[{"volume":11,"file_date_updated":"2023-01-30T11:50:53Z","article_type":"original","publisher":"eLife Sciences Publications","intvolume":"        11","isi":1,"date_created":"2023-01-16T10:04:15Z","month":"09","article_number":"79848","status":"public","citation":{"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>.","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>","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.","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>","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.","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>.","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022)."},"quality_controlled":"1","author":[{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","last_name":"Sumser","first_name":"Anton L"},{"first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","publication":"eLife","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","pmid":1,"oa":1,"ddc":["570"],"_id":"12288","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","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."}],"date_published":"2022-09-15T00:00:00Z","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"file":[{"success":1,"file_id":"12463","date_updated":"2023-01-30T11:50:53Z","file_name":"2022_eLife_Sumser.pdf","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T11:50:53Z","content_type":"application/pdf","creator":"dernst","file_size":8506811}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publication_identifier":{"eissn":["2050-084X"]},"scopus_import":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T10:29:48Z","type":"journal_article","oa_version":"Published Version","day":"15","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.7554/elife.79848","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"has_accepted_license":"1","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)."},{"scopus_import":"1","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"external_id":{"pmid":["36478632"]},"date_published":"2022-12-07T00:00:00Z","page":"2240-2251","department":[{"_id":"XiFe"}],"doi":"10.1111/jipb.13422","language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2023-05-08T10:59:00Z","type":"journal_article","day":"07","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","date_created":"2023-02-23T09:15:57Z","status":"public","intvolume":"        64","article_type":"review","publisher":"Wiley","issue":"12","volume":64,"abstract":[{"lang":"eng","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."}],"publication_status":"published","pmid":1,"publication":"Journal of Integrative Plant Biology","title":"DNA methylation dynamics during germline development","_id":"12670","oa":1,"year":"2022","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13422"}],"citation":{"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>.","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>","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.","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>","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","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>."},"author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"extern":"1","quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1038/s42004-022-00658-8","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2023-08-02T06:41:54Z","oa_version":"Published Version","day":"30","publication_identifier":{"eissn":["2399-3669"]},"scopus_import":"1","date_published":"2022-03-30T00:00:00Z","keyword":["Materials Chemistry","Biochemistry","Environmental Chemistry","General Chemistry"],"publication":"Communications Chemistry","title":"Encapsulation within a coordination cage modulates the reactivity of redox-active dyes","oa":1,"_id":"13347","publication_status":"published","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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>.","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.","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>","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.","short":"O. Yanshyna, M.J. Białek, O.V. Chashchikhin, R. Klajn, Communications Chemistry 5 (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>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s42004-022-00658-8"}],"author":[{"last_name":"Yanshyna","first_name":"Oksana","full_name":"Yanshyna, Oksana"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"last_name":"Chashchikhin","first_name":"Oleg V.","full_name":"Chashchikhin, Oleg V."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"}],"extern":"1","quality_controlled":"1","year":"2022","intvolume":"         5","date_created":"2023-08-01T09:30:47Z","month":"03","status":"public","article_number":"44","volume":5,"article_type":"original","publisher":"Springer Nature"},{"language":[{"iso":"eng"}],"doi":"10.1021/jacs.2c08901","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-02T06:39:50Z","day":"15","scopus_import":"1","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_published":"2022-11-15T00:00:00Z","page":"21244-21254","publication":"Journal of the American Chemical Society","title":"Altering the properties of spiropyran switches using coordination cages with different symmetries","_id":"13348","oa":1,"abstract":[{"lang":"eng","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."}],"publication_status":"published","citation":{"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>","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>.","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>","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.","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.","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>.","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."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c08901"}],"quality_controlled":"1","extern":"1","author":[{"full_name":"Wang, Jinhua","last_name":"Wang","first_name":"Jinhua"},{"full_name":"Avram, Liat","last_name":"Avram","first_name":"Liat"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"full_name":"Białek, Michał J.","first_name":"Michał J.","last_name":"Białek"},{"last_name":"Stawski","first_name":"Wojciech","full_name":"Stawski, Wojciech"},{"last_name":"Feller","first_name":"Moran","full_name":"Feller, Moran"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"year":"2022","intvolume":"       144","month":"11","date_created":"2023-08-01T09:31:01Z","status":"public","volume":144,"issue":"46","publisher":"American Chemical Society","article_type":"original"},{"page":"2362-2379","external_id":{"pmid":["36133801"]},"keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"date_published":"2022-09-08T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","oa_version":"Published Version","date_updated":"2023-08-02T09:39:35Z","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.chempr.2022.05.008","issue":"9","volume":8,"publisher":"Elsevier","article_type":"original","intvolume":"         8","status":"public","month":"09","date_created":"2023-08-01T09:32:14Z","extern":"1","author":[{"last_name":"Gemen","first_name":"Julius","full_name":"Gemen, Julius"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"full_name":"Kazes, Miri","last_name":"Kazes","first_name":"Miri"},{"last_name":"Shimon","first_name":"Linda J.W.","full_name":"Shimon, Linda J.W."},{"full_name":"Feller, Moran","first_name":"Moran","last_name":"Feller"},{"full_name":"Semenov, Sergey N.","first_name":"Sergey N.","last_name":"Semenov"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"first_name":"Dan","last_name":"Oron","full_name":"Oron, Dan"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"quality_controlled":"1","citation":{"ista":"Gemen J, Białek MJ, Kazes M, Shimon LJW, Feller M, Semenov SN, Diskin-Posner Y, Oron D, Klajn R. 2022. Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. Chem. 8(9), 2362–2379.","short":"J. Gemen, M.J. Białek, M. Kazes, L.J.W. Shimon, M. Feller, S.N. Semenov, Y. Diskin-Posner, D. Oron, R. Klajn, Chem 8 (2022) 2362–2379.","chicago":"Gemen, Julius, Michał J. Białek, Miri Kazes, Linda J.W. Shimon, Moran Feller, Sergey N. Semenov, Yael Diskin-Posner, Dan Oron, and Rafal Klajn. “Ternary Host-Guest Complexes with Rapid Exchange Kinetics and Photoswitchable Fluorescence.” <i>Chem</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.chempr.2022.05.008\">https://doi.org/10.1016/j.chempr.2022.05.008</a>.","ama":"Gemen J, Białek MJ, Kazes M, et al. Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. <i>Chem</i>. 2022;8(9):2362-2379. doi:<a href=\"https://doi.org/10.1016/j.chempr.2022.05.008\">10.1016/j.chempr.2022.05.008</a>","ieee":"J. Gemen <i>et al.</i>, “Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence,” <i>Chem</i>, vol. 8, no. 9. Elsevier, pp. 2362–2379, 2022.","apa":"Gemen, J., Białek, M. J., Kazes, M., Shimon, L. J. W., Feller, M., Semenov, S. N., … Klajn, R. (2022). Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. <i>Chem</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chempr.2022.05.008\">https://doi.org/10.1016/j.chempr.2022.05.008</a>","mla":"Gemen, Julius, et al. “Ternary Host-Guest Complexes with Rapid Exchange Kinetics and Photoswitchable Fluorescence.” <i>Chem</i>, vol. 8, no. 9, Elsevier, 2022, pp. 2362–79, doi:<a href=\"https://doi.org/10.1016/j.chempr.2022.05.008\">10.1016/j.chempr.2022.05.008</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2022.05.008"}],"year":"2022","_id":"13350","oa":1,"pmid":1,"publication":"Chem","title":"Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence","abstract":[{"lang":"eng","text":"Confinement within molecular cages can dramatically modify the physicochemical properties of the encapsulated guest molecules, but such host-guest complexes have mainly been studied in a static context. Combining confinement effects with fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular systems—and ultimately materials—whose desired properties could be tailored “on demand” rapidly and reversibly. Here, we demonstrate rapid guest exchange between inclusion complexes of an open-window coordination cage that can simultaneously accommodate two guest molecules. Working with two types of guests, anthracene derivatives and BODIPY dyes, we show that the former can substantially modify the optical properties of the latter upon noncovalent heterodimer formation. We also studied the light-induced covalent dimerization of encapsulated anthracenes and found large effects of confinement on reaction rates. By coupling the photodimerization with the rapid guest exchange, we developed a new way to modulate fluorescence using external irradiation."}],"publication_status":"published"},{"page":"1183-1186","date_published":"2022-05-12T00:00:00Z","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"publication_identifier":{"eissn":["2451-9294"],"issn":["2451-9308"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"12","type":"journal_article","date_updated":"2023-08-02T07:24:57Z","oa_version":"Published Version","doi":"10.1016/j.chempr.2022.04.022","language":[{"iso":"eng"}],"volume":8,"issue":"5","publisher":"Elsevier","article_type":"original","intvolume":"         8","status":"public","date_created":"2023-08-01T09:32:27Z","month":"05","quality_controlled":"1","extern":"1","author":[{"full_name":"Gemen, Julius","first_name":"Julius","last_name":"Gemen"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"citation":{"apa":"Gemen, J., &#38; Klajn, R. (2022). Electron catalysis expands the supramolecular chemist’s toolbox. <i>Chem</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chempr.2022.04.022\">https://doi.org/10.1016/j.chempr.2022.04.022</a>","mla":"Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular Chemist’s Toolbox.” <i>Chem</i>, vol. 8, no. 5, Elsevier, 2022, pp. 1183–86, doi:<a href=\"https://doi.org/10.1016/j.chempr.2022.04.022\">10.1016/j.chempr.2022.04.022</a>.","chicago":"Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular Chemist’s Toolbox.” <i>Chem</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.chempr.2022.04.022\">https://doi.org/10.1016/j.chempr.2022.04.022</a>.","short":"J. Gemen, R. Klajn, Chem 8 (2022) 1183–1186.","ista":"Gemen J, Klajn R. 2022. Electron catalysis expands the supramolecular chemist’s toolbox. Chem. 8(5), 1183–1186.","ama":"Gemen J, Klajn R. Electron catalysis expands the supramolecular chemist’s toolbox. <i>Chem</i>. 2022;8(5):1183-1186. doi:<a href=\"https://doi.org/10.1016/j.chempr.2022.04.022\">10.1016/j.chempr.2022.04.022</a>","ieee":"J. Gemen and R. Klajn, “Electron catalysis expands the supramolecular chemist’s toolbox,” <i>Chem</i>, vol. 8, no. 5. Elsevier, pp. 1183–1186, 2022."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2022.04.022"}],"year":"2022","oa":1,"_id":"13351","publication":"Chem","title":"Electron catalysis expands the supramolecular chemist’s toolbox","publication_status":"published","abstract":[{"text":"Molecular recognition is at the heart of the noncovalent synthesis of supramolecular assemblies and, at higher length scales, supramolecular materials. In a recent publication in Nature, Stoddart and co-workers demonstrate that the formation of host-guest complexes can be catalyzed by one of the simplest possible catalysts: the electron.","lang":"eng"}]},{"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0009","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","day":"11","date_updated":"2025-05-26T09:05:09Z","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"scopus_import":"1","date_published":"2022-04-11T00:00:00Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"file":[{"file_size":1349672,"content_type":"application/pdf","creator":"dernst","date_created":"2022-08-02T06:14:32Z","relation":"main_file","access_level":"open_access","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","date_updated":"2022-08-02T06:14:32Z","file_id":"11719","success":1}],"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"publication_status":"published","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"oa":1,"ddc":["570"],"related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"_id":"10787","title":"The response of a metapopulation to a changing environment","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","pmid":1,"year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O"}],"quality_controlled":"1","citation":{"chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>."},"status":"public","date_created":"2022-02-21T16:08:10Z","month":"04","isi":1,"intvolume":"       377","article_type":"original","publisher":"The Royal Society","file_date_updated":"2022-08-02T06:14:32Z","volume":377,"issue":"1848"},{"page":"193-201","date_published":"2022-03-03T00:00:00Z","external_id":{"isi":["000763879400001"]},"keyword":["Process Chemistry and Technology","Biochemistry","Bioengineering","Catalysis"],"publication_identifier":{"issn":["2520-1158"]},"scopus_import":"1","day":"03","type":"journal_article","date_updated":"2023-10-17T13:06:28Z","oa_version":"Preprint","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (grant nos. 51773092, 21975124, 11874254, 51802187 and U2030206). It was further supported by Fujian science & technology innovation laboratory for energy devices of China (21C-LAB), Key Research Project of Zhejiang Laboratory (grant no. 2021PE0AC02) and the Cultivation Program for the Excellent Doctoral Dissertation of Nanjing Tech University. S.A.F. is indebted to IST Austria for support.","language":[{"iso":"eng"}],"doi":"10.1038/s41929-022-00752-z","department":[{"_id":"StFr"}],"publisher":"Springer Nature","article_type":"original","volume":5,"status":"public","date_created":"2022-03-04T07:50:10Z","month":"03","isi":1,"intvolume":"         5","year":"2022","author":[{"full_name":"Cao, Deqing","first_name":"Deqing","last_name":"Cao"},{"full_name":"Shen, Xiaoxiao","last_name":"Shen","first_name":"Xiaoxiao"},{"first_name":"Aiping","last_name":"Wang","full_name":"Wang, Aiping"},{"full_name":"Yu, Fengjiao","last_name":"Yu","first_name":"Fengjiao"},{"full_name":"Wu, Yuping","last_name":"Wu","first_name":"Yuping"},{"full_name":"Shi, Siqi","first_name":"Siqi","last_name":"Shi"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21203/rs.3.rs-750965/v1"}],"citation":{"apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (2022). Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>","mla":"Cao, Deqing, et al. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>, vol. 5, Springer Nature, 2022, pp. 193–201, doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Nature Catalysis 5 (2022) 193–201.","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>.","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. 2022. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. Nature Catalysis. 5, 193–201.","ieee":"D. Cao <i>et al.</i>, “Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries,” <i>Nature Catalysis</i>, vol. 5. Springer Nature, pp. 193–201, 2022.","ama":"Cao D, Shen X, Wang A, et al. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. 2022;5:193-201. doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>"},"publication_status":"published","abstract":[{"text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li–S and Li–O2 batteries by shuttling electrons or holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics but with the lowest possible overpotential. However, the dependence of kinetics and overpotential is unclear, which hinders informed improvement. Here, we find that when the redox potentials of mediators are tuned via, for example, Li+ concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediator and electrolyte. The acceleration originates from the overpotentials required to activate fast Li+/e− extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids therefore requires careful consideration of the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.","lang":"eng"}],"oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9978"}]},"_id":"10813","title":"Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries","publication":"Nature Catalysis"},{"publication_identifier":{"issn":["2211-1247"]},"date_published":"2022-04-05T00:00:00Z","file":[{"file_id":"11164","date_updated":"2022-04-15T09:06:25Z","success":1,"access_level":"open_access","file_name":"2022_CellReports_Villa.pdf","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","date_created":"2022-04-15T09:06:25Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":"7808644"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2022.110615","has_accepted_license":"1","department":[{"_id":"JoDa"},{"_id":"GaNo"}],"date_updated":"2024-03-25T23:30:25Z","type":"journal_article","oa_version":"Published Version","day":"05","article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-15T09:03:10Z","month":"04","status":"public","article_number":"110615","intvolume":"        39","isi":1,"file_date_updated":"2022-04-15T09:06:25Z","article_type":"original","publisher":"Elsevier","issue":"1","volume":39,"project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"publication":"Cell Reports","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","pmid":1,"ddc":["570"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12364"}]},"oa":1,"_id":"11160","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","citation":{"mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022."},"author":[{"first_name":"Carlo Emanuele","last_name":"Villa","full_name":"Villa, Carlo Emanuele"},{"full_name":"Cheroni, Cristina","first_name":"Cristina","last_name":"Cheroni"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"},{"full_name":"López-Tóbon, Alejandro","first_name":"Alejandro","last_name":"López-Tóbon"},{"first_name":"Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara"},{"first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto"},{"last_name":"Yahya","first_name":"Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87","full_name":"Yahya, Aysan Çerağ"},{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"full_name":"Gabriele, Michele","first_name":"Michele","last_name":"Gabriele"},{"orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Gabitto, Mariano","first_name":"Mariano","last_name":"Gabitto"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Testa, Giuseppe","first_name":"Giuseppe","last_name":"Testa"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"quality_controlled":"1"},{"author":[{"full_name":"Nicolas, William J.","first_name":"William J.","last_name":"Nicolas"},{"orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler"},{"full_name":"Dutka, Przemysław","last_name":"Dutka","first_name":"Przemysław"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"},{"first_name":"Grant","last_name":"Jensen","full_name":"Jensen, Grant"},{"first_name":"Elliot","last_name":"Meyerowitz","full_name":"Meyerowitz, Elliot"}],"quality_controlled":"1","citation":{"ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>."},"year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"11351","ddc":["570"],"oa":1,"pmid":1,"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","publication":"Current Biology","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"publication_status":"published","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"volume":32,"issue":"11","article_type":"original","publisher":"Elsevier","file_date_updated":"2022-08-05T06:29:18Z","isi":1,"intvolume":"        32","status":"public","month":"06","date_created":"2022-05-04T06:22:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"06","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-03T07:05:36Z","has_accepted_license":"1","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2022.04.024","acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","page":"P2375-2389","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"file":[{"date_created":"2022-08-05T06:29:18Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":12827717,"file_id":"11730","date_updated":"2022-08-05T06:29:18Z","success":1,"access_level":"open_access","checksum":"af3f24d97c016d844df237abef987639","file_name":"2022_CurrentBiology_Nicolas.pdf"}],"external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"date_published":"2022-06-06T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0960-9822"]}},{"scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"file":[{"creator":"dernst","content_type":"application/pdf","file_size":6945191,"date_created":"2022-05-13T09:10:51Z","relation":"main_file","access_level":"open_access","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","file_name":"2022_NatureCommunications_Radler.pdf","file_id":"11374","date_updated":"2022-05-13T09:10:51Z","success":1}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"external_id":{"isi":["000795171100037"]},"date_published":"2022-05-12T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"department":[{"_id":"MaLo"}],"has_accepted_license":"1","doi":"10.1038/s41467-022-30301-y","language":[{"iso":"eng"}],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","date_updated":"2024-02-21T12:35:18Z","type":"journal_article","day":"12","intvolume":"        13","isi":1,"month":"05","date_created":"2022-05-13T09:06:28Z","status":"public","article_number":"2635","volume":13,"file_date_updated":"2022-05-13T09:10:51Z","publisher":"Springer Nature","article_type":"original","publication":"Nature Communications","title":"In vitro reconstitution of Escherichia coli divisome activation","_id":"11373","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14280"},{"relation":"research_data","status":"public","id":"10934"}],"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}]},"ddc":["570"],"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"abstract":[{"lang":"eng","text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ."}],"publication_status":"published","citation":{"apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>"},"quality_controlled":"1","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp"},{"full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S."},{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","first_name":"Paulo R"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","first_name":"Maria D"},{"first_name":"David","last_name":"Michalik","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022"},{"scopus_import":"1","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"file":[{"date_created":"2022-06-20T07:51:32Z","relation":"main_file","file_size":463025,"creator":"dernst","content_type":"application/pdf","date_updated":"2022-06-20T07:51:32Z","file_id":"11455","success":1,"access_level":"open_access","file_name":"2022_BulletinMathBiology_Saona.pdf","checksum":"05a1fe7d10914a00c2bca9b447993a65"}],"external_id":{"isi":["000812509800001"]},"date_published":"2022-06-17T00:00:00Z","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"doi":"10.1007/s11538-022-01029-z","language":[{"iso":"eng"}],"ec_funded":1,"day":"17","oa_version":"Published Version","date_updated":"2023-08-03T07:20:53Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","article_number":"74","status":"public","month":"06","date_created":"2022-06-17T16:16:15Z","isi":1,"intvolume":"        84","article_type":"original","publisher":"Springer Nature","file_date_updated":"2022-06-20T07:51:32Z","volume":84,"issue":"8","abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"publication_status":"published","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"}],"_id":"11447","oa":1,"ddc":["510","570"],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"publication":"Bulletin of Mathematical Biology","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","author":[{"last_name":"Saona Urmeneta","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kseniia","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"citation":{"ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>"}},{"day":"05","date_updated":"2023-08-03T07:20:15Z","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","doi":"10.7554/elife.75842","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"has_accepted_license":"1","ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_published":"2022-05-05T00:00:00Z","file":[{"file_id":"11454","date_updated":"2022-06-20T07:44:19Z","success":1,"access_level":"open_access","checksum":"7573c28f44028ab0cc81faef30039e44","file_name":"2022_eLife_Somermeyer.pdf","date_created":"2022-06-20T07:44:19Z","relation":"main_file","file_size":5297213,"creator":"dernst","content_type":"application/pdf"}],"external_id":{"isi":["000799197200001"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publication_identifier":{"issn":["2050-084X"]},"scopus_import":"1","year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","first_name":"Louisa","last_name":"Gonzalez Somermeyer"},{"last_name":"Fleiss","first_name":"Aubin","full_name":"Fleiss, Aubin"},{"first_name":"Alexander S","last_name":"Mishin","full_name":"Mishin, Alexander S"},{"last_name":"Bozhanova","first_name":"Nina G","full_name":"Bozhanova, Nina G"},{"last_name":"Igolkina","first_name":"Anna A","full_name":"Igolkina, Anna A"},{"full_name":"Meiler, Jens","first_name":"Jens","last_name":"Meiler"},{"first_name":"Maria-Elisenda","last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda"},{"first_name":"Ekaterina V","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V"},{"full_name":"Sarkisyan, Karen S","first_name":"Karen S","last_name":"Sarkisyan"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"}],"quality_controlled":"1","citation":{"ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering."}],"project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"oa":1,"ddc":["570"],"_id":"11448","publication":"eLife","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","publisher":"eLife Sciences Publications","article_type":"original","file_date_updated":"2022-06-20T07:44:19Z","volume":11,"article_number":"75842","status":"public","date_created":"2022-06-18T09:06:59Z","month":"05","isi":1,"intvolume":"        11"},{"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"external_id":{"isi":["000812317300005"]},"file":[{"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","access_level":"open_access","success":1,"file_id":"12479","date_updated":"2023-02-02T08:20:29Z","file_size":920304,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-02-02T08:20:29Z"}],"date_published":"2022-08-01T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-03T11:55:42Z","day":"01","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"has_accepted_license":"1","doi":"10.1098/rstb.2021.0203","language":[{"iso":"eng"}],"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","volume":377,"issue":"1856","file_date_updated":"2023-02-02T08:20:29Z","publisher":"Royal Society of London","article_type":"original","intvolume":"       377","isi":1,"month":"08","date_created":"2022-07-08T11:41:56Z","article_number":"20210203","status":"public","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>."},"quality_controlled":"1","author":[{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","title":"Inversions and parallel evolution","_id":"11546","ddc":["570"],"oa":1,"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166"}],"abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"publication_status":"published"},{"file":[{"file_size":1545310,"creator":"dernst","content_type":"application/pdf","date_created":"2022-08-01T09:24:42Z","relation":"main_file","access_level":"open_access","checksum":"008156e5340e9789f0f6d82bde4d347a","file_name":"2022_BMCResearchNotes_Nikolic.pdf","date_updated":"2022-08-01T09:24:42Z","file_id":"11714","success":1}],"external_id":{"pmid":["35562780"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"date_published":"2022-05-13T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["1756-0500"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","date_updated":"2022-08-01T09:27:40Z","day":"13","department":[{"_id":"CaGu"}],"has_accepted_license":"1","doi":"10.1186/s13104-022-06061-9","language":[{"iso":"eng"}],"acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","volume":15,"file_date_updated":"2022-08-01T09:24:42Z","publisher":"Springer Nature","article_type":"letter_note","intvolume":"        15","month":"05","date_created":"2022-08-01T09:04:27Z","status":"public","article_number":"173","citation":{"mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>","ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173."},"quality_controlled":"1","author":[{"first_name":"Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sauert","first_name":"Martina","full_name":"Sauert, Martina"},{"full_name":"Albanese, Tanino G.","first_name":"Tanino G.","last_name":"Albanese"},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","pmid":1,"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","publication":"BMC Research Notes","_id":"11713","ddc":["570"],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"oa":1,"project":[{"_id":"26956E74-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","grant_number":"V00738"}],"abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}],"publication_status":"published"},{"volume":13,"article_type":"original","publisher":"Springer Nature","file_date_updated":"2022-08-26T11:51:40Z","isi":1,"intvolume":"        13","article_number":"4826","status":"public","month":"08","date_created":"2022-08-24T08:25:50Z","author":[{"first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","first_name":"Philipp"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L"},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"}],"quality_controlled":"1","citation":{"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.","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>","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>.","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>.","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>"},"year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"11951","ddc":["570"],"oa":1,"title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","publication":"Nature Communications","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"}],"publication_status":"published","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"file":[{"relation":"main_file","date_created":"2022-08-26T11:51:40Z","creator":"dernst","content_type":"application/pdf","file_size":5910357,"success":1,"file_id":"11990","date_updated":"2022-08-26T11:51:40Z","checksum":"405936d9e4d33625d80c093c9713a91f","file_name":"2022_NatureCommunications_BenSimon.pdf","access_level":"open_access"}],"external_id":{"isi":["000841396400008"]},"date_published":"2022-08-16T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"16","oa_version":"Published Version","date_updated":"2023-08-03T13:01:19Z","type":"journal_article","department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41467-022-32559-8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"ec_funded":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.)."},{"isi":1,"intvolume":"         5","status":"public","article_number":"e202201568","date_created":"2022-09-06T18:45:23Z","month":"09","volume":5,"issue":"11","article_type":"original","publisher":"Life Science Alliance","file_date_updated":"2022-09-08T06:41:14Z","ddc":["570"],"oa":1,"_id":"12051","publication":"Life Science Alliance","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","publication_status":"published","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"}],"quality_controlled":"1","author":[{"last_name":"Daiß","first_name":"Julia L","full_name":"Daiß, Julia L"},{"last_name":"Pilsl","first_name":"Michael","full_name":"Pilsl, Michael"},{"first_name":"Kristina","last_name":"Straub","full_name":"Straub, Kristina"},{"full_name":"Bleckmann, Andrea","first_name":"Andrea","last_name":"Bleckmann"},{"full_name":"Höcherl, Mona","last_name":"Höcherl","first_name":"Mona"},{"full_name":"Heiss, Florian B","first_name":"Florian B","last_name":"Heiss"},{"last_name":"Abascal-Palacios","first_name":"Guillermo","full_name":"Abascal-Palacios, Guillermo"},{"first_name":"Ewan P","last_name":"Ramsay","full_name":"Ramsay, Ewan P"},{"first_name":"Katarina","last_name":"Tluckova","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","full_name":"Tluckova, Katarina"},{"last_name":"Mars","first_name":"Jean-Clement","full_name":"Mars, Jean-Clement"},{"last_name":"Fürtges","first_name":"Torben","full_name":"Fürtges, Torben"},{"first_name":"Astrid","last_name":"Bruckmann","full_name":"Bruckmann, Astrid"},{"last_name":"Rudack","first_name":"Till","full_name":"Rudack, Till"},{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Lamour, Valérie","last_name":"Lamour","first_name":"Valérie"},{"first_name":"Konstantin","last_name":"Panov","full_name":"Panov, Konstantin"},{"full_name":"Vannini, Alessandro","last_name":"Vannini","first_name":"Alessandro"},{"full_name":"Moss, Tom","last_name":"Moss","first_name":"Tom"},{"full_name":"Engel, Christoph","first_name":"Christoph","last_name":"Engel"}],"citation":{"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>","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>.","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).","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>.","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>","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."},"year":"2022","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2575-1077"]},"date_published":"2022-09-01T00:00:00Z","external_id":{"isi":["000972702600001"]},"file":[{"relation":"main_file","date_created":"2022-09-08T06:41:14Z","creator":"dernst","content_type":"application/pdf","file_size":3183129,"success":1,"date_updated":"2022-09-08T06:41:14Z","file_id":"12062","checksum":"4201d876a3e5e8b65e319d03300014ad","file_name":"2022_LifeScienceAlliance_Daiss.pdf","access_level":"open_access"}],"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"language":[{"iso":"eng"}],"doi":"10.26508/lsa.202201568","department":[{"_id":"CaBe"}],"has_accepted_license":"1","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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"01","date_updated":"2023-08-03T13:39:36Z","type":"journal_article","oa_version":"Published Version"},{"issue":"4","volume":3,"file_date_updated":"2023-01-23T09:50:51Z","article_type":"letter_note","publisher":"Elsevier","intvolume":"         3","month":"12","date_created":"2023-01-12T11:56:38Z","article_number":"101866","status":"public","citation":{"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.","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>","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (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>.","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.","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>","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>."},"author":[{"last_name":"Hübschmann","first_name":"Verena","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Medina","last_name":"Korkut","orcid":"0000-0003-4309-2251","full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2022","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","publication":"STAR Protocols","_id":"12117","ddc":["570"],"oa":1,"related_material":{"record":[{"status":"public","relation":"other","id":"11478"}]},"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"}],"abstract":[{"lang":"eng","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"}],"publication_status":"published","file":[{"checksum":"3c71b8a60633d42c2f77c49025d5559b","file_name":"2022_STARProtocols_Huebschmann.pdf","access_level":"open_access","success":1,"file_id":"12340","date_updated":"2023-01-23T09:50:51Z","creator":"dernst","content_type":"application/pdf","file_size":6251945,"relation":"main_file","date_created":"2023-01-23T09:50:51Z"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"date_published":"2022-12-16T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["2666-1667"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","date_updated":"2023-11-02T12:21:32Z","day":"16","acknowledged_ssus":[{"_id":"Bio"}],"ec_funded":1,"has_accepted_license":"1","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.xpro.2022.101866","language":[{"iso":"eng"}],"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."},{"date_created":"2023-01-12T11:57:00Z","month":"12","status":"public","intvolume":"        57","isi":1,"publisher":"Elsevier","article_type":"original","volume":57,"issue":"23","publication_status":"published","abstract":[{"lang":"eng","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."}],"publication":"Developmental Cell","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","pmid":1,"_id":"12120","year":"2022","citation":{"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>","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.","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.","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>.","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.","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>.","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>"},"quality_controlled":"1","author":[{"last_name":"Xiao","first_name":"Huixin","full_name":"Xiao, Huixin"},{"full_name":"Hu, Yumei","last_name":"Hu","first_name":"Yumei"},{"full_name":"Wang, Yaping","first_name":"Yaping","last_name":"Wang"},{"full_name":"Cheng, Jinkui","first_name":"Jinkui","last_name":"Cheng"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"first_name":"Guojingwei","last_name":"Chen","full_name":"Chen, Guojingwei"},{"full_name":"Li, Qian","first_name":"Qian","last_name":"Li"},{"full_name":"Wang, Shuwei","last_name":"Wang","first_name":"Shuwei"},{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"last_name":"Wang","first_name":"Yi","full_name":"Wang, Yi"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Li, Zhen","first_name":"Zhen","last_name":"Li"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"}],"publication_identifier":{"issn":["1534-5807"]},"scopus_import":"1","date_published":"2022-12-05T00:00:00Z","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"page":"2638-2651.e6","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).","doi":"10.1016/j.devcel.2022.11.006","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"type":"journal_article","date_updated":"2023-10-04T08:23:20Z","oa_version":"None","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No"},{"file_date_updated":"2023-01-23T11:17:33Z","publisher":"Springer Nature","article_type":"original","volume":13,"month":"11","date_created":"2023-01-12T12:02:41Z","status":"public","article_number":"6960","intvolume":"        13","isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","citation":{"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>.","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>","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.","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).","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>.","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>","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."},"author":[{"last_name":"Huang","first_name":"Jian","full_name":"Huang, Jian"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"last_name":"Malik","first_name":"Shikha","full_name":"Malik, Shikha"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"first_name":"Va","last_name":"Xiong","full_name":"Xiong, Va"},{"first_name":"Tzahi","last_name":"Arazi","full_name":"Arazi, Tzahi"},{"last_name":"Owen","first_name":"Heather A.","full_name":"Owen, Heather A."},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhao","first_name":"Dazhong","full_name":"Zhao, Dazhong"}],"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","pmid":1,"title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","publication":"Nature Communications","_id":"12130","ddc":["580"],"oa":1,"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"file":[{"content_type":"application/pdf","creator":"dernst","file_size":3375249,"date_created":"2023-01-23T11:17:33Z","relation":"main_file","access_level":"open_access","file_name":"2022_NatureCommunications_Huang.pdf","checksum":"233922a7b9507d9d48591e6799e4526e","file_id":"12346","date_updated":"2023-01-23T11:17:33Z","success":1}],"external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"date_published":"2022-11-15T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-04T08:52:01Z","day":"15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","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.","department":[{"_id":"JiFr"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41467-022-34723-6"}]