[{"publication_identifier":{"issn":["0092-8674"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2023-04-27T00:00:00Z","file":[{"creator":"dernst","file_id":"12889","relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"2023_Cell_Knaus.pdf","date_updated":"2023-05-02T09:26:21Z","checksum":"47e94fbe19e86505b429cb7a5b503ce6","file_size":15712841,"date_created":"2023-05-02T09:26:21Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/feed-them-or-lose-them/"}],"record":[{"relation":"dissertation_contains","id":"13107","status":"public"}]},"project":[{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","month":"04","has_accepted_license":"1","publication":"Cell","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"day":"27","doi":"10.1016/j.cell.2023.02.037","abstract":[{"text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.","lang":"eng"}],"year":"2023","citation":{"apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25."},"date_updated":"2024-02-07T08:03:32Z","external_id":{"isi":["000991468700001"]},"isi":1,"volume":186,"acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","ddc":["570"],"article_processing_charge":"Yes (via OA deal)","date_created":"2023-04-05T08:15:40Z","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"publication_status":"published","intvolume":"       186","title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","scopus_import":"1","_id":"12802","issue":"9","author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus"},{"first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova","first_name":"Maria"},{"full_name":"Smogavec, Mateja","last_name":"Smogavec","first_name":"Mateja"},{"last_name":"Schwarz","first_name":"Lena A.","full_name":"Schwarz, Lena A."},{"last_name":"Gorkiewicz","first_name":"Sarah","full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Knittl-Frank, Christian","first_name":"Christian","last_name":"Knittl-Frank"},{"full_name":"Tassinari, Marianna","last_name":"Tassinari","first_name":"Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e"},{"last_name":"Maulide","first_name":"Nuno","full_name":"Maulide, Nuno"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","article_type":"original","ec_funded":1,"quality_controlled":"1","page":"1950-1967.e25","file_date_updated":"2023-05-02T09:26:21Z"},{"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"file":[{"date_updated":"2022-08-02T06:14:32Z","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","content_type":"application/pdf","date_created":"2022-08-02T06:14:32Z","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","file_size":1349672,"file_id":"11719","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}],"type":"journal_article","date_published":"2022-04-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","month":"04","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"oa_version":"Published Version","ddc":["570"],"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","volume":377,"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"isi":1,"year":"2022","citation":{"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>.","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).","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>","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.","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>."},"date_updated":"2025-05-26T09:05:09Z","abstract":[{"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)’.","lang":"eng"}],"day":"11","doi":"10.1098/rstb.2021.0009","file_date_updated":"2022-08-02T06:14:32Z","quality_controlled":"1","article_type":"original","publisher":"The Royal Society","issue":"1848","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Olusanya","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","pmid":1,"_id":"10787","intvolume":"       377","title":"The response of a metapopulation to a changing environment","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-02-21T16:08:10Z","article_processing_charge":"No","publication_status":"published"},{"file":[{"content_type":"application/pdf","file_name":"2021_Glia_Basilico.pdf","date_updated":"2022-03-04T08:55:27Z","file_size":5340294,"checksum":"f10a897290e66c0a062e04ba91db6c17","date_created":"2022-03-04T08:55:27Z","creator":"dernst","file_id":"10819","access_level":"open_access","success":1,"relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_published":"2022-01-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Cellular and Molecular Neuroscience","Neurology"],"oa_version":"Published Version","month":"01","publication":"Glia","has_accepted_license":"1","acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","volume":70,"ddc":["570"],"doi":"10.1002/glia.24101","day":"01","abstract":[{"text":"Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses.","lang":"eng"}],"date_updated":"2023-09-05T16:01:23Z","year":"2022","citation":{"ista":"Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 70(1), 173–195.","short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>.","ieee":"B. Basilico <i>et al.</i>, “Microglia control glutamatergic synapses in the adult mouse hippocampus,” <i>Glia</i>, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. 2022;70(1):173-195. doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. Wiley. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>"},"isi":1,"external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"publisher":"Wiley","article_type":"original","page":"173-195","quality_controlled":"1","file_date_updated":"2022-03-04T08:55:27Z","publication_status":"published","date_created":"2022-03-04T08:53:37Z","article_processing_charge":"No","department":[{"_id":"GaNo"}],"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","intvolume":"        70","_id":"10818","pmid":1,"scopus_import":"1","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"first_name":"Laura","last_name":"Ferrucci","full_name":"Ferrucci, Laura"},{"full_name":"Ratano, Patrizia","last_name":"Ratano","first_name":"Patrizia"},{"first_name":"Maria T.","last_name":"Golia","full_name":"Golia, Maria T."},{"full_name":"Grimaldi, Alfonso","last_name":"Grimaldi","first_name":"Alfonso"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"last_name":"Ferretti","first_name":"Valentina","full_name":"Ferretti, Valentina"},{"full_name":"Reverte, Ingrid","last_name":"Reverte","first_name":"Ingrid"},{"last_name":"Sanchini","first_name":"Caterina","full_name":"Sanchini, Caterina"},{"full_name":"Marrone, Maria C.","last_name":"Marrone","first_name":"Maria C."},{"first_name":"Maria","last_name":"Giubettini","full_name":"Giubettini, Maria"},{"full_name":"De Turris, Valeria","last_name":"De Turris","first_name":"Valeria"},{"full_name":"Salerno, Debora","last_name":"Salerno","first_name":"Debora"},{"full_name":"Garofalo, Stefano","first_name":"Stefano","last_name":"Garofalo"},{"full_name":"St‐Pierre, Marie‐Kim","first_name":"Marie‐Kim","last_name":"St‐Pierre"},{"last_name":"Carrier","first_name":"Micael","full_name":"Carrier, Micael"},{"last_name":"Renzi","first_name":"Massimiliano","full_name":"Renzi, Massimiliano"},{"first_name":"Francesca","last_name":"Pagani","full_name":"Pagani, Francesca"},{"full_name":"Modi, Brijesh","last_name":"Modi","first_name":"Brijesh"},{"last_name":"Raspa","first_name":"Marcello","full_name":"Raspa, Marcello"},{"full_name":"Scavizzi, Ferdinando","last_name":"Scavizzi","first_name":"Ferdinando"},{"last_name":"Gross","first_name":"Cornelius T.","full_name":"Gross, Cornelius T."},{"last_name":"Marinelli","first_name":"Silvia","full_name":"Marinelli, Silvia"},{"full_name":"Tremblay, Marie‐Ève","first_name":"Marie‐Ève","last_name":"Tremblay"},{"full_name":"Caprioli, Daniele","last_name":"Caprioli","first_name":"Daniele"},{"full_name":"Maggi, Laura","last_name":"Maggi","first_name":"Laura"},{"last_name":"Limatola","first_name":"Cristina","full_name":"Limatola, Cristina"},{"first_name":"Silvia","last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia"},{"last_name":"Ragozzino","first_name":"Davide","full_name":"Ragozzino, Davide"}],"issue":"1"},{"has_accepted_license":"1","publication":"Cell Reports","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","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","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","article_number":"110615","month":"04","keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-04-05T00:00:00Z","publication_identifier":{"issn":["2211-1247"]},"oa":1,"file":[{"content_type":"application/pdf","file_name":"2022_CellReports_Villa.pdf","date_updated":"2022-04-15T09:06:25Z","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","file_size":"7808644","date_created":"2022-04-15T09:06:25Z","creator":"dernst","file_id":"11164","success":1,"access_level":"open_access","relation":"main_file"}],"status":"public","related_material":{"record":[{"id":"12364","relation":"dissertation_contains","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"11160","pmid":1,"issue":"1","author":[{"full_name":"Villa, Carlo Emanuele","first_name":"Carlo Emanuele","last_name":"Villa"},{"full_name":"Cheroni, Cristina","last_name":"Cheroni","first_name":"Cristina"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096"},{"last_name":"López-Tóbon","first_name":"Alejandro","full_name":"López-Tóbon, Alejandro"},{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara","last_name":"Oliveira","first_name":"Bárbara"},{"full_name":"Sacco, Roberto","first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yahya, Aysan Çerağ","last_name":"Yahya","first_name":"Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gabriele, Michele","last_name":"Gabriele","first_name":"Michele"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli"},{"first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Gabitto, Mariano","first_name":"Mariano","last_name":"Gabitto"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Giuseppe","last_name":"Testa","full_name":"Testa, Giuseppe"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"date_created":"2022-04-15T09:03:10Z","department":[{"_id":"JoDa"},{"_id":"GaNo"}],"article_processing_charge":"Yes","publication_status":"published","intvolume":"        39","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-04-15T09:06:25Z","publisher":"Elsevier","article_type":"original","citation":{"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>","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>","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>.","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.","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>.","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).","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."},"year":"2022","date_updated":"2024-03-25T23:30:25Z","external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"isi":1,"day":"05","doi":"10.1016/j.celrep.2022.110615","abstract":[{"lang":"eng","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."}],"volume":39,"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.","ddc":["570"]},{"oa_version":"Published Version","month":"06","article_number":"102350","publication":"Current Opinion in Structural Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["Molecular Biology","Structural Biology"],"publication_identifier":{"issn":["0959-440X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-06-01T00:00:00Z","type":"journal_article","file":[{"creator":"dernst","file_id":"11725","success":1,"relation":"main_file","access_level":"open_access","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","content_type":"application/pdf","date_updated":"2022-08-05T05:56:03Z","file_size":815607,"checksum":"72bdde48853643a32d42b75f54965c44","date_created":"2022-08-05T05:56:03Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","department":[{"_id":"LeSa"}],"date_created":"2022-04-15T09:32:35Z","article_processing_charge":"Yes (via OA deal)","title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","intvolume":"        74","pmid":1,"_id":"11167","scopus_import":"1","author":[{"first_name":"Domen","last_name":"Kampjut","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","article_type":"original","quality_controlled":"1","file_date_updated":"2022-08-05T05:56:03Z","doi":"10.1016/j.sbi.2022.102350","day":"01","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"date_updated":"2023-08-03T06:31:06Z","citation":{"ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022)."},"year":"2022","isi":1,"external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"volume":74,"ddc":["570"]},{"article_type":"original","publisher":"Elsevier","file_date_updated":"2022-08-05T06:29:18Z","quality_controlled":"1","page":"P2375-2389","intvolume":"        32","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","department":[{"_id":"FlSc"}],"date_created":"2022-05-04T06:22:06Z","article_processing_charge":"No","publication_status":"published","issue":"11","author":[{"last_name":"Nicolas","first_name":"William J.","full_name":"Nicolas, William J."},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"first_name":"Elliot","last_name":"Meyerowitz","full_name":"Meyerowitz, Elliot"}],"scopus_import":"1","pmid":1,"_id":"11351","ddc":["570"],"volume":32,"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.","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"}],"day":"06","doi":"10.1016/j.cub.2022.04.024","external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"isi":1,"year":"2022","citation":{"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.","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>.","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>","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>","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.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","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>."},"date_updated":"2023-08-03T07:05:36Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"month":"06","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Current Biology","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":12827717,"checksum":"af3f24d97c016d844df237abef987639","date_created":"2022-08-05T06:29:18Z","content_type":"application/pdf","file_name":"2022_CurrentBiology_Nicolas.pdf","date_updated":"2022-08-05T06:29:18Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"11730"}],"oa":1,"publication_identifier":{"issn":["0960-9822"]},"type":"journal_article","date_published":"2022-06-06T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"isi":1,"external_id":{"isi":["000795171100037"]},"date_updated":"2024-02-21T12:35:18Z","year":"2022","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>","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>","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","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>.","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>.","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).","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."},"abstract":[{"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.","lang":"eng"}],"doi":"10.1038/s41467-022-30301-y","day":"12","ddc":["570"],"volume":13,"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.","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia S."},{"last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin","first_name":"Maria D"},{"full_name":"Michalik, David","last_name":"Michalik","first_name":"David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"_id":"11373","scopus_import":"1","title":"In vitro reconstitution of Escherichia coli divisome activation","intvolume":"        13","publication_status":"published","date_created":"2022-05-13T09:06:28Z","article_processing_charge":"No","department":[{"_id":"MaLo"}],"file_date_updated":"2022-05-13T09:10:51Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Springer Nature","date_published":"2022-05-12T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2041-1723"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"relation":"dissertation_contains","id":"14280","status":"public"},{"status":"public","id":"10934","relation":"research_data"}]},"file":[{"file_name":"2022_NatureCommunications_Radler.pdf","content_type":"application/pdf","date_updated":"2022-05-13T09:10:51Z","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","file_size":6945191,"date_created":"2022-05-13T09:10:51Z","creator":"dernst","file_id":"11374","relation":"main_file","success":1,"access_level":"open_access"}],"publication":"Nature Communications","has_accepted_license":"1","month":"05","article_number":"2635","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"}],"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"]},{"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-06-20T07:51:32Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"date_created":"2022-06-17T16:16:15Z","publication_status":"published","intvolume":"        84","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","scopus_import":"1","_id":"11447","issue":"8","author":[{"first_name":"Raimundo J","last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"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.","volume":84,"ddc":["510","570"],"day":"17","doi":"10.1007/s11538-022-01029-z","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."}],"citation":{"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>.","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.","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>","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>","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).","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>."},"year":"2022","date_updated":"2023-08-03T07:20:53Z","external_id":{"isi":["000812509800001"]},"isi":1,"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"],"language":[{"iso":"eng"}],"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"oa_version":"Published Version","article_number":"74","month":"06","has_accepted_license":"1","publication":"Bulletin of Mathematical Biology","file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"11455","creator":"dernst","date_created":"2022-06-20T07:51:32Z","checksum":"05a1fe7d10914a00c2bca9b447993a65","file_size":463025,"date_updated":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","content_type":"application/pdf"}],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-06-17T00:00:00Z"},{"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>","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>","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.","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>.","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>.","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).","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."},"year":"2022","date_updated":"2023-08-03T07:20:15Z","external_id":{"isi":["000799197200001"]},"isi":1,"day":"05","doi":"10.7554/elife.75842","abstract":[{"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.","lang":"eng"}],"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.","volume":11,"ddc":["570"],"scopus_import":"1","_id":"11448","author":[{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa","last_name":"Gonzalez Somermeyer"},{"full_name":"Fleiss, Aubin","last_name":"Fleiss","first_name":"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"},{"full_name":"Igolkina, Anna A","last_name":"Igolkina","first_name":"Anna A"},{"last_name":"Meiler","first_name":"Jens","full_name":"Meiler, Jens"},{"full_name":"Alaball Pujol, Maria-Elisenda","last_name":"Alaball Pujol","first_name":"Maria-Elisenda"},{"first_name":"Ekaterina V","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V"},{"last_name":"Sarkisyan","first_name":"Karen S","full_name":"Sarkisyan, Karen S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"}],"date_created":"2022-06-18T09:06:59Z","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        11","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-06-20T07:44:19Z","publisher":"eLife Sciences Publications","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-05-05T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"oa":1,"file":[{"creator":"dernst","file_id":"11454","success":1,"access_level":"open_access","relation":"main_file","file_name":"2022_eLife_Somermeyer.pdf","content_type":"application/pdf","date_updated":"2022-06-20T07:44:19Z","checksum":"7573c28f44028ab0cc81faef30039e44","file_size":5297213,"date_created":"2022-06-20T07:44:19Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","has_accepted_license":"1","publication":"eLife","project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"article_number":"75842","month":"05","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}]},{"file_date_updated":"2022-06-24T08:22:59Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"full_name":"Schaaf, Zachary A.","first_name":"Zachary A.","last_name":"Schaaf"},{"first_name":"Lyvin","last_name":"Tat","full_name":"Tat, Lyvin"},{"last_name":"Cannizzaro","first_name":"Noemi","full_name":"Cannizzaro, Noemi"},{"first_name":"Ralph","last_name":"Green","full_name":"Green, Ralph"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S.","last_name":"Zarbalis"}],"_id":"11460","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","intvolume":"        13","publication_status":"published","article_processing_charge":"No","date_created":"2022-06-23T14:28:55Z","department":[{"_id":"SiHi"}],"ddc":["570"],"volume":13,"acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","isi":1,"external_id":{"isi":["000814641400001"]},"date_updated":"2023-08-03T07:21:32Z","citation":{"ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27."},"year":"2022","abstract":[{"text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"doi":"10.1186/s13229-022-00508-3","day":"22","language":[{"iso":"eng"}],"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"publication":"Molecular Autism","has_accepted_license":"1","month":"06","article_number":"27","oa_version":"Published Version","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"11461","creator":"dernst","date_created":"2022-06-24T08:22:59Z","checksum":"525d2618e855139089bbfc3e3d49d1b2","file_size":7552298,"date_updated":"2022-06-24T08:22:59Z","file_name":"2022_MolecularAutism_Schaaf.pdf","content_type":"application/pdf"}],"date_published":"2022-06-22T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2040-2392"]}},{"day":"01","doi":"10.1098/rstb.2021.0203","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."}],"year":"2022","citation":{"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.","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>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (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>.","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.","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>","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>"},"date_updated":"2023-08-03T11:55:42Z","external_id":{"isi":["000812317300005"]},"isi":1,"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","volume":377,"ddc":["570"],"article_processing_charge":"Yes (via OA deal)","date_created":"2022-07-08T11:41:56Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","intvolume":"       377","title":"Inversions and parallel evolution","scopus_import":"1","_id":"11546","issue":"1856","author":[{"first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"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"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"publisher":"Royal Society of London","article_type":"original","quality_controlled":"1","file_date_updated":"2023-02-02T08:20:29Z","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-08-01T00:00:00Z","file":[{"relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"12479","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_size":920304,"date_created":"2023-02-02T08:20:29Z","content_type":"application/pdf","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","date_updated":"2023-02-02T08:20:29Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"oa_version":"Published Version","article_number":"20210203","month":"08","has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","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."}],"doi":"10.1186/s13104-022-06061-9","day":"13","external_id":{"pmid":["35562780"]},"date_updated":"2022-08-01T09:27:40Z","year":"2022","citation":{"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.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","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>.","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>.","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.","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>","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>"},"ddc":["570"],"volume":15,"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.","title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","intvolume":"        15","publication_status":"published","article_processing_charge":"No","date_created":"2022-08-01T09:04:27Z","department":[{"_id":"CaGu"}],"author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","first_name":"Nela","last_name":"Nikolic"},{"first_name":"Martina","last_name":"Sauert","full_name":"Sauert, Martina"},{"last_name":"Albanese","first_name":"Tanino G.","full_name":"Albanese, Tanino G."},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"_id":"11713","pmid":1,"scopus_import":"1","article_type":"letter_note","publisher":"Springer Nature","file_date_updated":"2022-08-01T09:24:42Z","quality_controlled":"1","oa":1,"publication_identifier":{"issn":["1756-0500"]},"date_published":"2022-05-13T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_name":"2022_BMCResearchNotes_Nikolic.pdf","date_updated":"2022-08-01T09:24:42Z","file_size":1545310,"checksum":"008156e5340e9789f0f6d82bde4d347a","date_created":"2022-08-01T09:24:42Z","creator":"dernst","file_id":"11714","relation":"main_file","success":1,"access_level":"open_access"}],"month":"05","article_number":"173","oa_version":"Published Version","project":[{"grant_number":"V00738","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","call_identifier":"FWF","_id":"26956E74-B435-11E9-9278-68D0E5697425"}],"publication":"BMC Research Notes","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"]},{"quality_controlled":"1","page":"408-416","publisher":"Springer Nature","article_type":"original","scopus_import":"1","pmid":1,"_id":"13352","issue":"4","author":[{"full_name":"Cai, Jiarong","first_name":"Jiarong","last_name":"Cai"},{"full_name":"Zhang, Wei","last_name":"Zhang","first_name":"Wei"},{"full_name":"Xu, Liguang","last_name":"Xu","first_name":"Liguang"},{"full_name":"Hao, Changlong","first_name":"Changlong","last_name":"Hao"},{"last_name":"Ma","first_name":"Wei","full_name":"Ma, Wei"},{"full_name":"Sun, Maozhong","first_name":"Maozhong","last_name":"Sun"},{"full_name":"Wu, Xiaoling","last_name":"Wu","first_name":"Xiaoling"},{"full_name":"Qin, Xian","last_name":"Qin","first_name":"Xian"},{"full_name":"Colombari, Felippe Mariano","last_name":"Colombari","first_name":"Felippe Mariano"},{"full_name":"de Moura, André Farias","last_name":"de Moura","first_name":"André Farias"},{"last_name":"Xu","first_name":"Jiahui","full_name":"Xu, Jiahui"},{"full_name":"Silva, Mariana Cristina","first_name":"Mariana Cristina","last_name":"Silva"},{"full_name":"Carneiro-Neto, Evaldo Batista","first_name":"Evaldo Batista","last_name":"Carneiro-Neto"},{"last_name":"Gomes","first_name":"Weverson Rodrigues","full_name":"Gomes, Weverson Rodrigues"},{"first_name":"Renaud A. L.","last_name":"Vallée","full_name":"Vallée, Renaud A. L."},{"full_name":"Pereira, Ernesto Chaves","last_name":"Pereira","first_name":"Ernesto Chaves"},{"first_name":"Xiaogang","last_name":"Liu","full_name":"Liu, Xiaogang"},{"full_name":"Xu, Chuanlai","first_name":"Chuanlai","last_name":"Xu"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"},{"full_name":"Kotov, Nicholas A.","last_name":"Kotov","first_name":"Nicholas A."},{"last_name":"Kuang","first_name":"Hua","full_name":"Kuang, Hua"}],"date_created":"2023-08-01T09:32:40Z","article_processing_charge":"No","publication_status":"published","intvolume":"        17","title":"Polarization-sensitive optoionic membranes from chiral plasmonic nanoparticles","volume":17,"extern":"1","year":"2022","citation":{"apa":"Cai, J., Zhang, W., Xu, L., Hao, C., Ma, W., Sun, M., … Kuang, H. (2022). Polarization-sensitive optoionic membranes from chiral plasmonic nanoparticles. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-022-01079-3\">https://doi.org/10.1038/s41565-022-01079-3</a>","ama":"Cai J, Zhang W, Xu L, et al. Polarization-sensitive optoionic membranes from chiral plasmonic nanoparticles. <i>Nature Nanotechnology</i>. 2022;17(4):408-416. doi:<a href=\"https://doi.org/10.1038/s41565-022-01079-3\">10.1038/s41565-022-01079-3</a>","chicago":"Cai, Jiarong, Wei Zhang, Liguang Xu, Changlong Hao, Wei Ma, Maozhong Sun, Xiaoling Wu, et al. “Polarization-Sensitive Optoionic Membranes from Chiral Plasmonic Nanoparticles.” <i>Nature Nanotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41565-022-01079-3\">https://doi.org/10.1038/s41565-022-01079-3</a>.","ieee":"J. Cai <i>et al.</i>, “Polarization-sensitive optoionic membranes from chiral plasmonic nanoparticles,” <i>Nature Nanotechnology</i>, vol. 17, no. 4. Springer Nature, pp. 408–416, 2022.","mla":"Cai, Jiarong, et al. “Polarization-Sensitive Optoionic Membranes from Chiral Plasmonic Nanoparticles.” <i>Nature Nanotechnology</i>, vol. 17, no. 4, Springer Nature, 2022, pp. 408–16, doi:<a href=\"https://doi.org/10.1038/s41565-022-01079-3\">10.1038/s41565-022-01079-3</a>.","short":"J. Cai, W. Zhang, L. Xu, C. Hao, W. Ma, M. Sun, X. Wu, X. Qin, F.M. Colombari, A.F. de Moura, J. Xu, M.C. Silva, E.B. Carneiro-Neto, W.R. Gomes, R.A.L. Vallée, E.C. Pereira, X. Liu, C. Xu, R. Klajn, N.A. Kotov, H. Kuang, Nature Nanotechnology 17 (2022) 408–416.","ista":"Cai J, Zhang W, Xu L, Hao C, Ma W, Sun M, Wu X, Qin X, Colombari FM, de Moura AF, Xu J, Silva MC, Carneiro-Neto EB, Gomes WR, Vallée RAL, Pereira EC, Liu X, Xu C, Klajn R, Kotov NA, Kuang H. 2022. Polarization-sensitive optoionic membranes from chiral plasmonic nanoparticles. Nature Nanotechnology. 17(4), 408–416."},"date_updated":"2023-08-02T09:44:31Z","external_id":{"pmid":["35288671"]},"day":"14","doi":"10.1038/s41565-022-01079-3","abstract":[{"text":"Optoelectronic effects differentiating absorption of right and left circularly polarized photons in thin films of chiral materials are typically prohibitively small for their direct photocurrent observation. Chiral metasurfaces increase the electronic sensitivity to circular polarization, but their out-of-plane architecture entails manufacturing and performance trade-offs. Here, we show that nanoporous thin films of chiral nanoparticles enable high sensitivity to circular polarization due to light-induced polarization-dependent ion accumulation at nanoparticle interfaces. Self-assembled multilayers of gold nanoparticles modified with L-phenylalanine generate a photocurrent under right-handed circularly polarized light as high as 2.41 times higher than under left-handed circularly polarized light. The strong plasmonic coupling between the multiple nanoparticles producing planar chiroplasmonic modes facilitates the ejection of electrons, whose entrapment at the membrane–electrolyte interface is promoted by a thick layer of enantiopure phenylalanine. Demonstrated detection of light ellipticity with equal sensitivity at all incident angles mimics phenomenological aspects of polarization vision in marine animals. The simplicity of self-assembly and sensitivity of polarization detection found in optoionic membranes opens the door to a family of miniaturized fluidic devices for chiral photonics.","lang":"eng"}],"keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"language":[{"iso":"eng"}],"publication":"Nature Nanotechnology","oa_version":"Published Version","month":"03","main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03623036/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","date_published":"2022-03-14T00:00:00Z","publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"oa":1},{"issue":"9","author":[{"last_name":"Heide","first_name":"Christian","full_name":"Heide, Christian"},{"first_name":"Yuki","last_name":"Kobayashi","full_name":"Kobayashi, Yuki"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Jain","first_name":"Deepti","full_name":"Jain, Deepti"},{"first_name":"Jonathan A.","last_name":"Sobota","full_name":"Sobota, Jonathan A."},{"full_name":"Hashimoto, Makoto","last_name":"Hashimoto","first_name":"Makoto"},{"full_name":"Kirchmann, Patrick S.","first_name":"Patrick S.","last_name":"Kirchmann"},{"full_name":"Oh, Seongshik","last_name":"Oh","first_name":"Seongshik"},{"full_name":"Heinz, Tony F.","first_name":"Tony F.","last_name":"Heinz"},{"first_name":"David A.","last_name":"Reis","full_name":"Reis, David A."},{"first_name":"Shambhu","last_name":"Ghimire","full_name":"Ghimire, Shambhu"}],"scopus_import":"1","_id":"13991","intvolume":"        16","title":"Probing topological phase transitions using high-harmonic generation","date_created":"2023-08-09T13:07:51Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","page":"620-624","article_type":"original","publisher":"Springer Nature","citation":{"ista":"Heide C, Kobayashi Y, Baykusheva DR, Jain D, Sobota JA, Hashimoto M, Kirchmann PS, Oh S, Heinz TF, Reis DA, Ghimire S. 2022. Probing topological phase transitions using high-harmonic generation. Nature Photonics. 16(9), 620–624.","short":"C. Heide, Y. Kobayashi, D.R. Baykusheva, D. Jain, J.A. Sobota, M. Hashimoto, P.S. Kirchmann, S. Oh, T.F. Heinz, D.A. Reis, S. Ghimire, Nature Photonics 16 (2022) 620–624.","mla":"Heide, Christian, et al. “Probing Topological Phase Transitions Using High-Harmonic Generation.” <i>Nature Photonics</i>, vol. 16, no. 9, Springer Nature, 2022, pp. 620–24, doi:<a href=\"https://doi.org/10.1038/s41566-022-01050-7\">10.1038/s41566-022-01050-7</a>.","chicago":"Heide, Christian, Yuki Kobayashi, Denitsa Rangelova Baykusheva, Deepti Jain, Jonathan A. Sobota, Makoto Hashimoto, Patrick S. Kirchmann, et al. “Probing Topological Phase Transitions Using High-Harmonic Generation.” <i>Nature Photonics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41566-022-01050-7\">https://doi.org/10.1038/s41566-022-01050-7</a>.","ieee":"C. Heide <i>et al.</i>, “Probing topological phase transitions using high-harmonic generation,” <i>Nature Photonics</i>, vol. 16, no. 9. Springer Nature, pp. 620–624, 2022.","ama":"Heide C, Kobayashi Y, Baykusheva DR, et al. Probing topological phase transitions using high-harmonic generation. <i>Nature Photonics</i>. 2022;16(9):620-624. doi:<a href=\"https://doi.org/10.1038/s41566-022-01050-7\">10.1038/s41566-022-01050-7</a>","apa":"Heide, C., Kobayashi, Y., Baykusheva, D. R., Jain, D., Sobota, J. A., Hashimoto, M., … Ghimire, S. (2022). Probing topological phase transitions using high-harmonic generation. <i>Nature Photonics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41566-022-01050-7\">https://doi.org/10.1038/s41566-022-01050-7</a>"},"year":"2022","date_updated":"2023-08-22T07:20:09Z","abstract":[{"text":"The prediction and realization of topological insulators have sparked great interest in experimental approaches to the classification of materials1,2,3. The phase transition between non-trivial and trivial topological states is important, not only for basic materials science but also for next-generation technology, such as dissipation-free electronics4. It is therefore crucial to develop advanced probes that are suitable for a wide range of samples and environments. Here we demonstrate that circularly polarized laser-field-driven high-harmonic generation is distinctly sensitive to the non-trivial and trivial topological phases in the prototypical three-dimensional topological insulator bismuth selenide5. The phase transition is chemically initiated by reducing the spin–orbit interaction strength through the substitution of bismuth with indium atoms6,7. We find strikingly different high-harmonic responses of trivial and non-trivial topological surface states that manifest themselves as a conversion efficiency and elliptical dichroism that depend both on the driving laser ellipticity and the crystal orientation. The origins of the anomalous high-harmonic response are corroborated by calculations using the semiconductor optical Bloch equations with pairs of surface and bulk bands. As a purely optical approach, this method offers sensitivity to the electronic structure of the material, including its nonlinear response, and is compatible with a wide range of samples and sample environments.","lang":"eng"}],"day":"01","doi":"10.1038/s41566-022-01050-7","extern":"1","volume":16,"publication":"Nature Photonics","month":"09","oa_version":"None","keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-09-01T00:00:00Z","publication_identifier":{"eissn":["1749-4893"],"issn":["1749-4885"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"article_number":"4826","month":"08","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"has_accepted_license":"1","publication":"Nature Communications","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"11990","creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2022-08-26T11:51:40Z","file_name":"2022_NatureCommunications_BenSimon.pdf","content_type":"application/pdf","date_created":"2022-08-26T11:51:40Z","file_size":5910357,"checksum":"405936d9e4d33625d80c093c9713a91f"}],"oa":1,"publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","date_published":"2022-08-16T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"Springer Nature","file_date_updated":"2022-08-26T11:51:40Z","ec_funded":1,"quality_controlled":"1","intvolume":"        13","title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","date_created":"2022-08-24T08:25:50Z","department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"article_processing_charge":"No","publication_status":"published","author":[{"full_name":"Ben Simon, Yoav","last_name":"Ben Simon","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"_id":"11951","ddc":["570"],"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.).","volume":13,"abstract":[{"lang":"eng","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."}],"day":"16","doi":"10.1038/s41467-022-32559-8","external_id":{"isi":["000841396400008"]},"isi":1,"citation":{"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>","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>","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.","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>.","mla":"Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>, vol. 13, 4826, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>.","short":"Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas, Nature Communications 13 (2022).","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."},"year":"2022","date_updated":"2023-08-03T13:01:19Z"},{"file":[{"file_id":"12062","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-09-08T06:41:14Z","content_type":"application/pdf","file_name":"2022_LifeScienceAlliance_Daiss.pdf","date_created":"2022-09-08T06:41:14Z","checksum":"4201d876a3e5e8b65e319d03300014ad","file_size":3183129}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-09-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2575-1077"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"publication":"Life Science Alliance","has_accepted_license":"1","oa_version":"Published Version","month":"09","article_number":"e202201568","acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","volume":5,"ddc":["570"],"date_updated":"2023-08-03T13:39:36Z","year":"2022","citation":{"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>.","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.","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>","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>","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.","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).","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>."},"isi":1,"external_id":{"isi":["000972702600001"]},"doi":"10.26508/lsa.202201568","day":"01","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","file_date_updated":"2022-09-08T06:41:14Z","publisher":"Life Science Alliance","article_type":"original","_id":"12051","author":[{"full_name":"Daiß, Julia L","first_name":"Julia L","last_name":"Daiß"},{"full_name":"Pilsl, Michael","first_name":"Michael","last_name":"Pilsl"},{"full_name":"Straub, Kristina","first_name":"Kristina","last_name":"Straub"},{"full_name":"Bleckmann, Andrea","first_name":"Andrea","last_name":"Bleckmann"},{"last_name":"Höcherl","first_name":"Mona","full_name":"Höcherl, Mona"},{"full_name":"Heiss, Florian B","last_name":"Heiss","first_name":"Florian B"},{"first_name":"Guillermo","last_name":"Abascal-Palacios","full_name":"Abascal-Palacios, Guillermo"},{"full_name":"Ramsay, Ewan P","first_name":"Ewan P","last_name":"Ramsay"},{"full_name":"Tluckova, Katarina","first_name":"Katarina","last_name":"Tluckova","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jean-Clement","last_name":"Mars","full_name":"Mars, Jean-Clement"},{"full_name":"Fürtges, Torben","last_name":"Fürtges","first_name":"Torben"},{"full_name":"Bruckmann, Astrid","last_name":"Bruckmann","first_name":"Astrid"},{"last_name":"Rudack","first_name":"Till","full_name":"Rudack, Till"},{"first_name":"Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lamour, Valérie","last_name":"Lamour","first_name":"Valérie"},{"full_name":"Panov, Konstantin","last_name":"Panov","first_name":"Konstantin"},{"full_name":"Vannini, Alessandro","last_name":"Vannini","first_name":"Alessandro"},{"last_name":"Moss","first_name":"Tom","full_name":"Moss, Tom"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"}],"issue":"11","publication_status":"published","article_processing_charge":"No","department":[{"_id":"CaBe"}],"date_created":"2022-09-06T18:45:23Z","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","intvolume":"         5"},{"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","intvolume":"         3","publication_status":"published","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"article_processing_charge":"No","date_created":"2023-01-12T11:56:38Z","author":[{"first_name":"Verena","last_name":"Hübschmann","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korkut","first_name":"Medina","full_name":"Korkut, Medina","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","_id":"12117","scopus_import":"1","article_type":"letter_note","publisher":"Elsevier","file_date_updated":"2023-01-23T09:50:51Z","quality_controlled":"1","ec_funded":1,"abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"doi":"10.1016/j.xpro.2022.101866","day":"16","date_updated":"2023-11-02T12:21:32Z","citation":{"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>.","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.","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>","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","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>.","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022)."},"year":"2022","ddc":["570"],"volume":3,"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.","month":"12","article_number":"101866","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"},{"grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"publication":"STAR Protocols","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"oa":1,"publication_identifier":{"issn":["2666-1667"]},"date_published":"2022-12-16T00:00:00Z","type":"journal_article","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"},"related_material":{"record":[{"status":"public","id":"11478","relation":"other"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"content_type":"application/pdf","file_name":"2022_STARProtocols_Huebschmann.pdf","date_updated":"2023-01-23T09:50:51Z","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_size":6251945,"date_created":"2023-01-23T09:50:51Z","creator":"dernst","file_id":"12340","relation":"main_file","success":1,"access_level":"open_access"}]},{"isi":1,"external_id":{"isi":["000919603800005"],"pmid":["36473460"]},"date_updated":"2023-10-04T08:23:20Z","year":"2022","citation":{"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.","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>"},"abstract":[{"text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.","lang":"eng"}],"doi":"10.1016/j.devcel.2022.11.006","day":"05","volume":57,"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).","author":[{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"last_name":"Hu","first_name":"Yumei","full_name":"Hu, Yumei"},{"full_name":"Wang, Yaping","first_name":"Yaping","last_name":"Wang"},{"first_name":"Jinkui","last_name":"Cheng","full_name":"Cheng, Jinkui"},{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"last_name":"Chen","first_name":"Guojingwei","full_name":"Chen, Guojingwei"},{"full_name":"Li, Qian","first_name":"Qian","last_name":"Li"},{"full_name":"Wang, Shuwei","first_name":"Shuwei","last_name":"Wang"},{"first_name":"Yalu","last_name":"Wang","full_name":"Wang, Yalu"},{"last_name":"Wang","first_name":"Shao-Shuai","full_name":"Wang, Shao-Shuai"},{"full_name":"Wang, Yi","first_name":"Yi","last_name":"Wang"},{"full_name":"Xuan, Wei","first_name":"Wei","last_name":"Xuan"},{"full_name":"Li, Zhen","last_name":"Li","first_name":"Zhen"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"}],"issue":"23","_id":"12120","pmid":1,"scopus_import":"1","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","intvolume":"        57","publication_status":"published","date_created":"2023-01-12T11:57:00Z","department":[{"_id":"JiFr"}],"article_processing_charge":"No","page":"2638-2651.e6","quality_controlled":"1","article_type":"original","publisher":"Elsevier","date_published":"2022-12-05T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1534-5807"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Developmental Cell","month":"12","oa_version":"None","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"]},{"has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"6960","month":"11","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-11-15T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"oa":1,"file":[{"file_id":"12346","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2023-01-23T11:17:33Z","content_type":"application/pdf","file_name":"2022_NatureCommunications_Huang.pdf","date_created":"2023-01-23T11:17:33Z","file_size":3375249,"checksum":"233922a7b9507d9d48591e6799e4526e"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","pmid":1,"_id":"12130","author":[{"full_name":"Huang, Jian","first_name":"Jian","last_name":"Huang"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"full_name":"Malik, Shikha","first_name":"Shikha","last_name":"Malik"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"last_name":"Xiong","first_name":"Va","full_name":"Xiong, Va"},{"first_name":"Tzahi","last_name":"Arazi","full_name":"Arazi, Tzahi"},{"full_name":"Owen, Heather A.","last_name":"Owen","first_name":"Heather A."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhao, Dazhong","last_name":"Zhao","first_name":"Dazhong"}],"date_created":"2023-01-12T12:02:41Z","article_processing_charge":"No","department":[{"_id":"JiFr"}],"publication_status":"published","intvolume":"        13","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","quality_controlled":"1","file_date_updated":"2023-01-23T11:17:33Z","publisher":"Springer Nature","article_type":"original","citation":{"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>","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>","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>.","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.","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).","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>.","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."},"year":"2022","date_updated":"2023-08-04T08:52:01Z","external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"isi":1,"day":"15","doi":"10.1038/s41467-022-34723-6","abstract":[{"lang":"eng","text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants."}],"volume":13,"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.","ddc":["580"]},{"doi":"10.3389/fncel.2022.1022431","day":"04","abstract":[{"lang":"eng","text":"Microglia are dynamic cells, constantly surveying their surroundings and interacting with neurons and synapses. Indeed, a wealth of knowledge has revealed a critical role of microglia in modulating synaptic transmission and plasticity in the developing brain. In the past decade, novel pharmacological and genetic strategies have allowed the acute removal of microglia, opening the possibility to explore and understand the role of microglia also in the adult brain. In this review, we summarized and discussed the contribution of microglia depletion strategies to the current understanding of the role of microglia on synaptic function, learning and memory, and behavior both in physiological and pathological conditions. We first described the available microglia depletion methods highlighting their main strengths and weaknesses. We then reviewed the impact of microglia depletion on structural and functional synaptic plasticity. Next, we focused our analysis on the effects of microglia depletion on behavior, including general locomotor activity, sensory perception, motor function, sociability, learning and memory both in healthy animals and animal models of disease. Finally, we integrated the findings from the reviewed studies and discussed the emerging roles of microglia on the maintenance of synaptic function, learning, memory strength and forgetfulness, and the implications of microglia depletion in models of brain disease."}],"date_updated":"2023-08-04T08:56:10Z","year":"2022","citation":{"apa":"Basilico, B., Ferrucci, L., Khan, A., Di Angelantonio, S., Ragozzino, D., &#38; Reverte, I. (2022). What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncel.2022.1022431\">https://doi.org/10.3389/fncel.2022.1022431</a>","ama":"Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I. What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. <i>Frontiers in Cellular Neuroscience</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fncel.2022.1022431\">10.3389/fncel.2022.1022431</a>","chicago":"Basilico, Bernadette, Laura Ferrucci, Azka Khan, Silvia Di Angelantonio, Davide Ragozzino, and Ingrid Reverte. “What Microglia Depletion Approaches Tell Us about the Role of Microglia on Synaptic Function and Behavior.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fncel.2022.1022431\">https://doi.org/10.3389/fncel.2022.1022431</a>.","ieee":"B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, and I. Reverte, “What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior,” <i>Frontiers in Cellular Neuroscience</i>, vol. 16. Frontiers Media, 2022.","mla":"Basilico, Bernadette, et al. “What Microglia Depletion Approaches Tell Us about the Role of Microglia on Synaptic Function and Behavior.” <i>Frontiers in Cellular Neuroscience</i>, vol. 16, 1022431, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fncel.2022.1022431\">10.3389/fncel.2022.1022431</a>.","short":"B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, I. Reverte, Frontiers in Cellular Neuroscience 16 (2022).","ista":"Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I. 2022. What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. Frontiers in Cellular Neuroscience. 16, 1022431."},"isi":1,"external_id":{"pmid":["36406752"],"isi":["000886526600001"]},"acknowledgement":"The write-up of the review was supported by Sapienza University of Rome (Fondi di Ateneo, grant numbers #MA32117A7B698029 and #PH12017270934C3C to SD), Regione Lazio (POR FSE 2014/20, grant number #19036AP000000019 to SD), Fulbright 2019 (grant number\r\n#FSP-P005556 to SD), Institute Pasteur Italia (Fondi Cenci Bolognetti #363 to DR), and Network of European Funding for Neuroscience Research (ERA-NET NEURON Transnational\r\nResearch Projects on Neurodevelopmental Disorders 2021, grant acronym #JTC2021-SHANKAstro to DR).","volume":16,"ddc":["570"],"publication_status":"published","date_created":"2023-01-12T12:04:50Z","department":[{"_id":"GaNo"}],"article_processing_charge":"No","title":"What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior","intvolume":"        16","_id":"12140","pmid":1,"scopus_import":"1","author":[{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"full_name":"Ferrucci, Laura","first_name":"Laura","last_name":"Ferrucci"},{"first_name":"Azka","last_name":"Khan","full_name":"Khan, Azka"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","first_name":"Davide","last_name":"Ragozzino"},{"full_name":"Reverte, Ingrid","first_name":"Ingrid","last_name":"Reverte"}],"publisher":"Frontiers Media","article_type":"original","quality_controlled":"1","file_date_updated":"2023-01-24T09:16:29Z","publication_identifier":{"issn":["1662-5102"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-11-04T00:00:00Z","type":"journal_article","file":[{"file_id":"12352","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-01-24T09:16:29Z","content_type":"application/pdf","file_name":"2022_FrontiersNeuroscience_Basilico.pdf","date_created":"2023-01-24T09:16:29Z","file_size":6399987,"checksum":"84696213ecf99182c58a9f34b9ff2e23"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"11","article_number":"1022431","publication":"Frontiers in Cellular Neuroscience","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["Cellular and Molecular Neuroscience"]}]