abstract":[{"lang":"eng","text":"In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5′ overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system."}],"pmid":1,"article_number":"2987","oa_version":"Published Version","article_type":"original","publisher":"Springer Nature","date_created":"2024-03-20T10:41:59Z","publication":"Nature Communications","language":[{"iso":"eng"}],"status":"public","oa":1,"author":[{"orcid":"0000-0003-0456-0753","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"first_name":"Cristian","full_name":"Aparicio-Maldonado, Cristian","last_name":"Aparicio-Maldonado"},{"full_name":"Nobrega, Franklin L.","first_name":"Franklin L.","last_name":"Nobrega"},{"last_name":"Brouns","first_name":"Stan J. J.","full_name":"Brouns, Stan J. J."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"date_updated":"2024-06-04T06:16:38Z","intvolume":"        13","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-022-30673-1","open_access":"1"}],"date_published":"2022-05-27T00:00:00Z","citation":{"ista":"Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. 2022. Structural basis for broad anti-phage immunity by DISARM. Nature Communications. 13, 2987.","ama":"Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. Structural basis for broad anti-phage immunity by DISARM. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30673-1\">10.1038/s41467-022-30673-1</a>","mla":"Bravo, Jack Peter Kelly, et al. “Structural Basis for Broad Anti-Phage Immunity by DISARM.” <i>Nature Communications</i>, vol. 13, 2987, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30673-1\">10.1038/s41467-022-30673-1</a>.","short":"J.P.K. Bravo, C. Aparicio-Maldonado, F.L. Nobrega, S.J.J. Brouns, D.W. Taylor, Nature Communications 13 (2022).","chicago":"Bravo, Jack Peter Kelly, Cristian Aparicio-Maldonado, Franklin L. Nobrega, Stan J. J. Brouns, and David W. Taylor. “Structural Basis for Broad Anti-Phage Immunity by DISARM.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30673-1\">https://doi.org/10.1038/s41467-022-30673-1</a>.","ieee":"J. P. K. Bravo, C. Aparicio-Maldonado, F. L. Nobrega, S. J. J. Brouns, and D. W. Taylor, “Structural basis for broad anti-phage immunity by DISARM,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","apa":"Bravo, J. P. K., Aparicio-Maldonado, C., Nobrega, F. L., Brouns, S. J. J., &#38; Taylor, D. W. (2022). Structural basis for broad anti-phage immunity by DISARM. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30673-1\">https://doi.org/10.1038/s41467-022-30673-1</a>"},"article_processing_charge":"Yes","day":"27","publication_status":"published","volume":13},{"scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-30402-8","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"_id":"15134","type":"journal_article","month":"05","year":"2022","extern":"1","external_id":{"pmid":["35595728"]},"pmid":1,"abstract":[{"lang":"eng","text":"CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems."}],"title":"Structural rearrangements allow nucleic acid discrimination by type I-D Cascade","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2829","article_type":"original","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Nature Communications","publisher":"Springer Nature","date_created":"2024-03-20T10:42:05Z","oa":1,"author":[{"last_name":"Schwartz","first_name":"Evan A.","full_name":"Schwartz, Evan A."},{"full_name":"McBride, Tess M.","first_name":"Tess M.","last_name":"McBride"},{"last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"first_name":"Daniel","full_name":"Wrapp, Daniel","last_name":"Wrapp"},{"last_name":"Fineran","first_name":"Peter C.","full_name":"Fineran, Peter C."},{"full_name":"Fagerlund, Robert D.","first_name":"Robert D.","last_name":"Fagerlund"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"status":"public","intvolume":"        13","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-022-30402-8"}],"date_updated":"2024-06-04T06:14:28Z","date_published":"2022-05-20T00:00:00Z","volume":13,"publication_status":"published","day":"20","article_processing_charge":"Yes","citation":{"apa":"Schwartz, E. A., McBride, T. M., Bravo, J. P. K., Wrapp, D., Fineran, P. C., Fagerlund, R. D., &#38; Taylor, D. W. (2022). Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30402-8\">https://doi.org/10.1038/s41467-022-30402-8</a>","ieee":"E. A. Schwartz <i>et al.</i>, “Structural rearrangements allow nucleic acid discrimination by type I-D Cascade,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Schwartz, Evan A., Tess M. McBride, Jack Peter Kelly Bravo, Daniel Wrapp, Peter C. Fineran, Robert D. Fagerlund, and David W. Taylor. “Structural Rearrangements Allow Nucleic Acid Discrimination by Type I-D Cascade.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30402-8\">https://doi.org/10.1038/s41467-022-30402-8</a>.","short":"E.A. Schwartz, T.M. McBride, J.P.K. Bravo, D. Wrapp, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 13 (2022).","mla":"Schwartz, Evan A., et al. “Structural Rearrangements Allow Nucleic Acid Discrimination by Type I-D Cascade.” <i>Nature Communications</i>, vol. 13, 2829, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30402-8\">10.1038/s41467-022-30402-8</a>.","ista":"Schwartz EA, McBride TM, Bravo JPK, Wrapp D, Fineran PC, Fagerlund RD, Taylor DW. 2022. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nature Communications. 13, 2829.","ama":"Schwartz EA, McBride TM, Bravo JPK, et al. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30402-8\">10.1038/s41467-022-30402-8</a>"}},{"publisher":"Wiley","date_created":"2024-04-03T07:49:53Z","publication":"Proteins: Structure, Function, and Bioinformatics","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"258-269","article_type":"original","date_updated":"2024-10-09T21:08:44Z","quality_controlled":"1","intvolume":"        90","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.304337"}],"status":"public","oa":1,"author":[{"last_name":"Gisonno","first_name":"Romina A.","full_name":"Gisonno, Romina A."},{"last_name":"Masson","orcid":"0000-0002-2634-6283","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","full_name":"Masson, Tomas","first_name":"Tomas"},{"first_name":"Nahuel A.","full_name":"Ramella, Nahuel A.","last_name":"Ramella"},{"full_name":"Barrera, Exequiel E.","first_name":"Exequiel E.","last_name":"Barrera"},{"last_name":"Romanowski","first_name":"Víctor","full_name":"Romanowski, Víctor"},{"last_name":"Tricerri","full_name":"Tricerri, M. Alejandra","first_name":"M. Alejandra"}],"citation":{"ama":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. <i>Proteins: Structure, Function, and Bioinformatics</i>. 2022;90(1):258-269. doi:<a href=\"https://doi.org/10.1002/prot.26217\">10.1002/prot.26217</a>","ista":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. 2022. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics. 90(1), 258–269.","mla":"Gisonno, Romina A., et al. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” <i>Proteins: Structure, Function, and Bioinformatics</i>, vol. 90, no. 1, Wiley, 2022, pp. 258–69, doi:<a href=\"https://doi.org/10.1002/prot.26217\">10.1002/prot.26217</a>.","short":"R.A. Gisonno, T. Masson, N.A. Ramella, E.E. Barrera, V. Romanowski, M.A. Tricerri, Proteins: Structure, Function, and Bioinformatics 90 (2022) 258–269.","apa":"Gisonno, R. A., Masson, T., Ramella, N. A., Barrera, E. E., Romanowski, V., &#38; Tricerri, M. A. (2022). Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. <i>Proteins: Structure, Function, and Bioinformatics</i>. Wiley. <a href=\"https://doi.org/10.1002/prot.26217\">https://doi.org/10.1002/prot.26217</a>","chicago":"Gisonno, Romina A., Tomas Masson, Nahuel A. Ramella, Exequiel E. Barrera, Víctor Romanowski, and M. Alejandra Tricerri. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” <i>Proteins: Structure, Function, and Bioinformatics</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/prot.26217\">https://doi.org/10.1002/prot.26217</a>.","ieee":"R. A. Gisonno, T. Masson, N. A. Ramella, E. E. Barrera, V. Romanowski, and M. A. Tricerri, “Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior,” <i>Proteins: Structure, Function, and Bioinformatics</i>, vol. 90, no. 1. Wiley, pp. 258–269, 2022."},"article_processing_charge":"No","day":"01","publication_status":"published","volume":90,"corr_author":"1","date_published":"2022-01-01T00:00:00Z","publication_identifier":{"issn":["0887-3585"],"eissn":["1097-0134"]},"issue":"1","doi":"10.1002/prot.26217","department":[{"_id":"MaJö"}],"_id":"15268","keyword":["Molecular Biology","Biochemistry","Structural Biology"],"external_id":{"pmid":["34414600"]},"year":"2022","month":"01","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior","abstract":[{"text":"Apolipoprotein A‐I (apoA‐I) has a key function in the reverse cholesterol transport. However, aggregation of apoA‐I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural consequences introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA‐I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation‐prone regions (APRs) present in apoA‐I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA‐I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA‐I. Structural properties of full‐length apoA‐I models suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Compared to silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha‐helix bundle with the concomitant exposure of APR1 to the solvent, suggesting an insight into the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA‐I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region.","lang":"eng"}],"pmid":1},{"volume":5,"article_processing_charge":"No","citation":{"mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>.","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568.","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>","short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022).","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>.","apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>"},"day":"01","publication_status":"published","ddc":["570"],"date_published":"2022-09-01T00:00:00Z","has_accepted_license":"1","publication":"Life Science Alliance","language":[{"iso":"eng"}],"date_created":"2022-09-06T18:45:23Z","publisher":"Life Science Alliance","article_type":"original","oa_version":"Published Version","intvolume":"         5","quality_controlled":"1","date_updated":"2024-10-21T06:01:48Z","file":[{"file_size":3183129,"content_type":"application/pdf","creator":"dernst","relation":"main_file","success":1,"date_updated":"2022-09-08T06:41:14Z","checksum":"4201d876a3e5e8b65e319d03300014ad","file_name":"2022_LifeScienceAlliance_Daiss.pdf","file_id":"12062","access_level":"open_access","date_created":"2022-09-08T06:41:14Z"}],"isi":1,"author":[{"last_name":"Daiß","full_name":"Daiß, Julia L","first_name":"Julia L"},{"first_name":"Michael","full_name":"Pilsl, Michael","last_name":"Pilsl"},{"last_name":"Straub","full_name":"Straub, Kristina","first_name":"Kristina"},{"full_name":"Bleckmann, Andrea","first_name":"Andrea","last_name":"Bleckmann"},{"last_name":"Höcherl","full_name":"Höcherl, Mona","first_name":"Mona"},{"last_name":"Heiss","first_name":"Florian B","full_name":"Heiss, Florian B"},{"last_name":"Abascal-Palacios","first_name":"Guillermo","full_name":"Abascal-Palacios, Guillermo"},{"full_name":"Ramsay, Ewan P","first_name":"Ewan P","last_name":"Ramsay"},{"full_name":"Tluckova, Katarina","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","last_name":"Tluckova"},{"last_name":"Mars","full_name":"Mars, Jean-Clement","first_name":"Jean-Clement"},{"last_name":"Fürtges","full_name":"Fürtges, Torben","first_name":"Torben"},{"full_name":"Bruckmann, Astrid","first_name":"Astrid","last_name":"Bruckmann"},{"full_name":"Rudack, Till","first_name":"Till","last_name":"Rudack"},{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","last_name":"Bernecky"},{"last_name":"Lamour","full_name":"Lamour, Valérie","first_name":"Valérie"},{"full_name":"Panov, Konstantin","first_name":"Konstantin","last_name":"Panov"},{"last_name":"Vannini","first_name":"Alessandro","full_name":"Vannini, Alessandro"},{"last_name":"Moss","first_name":"Tom","full_name":"Moss, Tom"},{"full_name":"Engel, Christoph","first_name":"Christoph","last_name":"Engel"}],"oa":1,"status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000972702600001"]},"year":"2022","month":"09","type":"journal_article","article_number":"e202201568","acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","abstract":[{"text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","file_date_updated":"2022-09-08T06:41:14Z","scopus_import":"1","issue":"11","publication_identifier":{"issn":["2575-1077"]},"doi":"10.26508/lsa.202201568","_id":"12051","department":[{"_id":"CaBe"}],"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"]},{"oa":1,"author":[{"last_name":"Hübschmann","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","full_name":"Hübschmann, Verena"},{"last_name":"Korkut","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","full_name":"Korkut, Medina","first_name":"Medina"},{"last_name":"Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra"}],"file":[{"access_level":"open_access","date_created":"2023-01-23T09:50:51Z","file_name":"2022_STARProtocols_Huebschmann.pdf","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_id":"12340","creator":"dernst","relation":"main_file","success":1,"date_updated":"2023-01-23T09:50:51Z","content_type":"application/pdf","file_size":6251945}],"status":"public","intvolume":"         3","quality_controlled":"1","date_updated":"2025-06-11T13:58:47Z","article_type":"letter_note","oa_version":"Published Version","related_material":{"record":[{"relation":"other","status":"public","id":"11478"}]},"language":[{"iso":"eng"}],"publication":"STAR Protocols","date_created":"2023-01-12T11:56:38Z","publisher":"Elsevier","has_accepted_license":"1","date_published":"2022-12-16T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017"}],"corr_author":"1","volume":3,"day":"16","publication_status":"published","ddc":["570"],"article_processing_charge":"No","citation":{"mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>","ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022.","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>."},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"_id":"12117","acknowledged_ssus":[{"_id":"Bio"}],"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"scopus_import":"1","doi":"10.1016/j.xpro.2022.101866","issue":"4","publication_identifier":{"issn":["2666-1667"]},"file_date_updated":"2023-01-23T09:50:51Z","ec_funded":1,"pmid":1,"abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"101866","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","type":"journal_article","month":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2022","external_id":{"pmid":["36595902"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","abstract":[{"text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.","lang":"eng"}],"pmid":1,"acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","month":"12","type":"journal_article","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"year":"2022","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"department":[{"_id":"JiFr"}],"_id":"12120","doi":"10.1016/j.devcel.2022.11.006","issue":"23","publication_identifier":{"issn":["1534-5807"]},"scopus_import":"1","date_published":"2022-12-05T00:00:00Z","article_processing_charge":"No","citation":{"short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>."},"ddc":["580"],"day":"05","publication_status":"published","volume":57,"OA_type":"free access","status":"public","isi":1,"author":[{"last_name":"Xiao","full_name":"Xiao, Huixin","first_name":"Huixin"},{"last_name":"Hu","first_name":"Yumei","full_name":"Hu, Yumei"},{"last_name":"Wang","first_name":"Yaping","full_name":"Wang, Yaping"},{"last_name":"Cheng","full_name":"Cheng, Jinkui","first_name":"Jinkui"},{"last_name":"Wang","full_name":"Wang, Jinyi","first_name":"Jinyi"},{"full_name":"Chen, Guojingwei","first_name":"Guojingwei","last_name":"Chen"},{"full_name":"Li, Qian","first_name":"Qian","last_name":"Li"},{"last_name":"Wang","first_name":"Shuwei","full_name":"Wang, Shuwei"},{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"full_name":"Wang, Shao-Shuai","first_name":"Shao-Shuai","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Yi","first_name":"Yi"},{"last_name":"Xuan","full_name":"Xuan, Wei","first_name":"Wei"},{"full_name":"Li, Zhen","first_name":"Zhen","last_name":"Li"},{"last_name":"Guo","full_name":"Guo, Yan","first_name":"Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"oa":1,"date_updated":"2026-06-18T17:23:10Z","OA_place":"publisher","intvolume":"        57","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.11.006","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","page":"2638-2651.e6","article_type":"original","date_created":"2023-01-12T11:57:00Z","publisher":"Elsevier","publication":"Developmental Cell","language":[{"iso":"eng"}]},{"volume":13,"citation":{"short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"article_processing_charge":"No","ddc":["580"],"publication_status":"published","day":"15","date_published":"2022-11-15T00:00:00Z","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"date_created":"2023-01-12T12:02:41Z","publisher":"Springer Nature","article_type":"original","oa_version":"Published Version","quality_controlled":"1","intvolume":"        13","date_updated":"2025-07-08T09:01:02Z","isi":1,"file":[{"file_size":3375249,"content_type":"application/pdf","relation":"main_file","creator":"dernst","date_updated":"2023-01-23T11:17:33Z","success":1,"checksum":"233922a7b9507d9d48591e6799e4526e","file_name":"2022_NatureCommunications_Huang.pdf","file_id":"12346","access_level":"open_access","date_created":"2023-01-23T11:17:33Z"}],"oa":1,"author":[{"full_name":"Huang, Jian","first_name":"Jian","last_name":"Huang"},{"first_name":"Lei","full_name":"Zhao, Lei","last_name":"Zhao"},{"last_name":"Malik","first_name":"Shikha","full_name":"Malik, Shikha"},{"last_name":"Gentile","full_name":"Gentile, Benjamin R.","first_name":"Benjamin R."},{"last_name":"Xiong","full_name":"Xiong, Va","first_name":"Va"},{"first_name":"Tzahi","full_name":"Arazi, Tzahi","last_name":"Arazi"},{"last_name":"Owen","full_name":"Owen, Heather A.","first_name":"Heather A."},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhao","first_name":"Dazhong","full_name":"Zhao, Dazhong"}],"status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"year":"2022","month":"11","type":"journal_article","article_number":"6960","acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","abstract":[{"lang":"eng","text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants."}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","file_date_updated":"2023-01-23T11:17:33Z","scopus_import":"1","doi":"10.1038/s41467-022-34723-6","publication_identifier":{"eissn":["2041-1723"]},"_id":"12130","department":[{"_id":"JiFr"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"]},{"oa_version":"Published Version","article_type":"original","date_created":"2023-01-12T12:08:51Z","publisher":"Elsevier","language":[{"iso":"eng"}],"publication":"Current Opinion in Systems Biology","status":"public","oa":1,"author":[{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"last_name":"Tkačik","orcid":"1","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2023-01-24T12:14:10Z","success":1,"relation":"main_file","creator":"dernst","file_size":2214944,"content_type":"application/pdf","date_created":"2023-01-24T12:14:10Z","access_level":"open_access","file_id":"12362","file_name":"2022_CurrentBiology_Zoller.pdf","checksum":"97ef01e0cc60cdc84f45640a0f248fb0"}],"date_updated":"2025-06-11T13:47:43Z","intvolume":"        31","quality_controlled":"1","corr_author":"1","date_published":"2022-09-01T00:00:00Z","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27"}],"day":"01","publication_status":"published","ddc":["570"],"citation":{"ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022)."},"article_processing_charge":"Yes (via OA deal)","volume":31,"has_accepted_license":"1","doi":"10.1016/j.coisb.2022.100435","issue":"9","publication_identifier":{"issn":["2452-3100"]},"scopus_import":"1","file_date_updated":"2023-01-24T12:14:10Z","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"department":[{"_id":"GaTk"}],"_id":"12156","type":"journal_article","month":"09","year":"2022","external_id":{"pmid":["36590072"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Eukaryotic gene regulation at equilibrium, or non?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","article_number":"100435"},{"has_accepted_license":"1","volume":11,"publication_status":"published","day":"26","ddc":["570"],"citation":{"ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"article_processing_charge":"No","date_published":"2022-09-26T00:00:00Z","corr_author":"1","quality_controlled":"1","intvolume":"        11","date_updated":"2024-10-09T21:03:38Z","oa":1,"author":[{"first_name":"Laura","full_name":"Hayward, Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","last_name":"Hayward"},{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"}],"isi":1,"file":[{"file_id":"12363","file_name":"2022_eLife_Hayward.pdf","checksum":"28de155b231ac1c8d4501c98b2fb359a","date_created":"2023-01-24T12:21:32Z","access_level":"open_access","file_size":18935612,"content_type":"application/pdf","success":1,"date_updated":"2023-01-24T12:21:32Z","creator":"dernst","relation":"main_file"}],"status":"public","language":[{"iso":"eng"}],"publication":"eLife","publisher":"eLife Sciences Publications","date_created":"2023-01-12T12:09:00Z","article_type":"original","oa_version":"Published Version","article_number":"66697","acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","abstract":[{"lang":"eng","text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species."}],"title":"Polygenic adaptation after a sudden change in environment","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","external_id":{"isi":["000890735600001"]},"type":"journal_article","month":"09","_id":"12157","department":[{"_id":"NiBa"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"file_date_updated":"2023-01-24T12:21:32Z","scopus_import":"1","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/elife.66697"},{"article_type":"original","oa_version":"Published Version","publication":"Nature Communications","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2023-01-16T09:45:09Z","file":[{"date_created":"2023-01-27T07:19:11Z","access_level":"open_access","file_id":"12411","file_name":"2022_NatureCommunications_Prehal.pdf","checksum":"5034336dbf0f860030ef745c08df9e0e","success":1,"date_updated":"2023-01-27T07:19:11Z","relation":"main_file","creator":"dernst","file_size":4216931,"content_type":"application/pdf"}],"isi":1,"oa":1,"author":[{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"last_name":"von Mentlen","first_name":"Jean-Marc","full_name":"von Mentlen, Jean-Marc"},{"last_name":"Drvarič Talian","full_name":"Drvarič Talian, Sara","first_name":"Sara"},{"last_name":"Vizintin","full_name":"Vizintin, Alen","first_name":"Alen"},{"last_name":"Dominko","full_name":"Dominko, Robert","first_name":"Robert"},{"first_name":"Heinz","full_name":"Amenitsch, Heinz","last_name":"Amenitsch"},{"last_name":"Porcar","full_name":"Porcar, Lionel","first_name":"Lionel"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"},{"last_name":"Wood","full_name":"Wood, Vanessa","first_name":"Vanessa"}],"status":"public","intvolume":"        13","quality_controlled":"1","date_updated":"2024-10-09T21:03:47Z","date_published":"2022-10-24T00:00:00Z","corr_author":"1","volume":13,"citation":{"apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>","chicago":"Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin, Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger, and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>.","ieee":"C. Prehal <i>et al.</i>, “On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).","mla":"Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>, vol. 13, 6326, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>.","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>","ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326."},"article_processing_charge":"No","ddc":["540"],"day":"24","publication_status":"published","has_accepted_license":"1","scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-33931-4","file_date_updated":"2023-01-27T07:19:11Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"_id":"12208","department":[{"_id":"StFr"}],"month":"10","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000871563700006"],"pmid":["36280671"]},"year":"2022","abstract":[{"lang":"eng","text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells."}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","article_number":"6326","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for the access to the Austrian SAXS beamline and TU Graz for support through the Lead Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition, the authors acknowledge access to the D-22SANS beamline at the ILL neutron source. Electron microscopy measurements were performed at the Scientific Scenter for Optical and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P. and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F. is indebted to IST Austria for support. "},{"has_accepted_license":"1","date_published":"2022-09-05T00:00:00Z","project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288"}],"volume":13,"article_processing_charge":"No","citation":{"short":"S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, Nature Communications 13 (2022).","ista":"Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 13, 5219.","ama":"Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>","mla":"Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>, vol. 13, 5219, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>.","ieee":"S. Randriamanantsoa <i>et al.</i>, “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>.","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>"},"day":"05","publication_status":"published","ddc":["570"],"isi":1,"file":[{"date_updated":"2023-01-27T08:14:48Z","success":1,"relation":"main_file","creator":"dernst","file_size":22645149,"content_type":"application/pdf","date_created":"2023-01-27T08:14:48Z","access_level":"open_access","file_id":"12416","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","checksum":"295261b5172274fd5b8f85a6a6058828"}],"oa":1,"author":[{"last_name":"Randriamanantsoa","first_name":"S.","full_name":"Randriamanantsoa, S."},{"first_name":"A.","full_name":"Papargyriou, A.","last_name":"Papargyriou"},{"last_name":"Maurer","full_name":"Maurer, H. C.","first_name":"H. C."},{"last_name":"Peschke","full_name":"Peschke, K.","first_name":"K."},{"full_name":"Schuster, M.","first_name":"M.","last_name":"Schuster"},{"first_name":"G.","full_name":"Zecchin, G.","last_name":"Zecchin"},{"last_name":"Steiger","full_name":"Steiger, K.","first_name":"K."},{"full_name":"Öllinger, R.","first_name":"R.","last_name":"Öllinger"},{"last_name":"Saur","full_name":"Saur, D.","first_name":"D."},{"last_name":"Scheel","first_name":"C.","full_name":"Scheel, C."},{"last_name":"Rad","first_name":"R.","full_name":"Rad, R."},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Reichert","full_name":"Reichert, M.","first_name":"M."},{"last_name":"Bausch","first_name":"A. R.","full_name":"Bausch, A. R."}],"status":"public","intvolume":"        13","quality_controlled":"1","date_updated":"2025-06-11T13:53:55Z","article_type":"original","related_material":{"record":[{"status":"public","id":"13068","relation":"research_data"}]},"oa_version":"Published Version","publication":"Nature Communications","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2023-01-16T09:46:53Z","abstract":[{"text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis.","lang":"eng"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","article_number":"5219","acknowledgement":"A.R.B. acknowledges the financial support of the European Research Council (ERC) through the funding of the grant Principles of Integrin Mechanics and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project ID 201269156). E.H. was supported by the European Union (European Research Council Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project 12, project ID 329628492). M.R. was supported by the German Research Foundation (DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt DEAL.","month":"09","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["36064947"],"isi":["000850348400025"]},"year":"2022","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"_id":"12217","department":[{"_id":"EdHa"}],"scopus_import":"1","doi":"10.1038/s41467-022-32806-y","publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"file_date_updated":"2023-01-27T08:14:48Z"},{"scopus_import":"1","publication_identifier":{"issn":["2399-3642"]},"doi":"10.1038/s42003-022-03446-1","file_date_updated":"2023-01-27T08:23:46Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"_id":"12224","department":[{"_id":"PreCl"}],"month":"06","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000811777900003"]},"year":"2022","abstract":[{"text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine <jats:italic>Mkln1</jats:italic> knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that <jats:italic>Mkln1</jats:italic> deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from <jats:italic>Mkln1</jats:italic> ablation.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","article_number":"589","acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_type":"original","oa_version":"Published Version","publication":"Communications Biology","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2023-01-16T09:48:19Z","file":[{"file_id":"12417","file_name":"2022_CommBiology_Muhia.pdf","checksum":"bd95be1e77090208b79bc45ea8785d0b","date_created":"2023-01-27T08:23:46Z","access_level":"open_access","file_size":3968356,"content_type":"application/pdf","success":1,"date_updated":"2023-01-27T08:23:46Z","creator":"dernst","relation":"main_file"}],"isi":1,"oa":1,"author":[{"id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","first_name":"Mary W","full_name":"Muhia, Mary W","last_name":"Muhia"},{"first_name":"PingAn","full_name":"YuanXiang, PingAn","last_name":"YuanXiang"},{"last_name":"Sedlacik","first_name":"Jan","full_name":"Sedlacik, Jan"},{"full_name":"Schwarz, Jürgen R.","first_name":"Jürgen R.","last_name":"Schwarz"},{"full_name":"Heisler, Frank F.","first_name":"Frank F.","last_name":"Heisler"},{"first_name":"Kira V.","full_name":"Gromova, Kira V.","last_name":"Gromova"},{"first_name":"Edda","full_name":"Thies, Edda","last_name":"Thies"},{"last_name":"Breiden","full_name":"Breiden, Petra","first_name":"Petra"},{"full_name":"Pechmann, Yvonne","first_name":"Yvonne","last_name":"Pechmann"},{"last_name":"Kreutz","first_name":"Michael R.","full_name":"Kreutz, Michael R."},{"last_name":"Kneussel","full_name":"Kneussel, Matthias","first_name":"Matthias"}],"status":"public","intvolume":"         5","quality_controlled":"1","date_updated":"2024-10-09T21:03:48Z","date_published":"2022-06-15T00:00:00Z","corr_author":"1","volume":5,"citation":{"apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>","ieee":"M. W. Muhia <i>et al.</i>, “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>.","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>, vol. 5, 589, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>.","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022)."},"article_processing_charge":"No","publication_status":"published","ddc":["570"],"day":"15","has_accepted_license":"1"},{"acknowledgement":"We thank the members of the Matsuda Laboratory for their helpful discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical assistance. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107 and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no. JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER (no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739 to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO. This work was partly supported by an Extramural Collaborative Research Grant of Cancer Research Institute, Kanazawa University.","abstract":[{"text":"Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration.","lang":"eng"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"year":"2022","month":"10","type":"journal_article","_id":"12238","department":[{"_id":"CaHe"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"scopus_import":"1","publication_identifier":{"issn":["1534-5807"]},"issue":"19","doi":"10.1016/j.devcel.2022.09.003","volume":57,"OA_type":"free access","article_processing_charge":"No","citation":{"chicago":"Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>.","ieee":"N. Hino <i>et al.</i>, “A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration,” <i>Developmental Cell</i>, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.","apa":"Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda, M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>","short":"N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji, K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57 (2022) 2290–2304.e7.","ama":"Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. 2022;57(19):2290-2304.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>","ista":"Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K, Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 57(19), 2290–2304.e7.","mla":"Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>."},"day":"01","ddc":["570"],"publication_status":"published","date_published":"2022-10-01T00:00:00Z","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.09.003","open_access":"1"}],"intvolume":"        57","date_updated":"2026-06-18T17:25:21Z","OA_place":"publisher","isi":1,"oa":1,"author":[{"id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino"},{"first_name":"Kimiya","full_name":"Matsuda, Kimiya","last_name":"Matsuda"},{"last_name":"Jikko","full_name":"Jikko, Yuya","first_name":"Yuya"},{"first_name":"Gembu","full_name":"Maryu, Gembu","last_name":"Maryu"},{"full_name":"Sakai, Katsuya","first_name":"Katsuya","last_name":"Sakai"},{"last_name":"Imamura","full_name":"Imamura, Ryu","first_name":"Ryu"},{"full_name":"Tsukiji, Shinya","first_name":"Shinya","last_name":"Tsukiji"},{"first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro","last_name":"Aoki"},{"last_name":"Terai","full_name":"Terai, Kenta","first_name":"Kenta"},{"full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirashima"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"last_name":"Matsuda","first_name":"Michiyuki","full_name":"Matsuda, Michiyuki"}],"status":"public","publication":"Developmental Cell","language":[{"iso":"eng"}],"publisher":"Elsevier","date_created":"2023-01-16T09:51:39Z","article_type":"original","oa_version":"Published Version","page":"2290-2304.e7"},{"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","article_number":"e10490","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"pmid":1,"external_id":{"pmid":["36124745"],"isi":["000856482800001"]},"year":"2022","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"09","type":"journal_article","department":[{"_id":"ToBo"}],"_id":"12261","acknowledged_ssus":[{"_id":"M-Shop"}],"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"file_date_updated":"2023-01-30T09:49:55Z","publication_identifier":{"eissn":["1744-4292"]},"issue":"9","doi":"10.15252/msb.202110490","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>.","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &#38; Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” <i>Molecular Systems Biology</i>, vol. 18, no. 9. Embo Press, 2022.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. 2022;18(9). doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>, vol. 18, no. 9, e10490, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>."},"ddc":["570"],"day":"01","publication_status":"published","volume":18,"date_published":"2022-09-01T00:00:00Z","date_updated":"2025-06-11T14:10:18Z","intvolume":"        18","quality_controlled":"1","status":"public","file":[{"date_created":"2023-01-30T09:49:55Z","access_level":"open_access","file_id":"12446","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","success":1,"date_updated":"2023-01-30T09:49:55Z","relation":"main_file","creator":"dernst","file_size":1098812,"content_type":"application/pdf"}],"isi":1,"oa":1,"author":[{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","last_name":"Angermayr"},{"full_name":"Pang, Tin Yau","first_name":"Tin Yau","last_name":"Pang"},{"full_name":"Chevereau, Guillaume","first_name":"Guillaume","last_name":"Chevereau"},{"full_name":"Mitosch, Karin","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch"},{"full_name":"Lercher, Martin J","first_name":"Martin J","last_name":"Lercher"},{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"date_created":"2023-01-16T09:58:34Z","publisher":"Embo Press","publication":"Molecular Systems Biology","language":[{"iso":"eng"}],"oa_version":"Published Version","article_type":"original"},{"type":"journal_article","month":"07","year":"2022","external_id":{"pmid":["35586945"],"isi":["000797302700001"]},"pmid":1,"abstract":[{"lang":"eng","text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system."}],"title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e54163","acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship","scopus_import":"1","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"doi":"10.15252/embr.202154163","issue":"7","keyword":["Genetics","Molecular Biology","Biochemistry"],"_id":"12275","department":[{"_id":"MaDe"}],"date_published":"2022-07-05T00:00:00Z","volume":23,"publication_status":"published","day":"05","ddc":["570"],"citation":{"ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. 2022;23(7). doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163.","mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>, vol. 23, no. 7, e54163, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>.","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” <i>EMBO Reports</i>, vol. 23, no. 7. Embo Press, 2022.","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>.","apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., &#38; Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>"},"article_processing_charge":"No","has_accepted_license":"1","article_type":"original","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"EMBO Reports","date_created":"2023-01-16T10:01:44Z","publisher":"Embo Press","author":[{"last_name":"Rahman","full_name":"Rahman, Maisha","first_name":"Maisha"},{"full_name":"Ramirez, Nelson","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425","last_name":"Ramirez"},{"last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A","first_name":"Carlos A"},{"full_name":"Bülow, Hannes E","first_name":"Hannes E","last_name":"Bülow"}],"oa":1,"isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15252/embr.202154163"}],"quality_controlled":"1","intvolume":"        23","date_updated":"2026-06-18T17:26:25Z"},{"scopus_import":"1","doi":"10.7554/elife.79848","publication_identifier":{"eissn":["2050-084X"]},"file_date_updated":"2023-01-30T11:50:53Z","ec_funded":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"_id":"12288","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"department":[{"_id":"MaJö"},{"_id":"PeJo"}],"type":"journal_article","month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"pmid":1,"abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"79848","acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","article_type":"original","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"eLife","publisher":"eLife Sciences Publications","date_created":"2023-01-16T10:04:15Z","oa":1,"author":[{"orcid":"0000-0002-4792-1881","last_name":"Sumser","first_name":"Anton L","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"},{"last_name":"Ben Simon","full_name":"Ben Simon, Yoav","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2023-01-30T11:50:53Z","access_level":"open_access","file_id":"12463","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","file_name":"2022_eLife_Sumser.pdf","success":1,"date_updated":"2023-01-30T11:50:53Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":8506811}],"isi":1,"status":"public","intvolume":"        11","quality_controlled":"1","date_updated":"2025-04-15T08:29:05Z","date_published":"2022-09-15T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","volume":11,"day":"15","publication_status":"published","ddc":["570"],"citation":{"ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022)."},"article_processing_charge":"No","has_accepted_license":"1"},{"year":"2022","extern":"1","external_id":{"pmid":["36478632"]},"type":"journal_article","month":"12","title":"DNA methylation dynamics during germline development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.","lang":"eng"}],"doi":"10.1111/jipb.13422","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"issue":"12","scopus_import":"1","department":[{"_id":"XiFe"}],"_id":"12670","keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"publication_status":"published","day":"07","article_processing_charge":"No","citation":{"short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>.","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022."},"volume":64,"date_published":"2022-12-07T00:00:00Z","date_created":"2023-02-23T09:15:57Z","publisher":"Wiley","language":[{"iso":"eng"}],"publication":"Journal of Integrative Plant Biology","page":"2240-2251","oa_version":"Published Version","article_type":"review","date_updated":"2024-10-14T12:03:14Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13422"}],"intvolume":"        64","status":"public","oa":1,"author":[{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}]},{"scopus_import":"1","doi":"10.1038/s42004-022-00658-8","publication_identifier":{"eissn":["2399-3669"]},"keyword":["Materials Chemistry","Biochemistry","Environmental Chemistry","General Chemistry"],"_id":"13347","month":"03","type":"journal_article","extern":"1","year":"2022","abstract":[{"lang":"eng","text":"Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible Pd<jats:sup>II</jats:sup><jats:sub>6</jats:sub>L<jats:sub>4</jats:sub> coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the Pd<jats:sup>II</jats:sup><jats:sub>6</jats:sub>L<jats:sub>4</jats:sub> cage disassembles to afford Pd<jats:sup>II</jats:sup><jats:sub>2</jats:sub>L<jats:sub>2</jats:sub> species, which lacks the ability to form inclusion complexes – a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Encapsulation within a coordination cage modulates the reactivity of redox-active dyes","article_number":"44","article_type":"original","oa_version":"Published Version","publication":"Communications Chemistry","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2023-08-01T09:30:47Z","author":[{"first_name":"Oksana","full_name":"Yanshyna, Oksana","last_name":"Yanshyna"},{"first_name":"Michał J.","full_name":"Białek, Michał J.","last_name":"Białek"},{"first_name":"Oleg V.","full_name":"Chashchikhin, Oleg V.","last_name":"Chashchikhin"},{"last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal"}],"oa":1,"status":"public","quality_controlled":"1","intvolume":"         5","main_file_link":[{"url":"https://doi.org/10.1038/s42004-022-00658-8","open_access":"1"}],"date_updated":"2024-10-14T12:09:07Z","date_published":"2022-03-30T00:00:00Z","volume":5,"article_processing_charge":"No","citation":{"ieee":"O. Yanshyna, M. J. Białek, O. V. Chashchikhin, and R. Klajn, “Encapsulation within a coordination cage modulates the reactivity of redox-active dyes,” <i>Communications Chemistry</i>, vol. 5. Springer Nature, 2022.","chicago":"Yanshyna, Oksana, Michał J. Białek, Oleg V. Chashchikhin, and Rafal Klajn. “Encapsulation within a Coordination Cage Modulates the Reactivity of Redox-Active Dyes.” <i>Communications Chemistry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42004-022-00658-8\">https://doi.org/10.1038/s42004-022-00658-8</a>.","apa":"Yanshyna, O., Białek, M. J., Chashchikhin, O. V., &#38; Klajn, R. (2022). Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. <i>Communications Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42004-022-00658-8\">https://doi.org/10.1038/s42004-022-00658-8</a>","ista":"Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. 2022. Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. Communications Chemistry. 5, 44.","ama":"Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. <i>Communications Chemistry</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42004-022-00658-8\">10.1038/s42004-022-00658-8</a>","mla":"Yanshyna, Oksana, et al. “Encapsulation within a Coordination Cage Modulates the Reactivity of Redox-Active Dyes.” <i>Communications Chemistry</i>, vol. 5, 44, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42004-022-00658-8\">10.1038/s42004-022-00658-8</a>.","short":"O. Yanshyna, M.J. Białek, O.V. Chashchikhin, R. Klajn, Communications Chemistry 5 (2022)."},"day":"30","publication_status":"published"},{"date_published":"2022-11-15T00:00:00Z","publication_status":"published","day":"15","citation":{"chicago":"Wang, Jinhua, Liat Avram, Yael Diskin-Posner, Michał J. Białek, Wojciech Stawski, Moran Feller, and Rafal Klajn. “Altering the Properties of Spiropyran Switches Using Coordination Cages with Different Symmetries.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/jacs.2c08901\">https://doi.org/10.1021/jacs.2c08901</a>.","ieee":"J. Wang <i>et al.</i>, “Altering the properties of spiropyran switches using coordination cages with different symmetries,” <i>Journal of the American Chemical Society</i>, vol. 144, no. 46. American Chemical Society, pp. 21244–21254, 2022.","apa":"Wang, J., Avram, L., Diskin-Posner, Y., Białek, M. J., Stawski, W., Feller, M., &#38; Klajn, R. (2022). Altering the properties of spiropyran switches using coordination cages with different symmetries. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.2c08901\">https://doi.org/10.1021/jacs.2c08901</a>","short":"J. Wang, L. Avram, Y. Diskin-Posner, M.J. Białek, W. Stawski, M. Feller, R. Klajn, Journal of the American Chemical Society 144 (2022) 21244–21254.","ama":"Wang J, Avram L, Diskin-Posner Y, et al. Altering the properties of spiropyran switches using coordination cages with different symmetries. <i>Journal of the American Chemical Society</i>. 2022;144(46):21244-21254. doi:<a href=\"https://doi.org/10.1021/jacs.2c08901\">10.1021/jacs.2c08901</a>","ista":"Wang J, Avram L, Diskin-Posner Y, Białek MJ, Stawski W, Feller M, Klajn R. 2022. Altering the properties of spiropyran switches using coordination cages with different symmetries. Journal of the American Chemical Society. 144(46), 21244–21254.","mla":"Wang, Jinhua, et al. “Altering the Properties of Spiropyran Switches Using Coordination Cages with Different Symmetries.” <i>Journal of the American Chemical Society</i>, vol. 144, no. 46, American Chemical Society, 2022, pp. 21244–54, doi:<a href=\"https://doi.org/10.1021/jacs.2c08901\">10.1021/jacs.2c08901</a>."},"article_processing_charge":"No","volume":144,"status":"public","oa":1,"author":[{"first_name":"Jinhua","full_name":"Wang, Jinhua","last_name":"Wang"},{"last_name":"Avram","first_name":"Liat","full_name":"Avram, Liat"},{"first_name":"Yael","full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner"},{"full_name":"Białek, Michał J.","first_name":"Michał J.","last_name":"Białek"},{"last_name":"Stawski","full_name":"Stawski, Wojciech","first_name":"Wojciech"},{"last_name":"Feller","first_name":"Moran","full_name":"Feller, Moran"},{"last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal"}],"date_updated":"2024-10-14T12:08:54Z","intvolume":"       144","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c08901"}],"quality_controlled":"1","page":"21244-21254","oa_version":"Published Version","article_type":"original","date_created":"2023-08-01T09:31:01Z","publisher":"American Chemical Society","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","title":"Altering the properties of spiropyran switches using coordination cages with different symmetries","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Molecular confinement effects can profoundly alter the physicochemical properties of the confined species. A plethora of organic molecules were encapsulated within the cavities of supramolecular hosts, and the impact of the cavity size and polarity was widely investigated. However, the extent to which the properties of the confined guests can be affected by the symmetry of the cage─which dictates the shape of the cavity─remains to be understood. Here we show that cage symmetry has a dramatic effect on the equilibrium between two isomers of the encapsulated spiropyran guests. Working with two Pd-based coordination cages featuring similarly sized but differently shaped hydrophobic cavities, we found a highly selective stabilization of the isomer whose shape matches that of the cavity of the cage. A Td-symmetric cage stabilized the spiropyrans’ colorless form and rendered them photochemically inert. In contrast, a D2h-symmetric cage favored the colored isomer, while maintaining reversible photoswitching between the two states of the encapsulated spiropyrans. We also show that the switching kinetics strongly depend on the substitution pattern on the spiropyran scaffold. This finding was used to fabricate a time-sensitive information storage medium with tunable lifetimes of the encoded messages.","lang":"eng"}],"type":"journal_article","month":"11","extern":"1","year":"2022","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"_id":"13348","doi":"10.1021/jacs.2c08901","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"issue":"46","scopus_import":"1"}]