[{"publication":"Bulletin of Mathematical Biology","language":[{"iso":"eng"}],"intvolume":"        84","scopus_import":"1","has_accepted_license":"1","isi":1,"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","oa":1,"date_updated":"2023-08-03T07:20:53Z","issue":"8","article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","day":"17","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"05a1fe7d10914a00c2bca9b447993a65","file_id":"11455","file_name":"2022_BulletinMathBiology_Saona.pdf","success":1,"date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":463025}],"publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"month":"06","author":[{"first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6246-1465","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","first_name":"Kseniia"}],"doi":"10.1007/s11538-022-01029-z","file_date_updated":"2022-06-20T07:51:32Z","article_type":"original","_id":"11447","ec_funded":1,"article_number":"74","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"date_created":"2022-06-17T16:16:15Z","citation":{"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>","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","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>","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","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."},"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"],"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.","year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"quality_controlled":"1","volume":84,"publisher":"Springer Nature","date_published":"2022-06-17T00:00:00Z","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"}],"external_id":{"isi":["000812509800001"]},"abstract":[{"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.","lang":"eng"}],"ddc":["510","570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published"},{"year":"2022","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.","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_created":"2022-06-18T09:06:59Z","citation":{"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.","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>.","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>.","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","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).","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>"},"article_number":"75842","ec_funded":1,"article_type":"original","_id":"11448","file_date_updated":"2022-06-20T07:44:19Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.7554/elife.75842","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering."}],"external_id":{"isi":["000799197200001"]},"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2022-05-05T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","volume":11,"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"article_processing_charge":"No","oa":1,"date_updated":"2023-08-03T07:20:15Z","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"        11","language":[{"iso":"eng"}],"publication":"eLife","author":[{"first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fleiss","full_name":"Fleiss, Aubin","first_name":"Aubin"},{"first_name":"Alexander S","full_name":"Mishin, Alexander S","last_name":"Mishin"},{"last_name":"Bozhanova","first_name":"Nina G","full_name":"Bozhanova, Nina G"},{"last_name":"Igolkina","full_name":"Igolkina, Anna A","first_name":"Anna A"},{"last_name":"Meiler","full_name":"Meiler, Jens","first_name":"Jens"},{"last_name":"Alaball Pujol","first_name":"Maria-Elisenda","full_name":"Alaball Pujol, Maria-Elisenda"},{"full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V","last_name":"Putintseva"},{"full_name":"Sarkisyan, Karen S","first_name":"Karen S","last_name":"Sarkisyan"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"publication_identifier":{"issn":["2050-084X"]},"month":"05","file":[{"date_created":"2022-06-20T07:44:19Z","date_updated":"2022-06-20T07:44:19Z","success":1,"file_name":"2022_eLife_Somermeyer.pdf","checksum":"7573c28f44028ab0cc81faef30039e44","file_id":"11454","access_level":"open_access","relation":"main_file","file_size":5297213,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"05","status":"public","type":"journal_article"},{"article_type":"original","_id":"11546","file_date_updated":"2023-02-02T08:20:29Z","doi":"10.1098/rstb.2021.0203","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"date_created":"2022-07-08T11:41:56Z","citation":{"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>.","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>.","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.","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.","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>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (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>"},"year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","article_number":"20210203","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","volume":377,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2022-08-01T00:00:00Z","publisher":"Royal Society of London","publication_status":"published","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."}],"external_id":{"isi":["000812317300005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","title":"Inversions and parallel evolution","issue":"1856","article_processing_charge":"Yes (via OA deal)","oa":1,"date_updated":"2023-08-03T11:55:42Z","scopus_import":"1","has_accepted_license":"1","intvolume":"       377","isi":1,"type":"journal_article","status":"public","author":[{"orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"file":[{"file_id":"12479","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","success":1,"date_updated":"2023-02-02T08:20:29Z","date_created":"2023-02-02T08:20:29Z","creator":"dernst","file_size":920304,"access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"01","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"08"},{"doi":"10.1186/s13104-022-06061-9","_id":"11713","article_type":"letter_note","file_date_updated":"2022-08-01T09:24:42Z","article_number":"173","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"year":"2022","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.","keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"date_created":"2022-08-01T09:04:27Z","citation":{"mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","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.","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>.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","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>"},"date_published":"2022-05-13T00:00:00Z","publisher":"Springer Nature","volume":15,"quality_controlled":"1","department":[{"_id":"CaGu"}],"project":[{"call_identifier":"FWF","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","_id":"26956E74-B435-11E9-9278-68D0E5697425","grant_number":"V00738"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}],"external_id":{"pmid":["35562780"]},"publication_status":"published","publication":"BMC Research Notes","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"        15","scopus_import":"1","article_processing_charge":"No","date_updated":"2022-08-01T09:27:40Z","oa":1,"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","status":"public","type":"journal_article","pmid":1,"month":"05","publication_identifier":{"issn":["1756-0500"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"008156e5340e9789f0f6d82bde4d347a","file_name":"2022_BMCResearchNotes_Nikolic.pdf","file_id":"11714","success":1,"date_updated":"2022-08-01T09:24:42Z","date_created":"2022-08-01T09:24:42Z","creator":"dernst","file_size":1545310,"relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"day":"13","oa_version":"Published Version","author":[{"orcid":"0000-0001-9068-6090","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","first_name":"Nela"},{"last_name":"Sauert","first_name":"Martina","full_name":"Sauert, Martina"},{"first_name":"Tanino G.","full_name":"Albanese, Tanino G.","last_name":"Albanese"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}]},{"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.).","year":"2022","date_created":"2022-08-24T08:25:50Z","citation":{"ama":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>","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.","short":"Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas, Nature Communications 13 (2022).","chicago":"Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>.","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>.","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.","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>"},"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"ec_funded":1,"article_number":"4826","file_date_updated":"2022-08-26T11:51:40Z","_id":"11951","article_type":"original","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"doi":"10.1038/s41467-022-32559-8","publication_status":"published","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000841396400008"]},"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."}],"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","date_published":"2022-08-16T00:00:00Z","department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"volume":13,"quality_controlled":"1","date_updated":"2023-08-03T13:01:19Z","oa":1,"article_processing_charge":"No","title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","isi":1,"intvolume":"        13","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Nature Communications","author":[{"full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","full_name":"Käfer, Karola"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"month":"08","publication_identifier":{"issn":["2041-1723"]},"oa_version":"Published Version","day":"16","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":5910357,"creator":"dernst","date_updated":"2022-08-26T11:51:40Z","date_created":"2022-08-26T11:51:40Z","file_id":"11990","checksum":"405936d9e4d33625d80c093c9713a91f","file_name":"2022_NatureCommunications_BenSimon.pdf","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","type":"journal_article"},{"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"abstract":[{"lang":"eng","text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1"}],"project":[{"call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571"},{"grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2022-12-16T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":3,"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"year":"2022","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.","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"date_created":"2023-01-12T11:56:38Z","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>.","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).","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>","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>"},"article_number":"101866","related_material":{"record":[{"status":"public","relation":"other","id":"11478"}]},"ec_funded":1,"article_type":"letter_note","_id":"12117","file_date_updated":"2023-01-23T09:50:51Z","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.xpro.2022.101866","author":[{"id":"32B7C918-F248-11E8-B48F-1D18A9856A87","last_name":"Hübschmann","full_name":"Hübschmann, Verena","first_name":"Verena"},{"orcid":"0000-0003-4309-2251","last_name":"Korkut","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina","full_name":"Korkut, Medina"},{"first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2666-1667"]},"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"12340","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_name":"2022_STARProtocols_Huebschmann.pdf","success":1,"date_updated":"2023-01-23T09:50:51Z","date_created":"2023-01-23T09:50:51Z","creator":"dernst","file_size":6251945,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","day":"16","status":"public","type":"journal_article","article_processing_charge":"No","issue":"4","oa":1,"date_updated":"2023-11-02T12:21:32Z","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","scopus_import":"1","has_accepted_license":"1","intvolume":"         3","language":[{"iso":"eng"}],"publication":"STAR Protocols"},{"publication":"Developmental Cell","language":[{"iso":"eng"}],"isi":1,"intvolume":"        57","scopus_import":"1","issue":"23","article_processing_charge":"No","date_updated":"2023-10-04T08:23:20Z","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","status":"public","type":"journal_article","pmid":1,"publication_identifier":{"issn":["1534-5807"]},"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"05","author":[{"first_name":"Huixin","full_name":"Xiao, Huixin","last_name":"Xiao"},{"last_name":"Hu","first_name":"Yumei","full_name":"Hu, Yumei"},{"last_name":"Wang","full_name":"Wang, Yaping","first_name":"Yaping"},{"first_name":"Jinkui","full_name":"Cheng, Jinkui","last_name":"Cheng"},{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"full_name":"Chen, Guojingwei","first_name":"Guojingwei","last_name":"Chen"},{"last_name":"Li","full_name":"Li, Qian","first_name":"Qian"},{"first_name":"Shuwei","full_name":"Wang, Shuwei","last_name":"Wang"},{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"last_name":"Wang","full_name":"Wang, Shao-Shuai","first_name":"Shao-Shuai"},{"first_name":"Yi","full_name":"Wang, Yi","last_name":"Wang"},{"first_name":"Wei","full_name":"Xuan, Wei","last_name":"Xuan"},{"last_name":"Li","full_name":"Li, Zhen","first_name":"Zhen"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"last_name":"Gong","full_name":"Gong, Zhizhong","first_name":"Zhizhong"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"doi":"10.1016/j.devcel.2022.11.006","article_type":"original","_id":"12120","year":"2022","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).","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"date_created":"2023-01-12T11:57:00Z","citation":{"short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","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>.","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>"},"date_published":"2022-12-05T00:00:00Z","publisher":"Elsevier","volume":57,"quality_controlled":"1","page":"2638-2651.e6","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth."}],"external_id":{"isi":["000919603800005"],"pmid":["36473460"]},"publication_status":"published"},{"date_published":"2022-11-15T00:00:00Z","publisher":"Springer Nature","volume":13,"quality_controlled":"1","department":[{"_id":"JiFr"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["580"],"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."}],"external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"publication_status":"published","doi":"10.1038/s41467-022-34723-6","_id":"12130","article_type":"original","file_date_updated":"2023-01-23T11:17:33Z","article_number":"6960","year":"2022","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.","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_created":"2023-01-12T12:02:41Z","citation":{"short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","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.","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>","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.","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>"},"status":"public","type":"journal_article","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2023-01-23T11:17:33Z","date_created":"2023-01-23T11:17:33Z","checksum":"233922a7b9507d9d48591e6799e4526e","file_name":"2022_NatureCommunications_Huang.pdf","file_id":"12346","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":3375249,"creator":"dernst"}],"oa_version":"Published Version","day":"15","author":[{"last_name":"Huang","first_name":"Jian","full_name":"Huang, Jian"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"full_name":"Malik, Shikha","first_name":"Shikha","last_name":"Malik"},{"last_name":"Gentile","full_name":"Gentile, Benjamin R.","first_name":"Benjamin R."},{"full_name":"Xiong, Va","first_name":"Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","first_name":"Tzahi","last_name":"Arazi"},{"full_name":"Owen, Heather A.","first_name":"Heather A.","last_name":"Owen"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"Dazhong","full_name":"Zhao, Dazhong","last_name":"Zhao"}],"publication":"Nature Communications","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","has_accepted_license":"1","intvolume":"        13","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T08:52:01Z","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis"},{"article_number":"2868","year":"2021","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_created":"2023-02-20T08:11:29Z","citation":{"chicago":"Miles, Evan, Michael McCarthy, Amaury Dehecq, Marin Kneib, Stefan Fugger, and Francesca Pellicciotti. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>.","ista":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. 2021. Health and sustainability of glaciers in High Mountain Asia. Nature Communications. 12, 2868.","mla":"Miles, Evan, et al. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>, vol. 12, 2868, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>.","ama":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>","ieee":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, and F. Pellicciotti, “Health and sustainability of glaciers in High Mountain Asia,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","short":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, F. Pellicciotti, Nature Communications 12 (2021).","apa":"Miles, E., McCarthy, M., Dehecq, A., Kneib, M., Fugger, S., &#38; Pellicciotti, F. (2021). Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>"},"doi":"10.1038/s41467-021-23073-4","article_type":"original","_id":"12585","abstract":[{"lang":"eng","text":"Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly."}],"publication_status":"published","date_published":"2021-05-17T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","volume":12,"extern":"1","intvolume":"        12","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-02-28T13:21:51Z","oa":1,"title":"Health and sustainability of glaciers in High Mountain Asia","publication":"Nature Communications","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","main_file_link":[{"url":"https://doi.org/10.1038/s41467-021-23073-4","open_access":"1"}],"oa_version":"Published Version","author":[{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"full_name":"McCarthy, Michael","first_name":"Michael","last_name":"McCarthy"},{"last_name":"Dehecq","first_name":"Amaury","full_name":"Dehecq, Amaury"},{"last_name":"Kneib","first_name":"Marin","full_name":"Kneib, Marin"},{"full_name":"Fugger, Stefan","first_name":"Stefan","last_name":"Fugger"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca"}],"status":"public","type":"journal_article"},{"department":[{"_id":"GradSch"}],"quality_controlled":"1","volume":524,"publisher":"Elsevier ","date_published":"2021-04-24T00:00:00Z","publication_status":"published","external_id":{"isi":["000659161500002"]},"abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"article_type":"original","_id":"9387","doi":"10.1016/j.jtbi.2021.110729","citation":{"short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier , 2021.","chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>.","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>"},"date_created":"2021-05-12T05:58:42Z","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","year":"2021","article_number":"110729","status":"public","type":"journal_article","author":[{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","orcid":"0000-0002-6246-1465","first_name":"Kseniia","full_name":"Khudiakova, Kseniia"},{"last_name":"Neretina","first_name":"Tatiana Yu.","full_name":"Neretina, Tatiana Yu."},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"oa_version":"Preprint","day":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0022-5193"]},"month":"04","language":[{"iso":"eng"}],"publication":"Journal of Theoretical Biology","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","oa":1,"date_updated":"2023-08-08T13:32:40Z","article_processing_charge":"No","intvolume":"       524","isi":1},{"publication_identifier":{"eissn":["1749-6632"],"issn":["0077-8923"]},"month":"12","day":"01","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1111/nyas.14674","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bian, Tong","first_name":"Tong","last_name":"Bian"},{"first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"}],"pmid":1,"status":"public","type":"journal_article","scopus_import":"1","intvolume":"      1505","date_updated":"2023-08-07T10:01:10Z","oa":1,"issue":"1","article_processing_charge":"No","title":"Morphology control in crystalline nanoparticle–polymer aggregates","publication":"Annals of the New York Academy of Sciences","language":[{"iso":"eng"}],"ddc":["540"],"external_id":{"pmid":["34427923"]},"abstract":[{"lang":"eng","text":"Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained."}],"publication_status":"published","publisher":"Wiley","date_published":"2021-12-01T00:00:00Z","page":"191-201","extern":"1","quality_controlled":"1","volume":1505,"year":"2021","date_created":"2023-08-01T09:33:39Z","citation":{"apa":"Bian, T., &#38; Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer aggregates. <i>Annals of the New York Academy of Sciences</i>. Wiley. <a href=\"https://doi.org/10.1111/nyas.14674\">https://doi.org/10.1111/nyas.14674</a>","mla":"Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” <i>Annals of the New York Academy of Sciences</i>, vol. 1505, no. 1, Wiley, 2021, pp. 191–201, doi:<a href=\"https://doi.org/10.1111/nyas.14674\">10.1111/nyas.14674</a>.","chicago":"Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” <i>Annals of the New York Academy of Sciences</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nyas.14674\">https://doi.org/10.1111/nyas.14674</a>.","ista":"Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.","ieee":"T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer aggregates,” <i>Annals of the New York Academy of Sciences</i>, vol. 1505, no. 1. Wiley, pp. 191–201, 2021.","ama":"Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates. <i>Annals of the New York Academy of Sciences</i>. 2021;1505(1):191-201. doi:<a href=\"https://doi.org/10.1111/nyas.14674\">10.1111/nyas.14674</a>","short":"T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021) 191–201."},"keyword":["History and Philosophy of Science","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"doi":"10.1111/nyas.14674","article_type":"original","_id":"13356"},{"type":"journal_article","status":"public","month":"10","publication_identifier":{"eissn":["2041-1723"]},"file":[{"file_name":"2021_NatComm_Appel.pdf","file_id":"10169","checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"date_updated":"2021-10-21T13:51:49Z","date_created":"2021-10-21T13:51:49Z","creator":"cchlebak","file_size":5111706,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"19","author":[{"full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie","last_name":"Appel"},{"first_name":"Vedran","full_name":"Franke, Vedran","last_name":"Franke"},{"last_name":"Bruno","first_name":"Melania","full_name":"Bruno, Melania"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"last_name":"Kasiliauskaite","first_name":"Aiste","full_name":"Kasiliauskaite, Aiste"},{"last_name":"Kaufmann","full_name":"Kaufmann, Tanja","first_name":"Tanja"},{"last_name":"Schoeberl","first_name":"Ursula E.","full_name":"Schoeberl, Ursula E."},{"full_name":"Puchinger, Martin G.","first_name":"Martin G.","last_name":"Puchinger"},{"last_name":"Kostrhon","full_name":"Kostrhon, Sebastian","first_name":"Sebastian"},{"last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen","first_name":"Carmen"},{"first_name":"Marek","full_name":"Sebesta, Marek","last_name":"Sebesta"},{"last_name":"Beltzung","full_name":"Beltzung, Etienne","first_name":"Etienne"},{"last_name":"Mechtler","first_name":"Karl","full_name":"Mechtler, Karl"},{"last_name":"Lin","full_name":"Lin, Gen","first_name":"Gen"},{"last_name":"Vlasova","full_name":"Vlasova, Anna","first_name":"Anna"},{"last_name":"Leeb","first_name":"Martin","full_name":"Leeb, Martin"},{"full_name":"Pavri, Rushad","first_name":"Rushad","last_name":"Pavri"},{"first_name":"Alexander","full_name":"Stark, Alexander","last_name":"Stark"},{"last_name":"Akalin","full_name":"Akalin, Altuna","first_name":"Altuna"},{"first_name":"Richard","full_name":"Stefl, Richard","last_name":"Stefl"},{"last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A"},{"last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina"},{"last_name":"Slade","full_name":"Slade, Dea","first_name":"Dea"}],"publication":"Nature Communications","language":[{"iso":"eng"}],"isi":1,"intvolume":"        12","has_accepted_license":"1","article_processing_charge":"No","issue":"1","oa":1,"date_updated":"2023-08-14T08:02:31Z","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","date_published":"2021-10-19T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","volume":12,"department":[{"_id":"CaBe"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["610"],"abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"external_id":{"isi":["000709050300001"]},"publication_status":"published","doi":"10.1038/s41467-021-26360-2","_id":"10163","article_type":"original","file_date_updated":"2021-10-21T13:51:49Z","article_number":"6078","related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","description":"Preprint ","relation":"earlier_version"}]},"year":"2021","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"date_created":"2021-10-20T14:40:32Z","citation":{"apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>","ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021)."}},{"department":[{"_id":"GaNo"}],"volume":10,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_published":"2021-11-17T00:00:00Z","publication_status":"published","external_id":{"isi":["000720945900001"]},"abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-11-18T07:02:02Z","article_type":"original","_id":"10301","doi":"10.7554/elife.71575","citation":{"mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>, vol. 10, e71575, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>.","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>.","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ieee":"M. J. Conde-Dusman <i>et al.</i>, “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>"},"date_created":"2021-11-18T06:59:45Z","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","year":"2021","article_number":"e71575","type":"journal_article","status":"public","author":[{"full_name":"Conde-Dusman, María J","first_name":"María J","last_name":"Conde-Dusman"},{"last_name":"Dey","full_name":"Dey, Partha N","first_name":"Partha N"},{"last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar","first_name":"Óscar"},{"full_name":"Garcia Rabaneda, Luis E","first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","full_name":"García-Lira, Carmen","last_name":"García-Lira"},{"full_name":"Grand, Teddy","first_name":"Teddy","last_name":"Grand"},{"full_name":"Briz, Victor","first_name":"Victor","last_name":"Briz"},{"first_name":"Eric R","full_name":"Velasco, Eric R","last_name":"Velasco"},{"first_name":"Raül","full_name":"Andero Galí, Raül","last_name":"Andero Galí"},{"first_name":"Sergio","full_name":"Niñerola, Sergio","last_name":"Niñerola"},{"last_name":"Barco","full_name":"Barco, Angel","first_name":"Angel"},{"last_name":"Paoletti","full_name":"Paoletti, Pierre","first_name":"Pierre"},{"full_name":"Wesseling, John F","first_name":"John F","last_name":"Wesseling"},{"full_name":"Gardoni, Fabrizio","first_name":"Fabrizio","last_name":"Gardoni"},{"full_name":"Tavalin, Steven J","first_name":"Steven J","last_name":"Tavalin"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"oa_version":"Published Version","day":"17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":2477302,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"lgarciar","date_created":"2021-11-18T07:02:02Z","date_updated":"2021-11-18T07:02:02Z","success":1,"file_id":"10302","file_name":"elife-71575-v1.pdf","checksum":"59318e9e41507cec83c2f4070e6ad540"}],"month":"11","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"publication":"eLife","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","date_updated":"2023-08-14T11:50:50Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","intvolume":"        10","isi":1},{"author":[{"orcid":"0000-0002-3219-2022","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","first_name":"Mehmet Orkun"},{"full_name":"Frank, Anna","first_name":"Anna","last_name":"Frank"},{"full_name":"Tanaka, Hideaki","first_name":"Hideaki","last_name":"Tanaka"},{"full_name":"Kawamoto, Akihiro","first_name":"Akihiro","last_name":"Kawamoto"},{"full_name":"El-Mohsnawy, Eithar","first_name":"Eithar","last_name":"El-Mohsnawy"},{"first_name":"Takayuki","full_name":"Kato, Takayuki","last_name":"Kato"},{"first_name":"Keiichi","full_name":"Namba, Keiichi","last_name":"Namba"},{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"full_name":"Nowaczyk, Marc M.","first_name":"Marc M.","last_name":"Nowaczyk"},{"last_name":"Kurisu","full_name":"Kurisu, Genji","first_name":"Genji"}],"file":[{"file_id":"10318","file_name":"2021_CommBio_Çoruh.pdf","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"date_updated":"2021-11-19T15:09:18Z","date_created":"2021-11-19T15:09:18Z","creator":"cchlebak","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":6030261}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"08","oa_version":"Published Version","month":"03","publication_identifier":{"issn":["2399-3642"]},"status":"public","type":"journal_article","pmid":1,"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","article_processing_charge":"No","issue":"1","oa":1,"date_updated":"2023-08-14T11:51:19Z","has_accepted_license":"1","scopus_import":"1","intvolume":"         4","isi":1,"language":[{"iso":"eng"}],"publication":"Communications Biology","publication_status":"published","abstract":[{"text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.","lang":"eng"}],"external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"volume":4,"quality_controlled":"1","department":[{"_id":"LeSa"}],"date_published":"2021-03-08T00:00:00Z","publisher":"Springer ","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"date_created":"2021-11-19T11:37:29Z","citation":{"apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. Springer . <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>. Springer , 2021. <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>.","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>, vol. 4, no. 1, 304, Springer , 2021, doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>","ieee":"M. O. Çoruh <i>et al.</i>, “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” <i>Communications Biology</i>, vol. 4, no. 1. Springer , 2021."},"year":"2021","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","article_number":"304","_id":"10310","article_type":"original","file_date_updated":"2021-11-19T15:09:18Z","doi":"10.1038/s42003-021-01808-9"},{"publication":"Nature Communications","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"        12","isi":1,"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","date_updated":"2024-09-10T12:04:26Z","oa":1,"article_processing_charge":"No","issue":"1","status":"public","type":"journal_article","day":"24","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"kschuh","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":9358599,"success":1,"checksum":"337e0f7959c35ec959984cacdcb472ba","file_name":"2021_NatureCommunications_Morandell.pdf","file_id":"9430","date_created":"2021-05-28T12:39:43Z","date_updated":"2021-05-28T12:39:43Z"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"05","author":[{"first_name":"Jasmin","full_name":"Morandell, Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","full_name":"Schwarz, Lena A"},{"full_name":"Basilico, Bernadette","first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico"},{"first_name":"Saren","full_name":"Tasciyan, Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel","full_name":"Nicolas, Armel"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph"},{"first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe","first_name":"Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1038/s41467-021-23123-x","acknowledged_ssus":[{"_id":"PreCl"}],"file_date_updated":"2021-05-28T12:39:43Z","_id":"9429","article_type":"original","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"id":"7800","relation":"earlier_version","status":"public"},{"id":"12401","relation":"dissertation_contains","status":"public"}]},"article_number":"3058","citation":{"ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>"},"date_created":"2021-05-28T11:49:46Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","year":"2021","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"quality_controlled":"1","volume":12,"publisher":"Springer Nature","date_published":"2021-05-24T00:00:00Z","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy"},{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF"}],"external_id":{"isi":["000658769900010"]},"abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"ddc":["572"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published"},{"type":"journal_article","status":"public","author":[{"full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr"},{"last_name":"Ricana","full_name":"Ricana, Clifton L.","first_name":"Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R.","last_name":"Feathers"},{"last_name":"Klanschnig","full_name":"Klanschnig, Marco","first_name":"Marco"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas","first_name":"Andreas"},{"first_name":"Marc C.","full_name":"Johnson, Marc C.","last_name":"Johnson"},{"first_name":"Volker M.","full_name":"Vogt, Volker M.","last_name":"Vogt"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"}],"file":[{"date_updated":"2021-06-09T15:21:14Z","date_created":"2021-06-09T15:21:14Z","file_name":"2021_NatureCommunications_Obr.pdf","file_id":"9538","checksum":"53ccc53d09a9111143839dbe7784e663","success":1,"relation":"main_file","file_size":6166295,"access_level":"open_access","content_type":"application/pdf","creator":"kschuh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"28","publication_identifier":{"eissn":["2041-1723"]},"month":"05","language":[{"iso":"eng"}],"publication":"Nature Communications","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","issue":"1","article_processing_charge":"No","oa":1,"date_updated":"2023-08-08T13:53:53Z","has_accepted_license":"1","intvolume":"        12","scopus_import":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","volume":12,"department":[{"_id":"FlSc"}],"date_published":"2021-05-28T00:00:00Z","publisher":"Nature Research","publication_status":"published","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"external_id":{"isi":["000659145000011"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_type":"original","_id":"9431","file_date_updated":"2021-06-09T15:21:14Z","doi":"10.1038/s41467-021-23506-0","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"citation":{"apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226."},"date_created":"2021-05-28T14:25:50Z","year":"2021","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"article_number":"3226"},{"author":[{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"first_name":"Ingrid","full_name":"Rössler, Ingrid","last_name":"Rössler"},{"last_name":"Klein","first_name":"Isabella","full_name":"Klein, Isabella"},{"first_name":"Christina","full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder"},{"last_name":"Zisser","full_name":"Zisser, Gertrude","first_name":"Gertrude"},{"last_name":"Gruber","first_name":"Christian C.","full_name":"Gruber, Christian C."},{"last_name":"Gruber","full_name":"Gruber, Karl","first_name":"Karl"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"day":"09","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"cziletti","access_level":"open_access","file_size":3397292,"content_type":"application/pdf","relation":"main_file","success":1,"checksum":"40fc24c1310930990b52a8ad1142ee97","file_name":"2021_NatureComm_Prattes.pdf","file_id":"9556","date_created":"2021-06-15T18:55:59Z","date_updated":"2021-06-15T18:55:59Z"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"06","pmid":1,"type":"journal_article","status":"public","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","oa":1,"date_updated":"2023-08-08T14:05:26Z","issue":"1","article_processing_charge":"No","has_accepted_license":"1","intvolume":"        12","isi":1,"language":[{"iso":"eng"}],"publication":"Nature Communications","publication_status":"published","external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"EM-Fac"}],"quality_controlled":"1","volume":12,"publisher":"Springer Nature","date_published":"2021-06-09T00:00:00Z","citation":{"apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483."},"date_created":"2021-06-10T14:57:45Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","year":"2021","article_number":"3483","acknowledged_ssus":[{"_id":"EM-Fac"}],"file_date_updated":"2021-06-15T18:55:59Z","article_type":"original","_id":"9540","doi":"10.1038/s41467-021-23854-x"},{"type":"journal_article","status":"public","author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","full_name":"Vandael, David H","first_name":"David H"},{"last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","first_name":"Yuji"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"}],"oa_version":"Published Version","day":"18","file":[{"date_updated":"2021-12-17T11:34:50Z","date_created":"2021-12-17T11:34:50Z","file_id":"10563","checksum":"6036a8cdae95e1707c2a04d54e325ff4","file_name":"2021_NatureCommunications_Vandael.pdf","success":1,"file_size":3108845,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"kschuh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2041-1723"]},"month":"05","language":[{"iso":"eng"}],"publication":"Nature Communications","title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","oa":1,"date_updated":"2023-08-10T14:16:16Z","article_processing_charge":"No","issue":"1","intvolume":"        12","has_accepted_license":"1","scopus_import":"1","isi":1,"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"department":[{"_id":"PeJo"}],"volume":12,"quality_controlled":"1","publisher":"Springer","date_published":"2021-05-18T00:00:00Z","publication_status":"published","external_id":{"isi":["000655481800014"]},"abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"SSU"}],"file_date_updated":"2021-12-17T11:34:50Z","_id":"9778","article_type":"original","doi":"10.1038/s41467-021-23153-5","citation":{"apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>.","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912."},"date_created":"2021-08-06T07:22:55Z","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","year":"2021","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","description":"News on IST Homepage"}]},"article_number":"2912"},{"language":[{"iso":"eng"}],"publication":"Current Biology","title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","issue":"10","article_processing_charge":"No","oa":1,"date_updated":"2023-08-17T07:01:14Z","scopus_import":"1","intvolume":"        31","isi":1,"type":"journal_article","status":"public","pmid":1,"author":[{"first_name":"Stephanie","full_name":"Stahnke, Stephanie","last_name":"Stahnke"},{"last_name":"Döring","full_name":"Döring, Hermann","first_name":"Hermann"},{"full_name":"Kusch, Charly","first_name":"Charly","last_name":"Kusch"},{"full_name":"de Gorter, David J.J.","first_name":"David J.J.","last_name":"de Gorter"},{"first_name":"Sebastian","full_name":"Dütting, Sebastian","last_name":"Dütting"},{"last_name":"Guledani","full_name":"Guledani, Aleks","first_name":"Aleks"},{"last_name":"Pleines","full_name":"Pleines, Irina","first_name":"Irina"},{"full_name":"Schnoor, Michael","first_name":"Michael","last_name":"Schnoor"},{"first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geffers","full_name":"Geffers, Robert","first_name":"Robert"},{"last_name":"Rohde","first_name":"Manfred","full_name":"Rohde, Manfred"},{"full_name":"Müsken, Mathias","first_name":"Mathias","last_name":"Müsken"},{"full_name":"Kage, Frieda","first_name":"Frieda","last_name":"Kage"},{"last_name":"Steffen","first_name":"Anika","full_name":"Steffen, Anika"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"full_name":"Nieswandt, Bernhard","first_name":"Bernhard","last_name":"Nieswandt"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"full_name":"Stradal, Theresia E.B.","first_name":"Theresia E.B.","last_name":"Stradal"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"24","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.03.24.005835"}],"oa_version":"Preprint","month":"05","publication_identifier":{"issn":["0960-9822"]},"article_type":"original","_id":"10834","doi":"10.1016/j.cub.2021.02.043","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"citation":{"apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>.","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>"},"date_created":"2022-03-08T07:51:04Z","year":"2021","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","quality_controlled":"1","volume":31,"page":"2051-2064.e8","department":[{"_id":"MiSi"}],"date_published":"2021-05-24T00:00:00Z","publisher":"Elsevier","publication_status":"published","abstract":[{"lang":"eng","text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis."}],"external_id":{"pmid":["33711252"],"isi":["000654652200002"]}},{"type":"journal_article","status":"public","pmid":1,"author":[{"last_name":"Krishna","full_name":"Krishna, Shefali","first_name":"Shefali"},{"full_name":"Arrojo e Drigo, Rafael","first_name":"Rafael","last_name":"Arrojo e Drigo"},{"last_name":"Capitanio","full_name":"Capitanio, Juliana S.","first_name":"Juliana S."},{"first_name":"Ranjan","full_name":"Ramachandra, Ranjan","last_name":"Ramachandra"},{"last_name":"Ellisman","full_name":"Ellisman, Mark","first_name":"Mark"},{"first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"month":"11","publication_identifier":{"issn":["1534-5807"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"None","day":"08","language":[{"iso":"eng"}],"publication":"Developmental Cell","issue":"21","article_processing_charge":"No","date_updated":"2022-07-18T08:26:38Z","title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain","intvolume":"        56","scopus_import":"1","date_published":"2021-11-08T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":56,"extern":"1","page":"P2952-2965.e9","publication_status":"published","abstract":[{"lang":"eng","text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function."}],"external_id":{"pmid":["34715012"]},"_id":"11052","article_type":"original","doi":"10.1016/j.devcel.2021.10.008","year":"2021","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"citation":{"apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>.","short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>"},"date_created":"2022-04-07T07:43:14Z"}]