[{"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"article_number":"e1010149","article_type":"original","ec_funded":1,"publication":"PLOS Computational Biology","day":"14","doi":"10.1371/journal.pcbi.1010149","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Direct reciprocity between individuals that use different strategy spaces","pmid":1,"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"acknowledgement":"This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG 863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2022","department":[{"_id":"KrCh"}],"article_processing_charge":"No","citation":{"mla":"Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>, vol. 18, no. 6, e1010149, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","ista":"Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 18(6), e1010149.","ama":"Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. 2022;18(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>","apa":"Schmid, L., Hilbe, C., Chatterjee, K., &#38; Nowak, M. (2022). Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>","ieee":"L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between individuals that use different strategy spaces,” <i>PLOS Computational Biology</i>, vol. 18, no. 6. Public Library of Science, 2022.","chicago":"Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>."},"has_accepted_license":"1","publisher":"Public Library of Science","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"date_created":"2023-01-30T11:28:13Z","access_level":"open_access","checksum":"31b6b311b6731f1658277a9dfff6632c","creator":"dernst","file_id":"12460","relation":"main_file","success":1,"file_size":3143222,"date_updated":"2023-01-30T11:28:13Z","content_type":"application/pdf","file_name":"2022_PlosCompBio_Schmid.pdf"}],"date_updated":"2025-07-14T09:09:49Z","oa_version":"Published Version","ddc":["000","570"],"isi":1,"status":"public","month":"06","external_id":{"pmid":["35700167"],"isi":["000843626800031"]},"date_created":"2023-01-16T10:02:51Z","publication_status":"published","file_date_updated":"2023-01-30T11:28:13Z","abstract":[{"lang":"eng","text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate."}],"scopus_import":"1","intvolume":"        18","date_published":"2022-06-14T00:00:00Z","volume":18,"author":[{"last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","first_name":"Laura","full_name":"Schmid, Laura"},{"last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"issue":"6","quality_controlled":"1","_id":"12280"},{"type":"journal_article","article_processing_charge":"No","citation":{"chicago":"Atherton, Joseph, Melissa A Stouffer, Fiona Francis, and Carolyn A. Moores. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>.","apa":"Atherton, J., Stouffer, M. A., Francis, F., &#38; Moores, C. A. (2022). Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>","ieee":"J. Atherton, M. A. Stouffer, F. Francis, and C. A. Moores, “Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography,” <i>Journal of Cell Science</i>, vol. 135, no. 7. The Company of Biologists, 2022.","ama":"Atherton J, Stouffer MA, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. 2022;135(7). doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>","ista":"Atherton J, Stouffer MA, Francis F, Moores CA. 2022. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 135(7), 259234.","short":"J. Atherton, M.A. Stouffer, F. Francis, C.A. Moores, Journal of Cell Science 135 (2022).","mla":"Atherton, Joseph, et al. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>, vol. 135, no. 7, 259234, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>."},"publisher":"The Company of Biologists","has_accepted_license":"1","date_updated":"2023-08-04T10:28:34Z","oa_version":"Published Version","isi":1,"ddc":["570"],"month":"04","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"creator":"dernst","checksum":"4346ed32cb7c89a8ca051c7da68a9a1c","date_created":"2023-01-30T11:41:01Z","access_level":"open_access","file_id":"12461","relation":"main_file","file_name":"2022_JourCellBiology_Atherton.pdf","file_size":13868733,"success":1,"content_type":"application/pdf","date_updated":"2023-01-30T11:41:01Z"}],"scopus_import":"1","external_id":{"isi":["000783840400010"],"pmid":["35383828"]},"publication_status":"published","date_created":"2023-01-16T10:03:24Z","abstract":[{"text":"Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.","lang":"eng"}],"file_date_updated":"2023-01-30T11:41:01Z","issue":"7","quality_controlled":"1","_id":"12283","date_published":"2022-04-01T00:00:00Z","intvolume":"       135","author":[{"last_name":"Atherton","first_name":"Joseph","full_name":"Atherton, Joseph"},{"full_name":"Stouffer, Melissa A","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","last_name":"Stouffer"},{"full_name":"Francis, Fiona","first_name":"Fiona","last_name":"Francis"},{"full_name":"Moores, Carolyn A.","first_name":"Carolyn A.","last_name":"Moores"}],"volume":135,"article_number":"259234","article_type":"original","keyword":["Cell Biology"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"doi":"10.1242/jcs.259234","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Journal of Cell Science","day":"01","title":"Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography","acknowledgement":"J.A. was supported by a grant from the Medical Research Council (MRC), UK (MR/R000352/1) to C.A.M. Cryo-EM data were collected on equipment funded by the Wellcome Trust, UK (079605/Z/06/Z) and the Biotechnology and Biological Sciences Research Council (BBSRC) UK (BB/L014211/1). F.F.’s salary and institute were supported by Inserm (Institut National de la Santé et de la Recherche Médicale), CNRS (Centre National de la Recherche Scientifique) and Sorbonne Université. F.F.’s group was particularly supported by Agence Nationale de la\r\nRecherche (ANR-16-CE16-0011-03) and Seventh Framework Programme (EUHEALTH-\r\n2013, DESIRE, N° 60253; also funding M.S.’s salary) and the European Cooperation in Science and Technology (COST Action CA16118). Open Access funding provided by Birkbeck College: Birkbeck University of London. Deposited in PMC for immediate release.","year":"2022","department":[{"_id":"SiHi"}],"pmid":1},{"_id":"12288","quality_controlled":"1","volume":11,"author":[{"first_name":"Anton L","full_name":"Sumser, Anton L","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser"},{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"}],"date_published":"2022-09-15T00:00:00Z","intvolume":"        11","scopus_import":"1","abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"file_date_updated":"2023-01-30T11:50:53Z","publication_status":"published","date_created":"2023-01-16T10:04:15Z","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"month":"09","status":"public","isi":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2023-08-04T10:29:48Z","file":[{"relation":"main_file","file_name":"2022_eLife_Sumser.pdf","date_updated":"2023-01-30T11:50:53Z","content_type":"application/pdf","file_size":8506811,"success":1,"creator":"dernst","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","access_level":"open_access","date_created":"2023-01-30T11:50:53Z","file_id":"12463"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","has_accepted_license":"1","publisher":"eLife Sciences Publications","citation":{"mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>","ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>."},"article_processing_charge":"No","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"year":"2022","acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.7554/elife.79848","day":"15","publication":"eLife","ec_funded":1,"article_type":"original","article_number":"79848","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"oa":1},{"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"article_type":"review","publication":"Journal of Integrative Plant Biology","day":"07","doi":"10.1111/jipb.13422","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"DNA methylation dynamics during germline development","main_file_link":[{"url":"https://doi.org/10.1111/jipb.13422","open_access":"1"}],"extern":"1","pmid":1,"year":"2022","department":[{"_id":"XiFe"}],"article_processing_charge":"No","citation":{"ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022."},"publisher":"Wiley","type":"journal_article","date_updated":"2023-05-08T10:59:00Z","oa_version":"Published Version","month":"12","status":"public","date_created":"2023-02-23T09:15:57Z","publication_status":"published","external_id":{"pmid":["36478632"]},"abstract":[{"text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.","lang":"eng"}],"scopus_import":"1","date_published":"2022-12-07T00:00:00Z","intvolume":"        64","author":[{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"page":"2240-2251","volume":64,"issue":"12","quality_controlled":"1","_id":"12670"},{"type":"journal_article","citation":{"apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848)."},"has_accepted_license":"1","publisher":"The Royal Society","article_processing_charge":"No","isi":1,"ddc":["570"],"month":"04","status":"public","date_updated":"2025-05-26T09:05:09Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"file":[{"date_created":"2022-08-02T06:14:32Z","access_level":"open_access","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","creator":"dernst","file_id":"11719","relation":"main_file","success":1,"file_size":1349672,"content_type":"application/pdf","date_updated":"2022-08-02T06:14:32Z","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf"}],"scopus_import":"1","file_date_updated":"2022-08-02T06:14:32Z","abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"date_created":"2022-02-21T16:08:10Z","publication_status":"published","_id":"10787","quality_controlled":"1","issue":"1848","intvolume":"       377","date_published":"2022-04-11T00:00:00Z","volume":377,"author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya"}],"article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1098/rstb.2021.0009","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","day":"11","title":"The response of a metapopulation to a changing environment","year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"}],"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","pmid":1},{"month":"03","status":"public","date_updated":"2022-07-18T08:58:33Z","oa_version":"None","citation":{"ieee":"J. Liu and M. Hetzer, “Nuclear pore complex maintenance and implications for age-related diseases,” <i>Trends in Cell Biology</i>, vol. 32, no. 3. Elsevier, pp. P216-227, 2022.","apa":"Liu, J., &#38; Hetzer, M. (2022). Nuclear pore complex maintenance and implications for age-related diseases. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">https://doi.org/10.1016/j.tcb.2021.10.001</a>","chicago":"Liu, Jinqiang, and Martin Hetzer. “Nuclear Pore Complex Maintenance and Implications for Age-Related Diseases.” <i>Trends in Cell Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">https://doi.org/10.1016/j.tcb.2021.10.001</a>.","short":"J. Liu, M. Hetzer, Trends in Cell Biology 32 (2022) P216-227.","mla":"Liu, Jinqiang, and Martin Hetzer. “Nuclear Pore Complex Maintenance and Implications for Age-Related Diseases.” <i>Trends in Cell Biology</i>, vol. 32, no. 3, Elsevier, 2022, pp. P216-227, doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">10.1016/j.tcb.2021.10.001</a>.","ista":"Liu J, Hetzer M. 2022. Nuclear pore complex maintenance and implications for age-related diseases. Trends in Cell Biology. 32(3), P216-227.","ama":"Liu J, Hetzer M. Nuclear pore complex maintenance and implications for age-related diseases. <i>Trends in Cell Biology</i>. 2022;32(3):P216-227. doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">10.1016/j.tcb.2021.10.001</a>"},"publisher":"Elsevier","article_processing_charge":"No","type":"journal_article","date_published":"2022-03-01T00:00:00Z","intvolume":"        32","author":[{"last_name":"Liu","full_name":"Liu, Jinqiang","first_name":"Jinqiang"},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W"}],"volume":32,"page":"P216-227","_id":"11051","issue":"3","quality_controlled":"1","abstract":[{"text":"Nuclear pore complexes (NPCs) bridge the nucleus and the cytoplasm and are indispensable for crucial cellular activities, such as bidirectional molecular trafficking and gene transcription regulation. The discovery of long-lived proteins (LLPs) in NPCs from postmitotic cells raises the exciting possibility that the maintenance of NPC integrity might play an inherent role in lifelong cell function. Age-dependent deterioration of NPCs and loss of nuclear integrity have been linked to age-related decline in postmitotic cell function and degenerative diseases. In this review, we discuss our current understanding of NPC maintenance in proliferating and postmitotic cells, and how malfunction of nucleoporins (Nups) might contribute to the pathogenesis of various neurodegenerative and cardiovascular diseases.","lang":"eng"}],"external_id":{"pmid":["34782239"]},"date_created":"2022-04-07T07:43:01Z","publication_status":"published","scopus_import":"1","publication":"Trends in Cell Biology","day":"01","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","doi":"10.1016/j.tcb.2021.10.001","publication_identifier":{"issn":["0962-8924"]},"language":[{"iso":"eng"}],"keyword":["Cell Biology"],"article_type":"review","pmid":1,"extern":"1","year":"2022","title":"Nuclear pore complex maintenance and implications for age-related diseases"},{"file":[{"file_id":"11722","access_level":"open_access","date_created":"2022-08-02T11:07:58Z","creator":"dernst","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","content_type":"application/pdf","date_updated":"2022-08-02T11:07:58Z","file_size":7080863,"success":1,"file_name":"2022_JourStructuralBiology_Obr.pdf","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","month":"06","ddc":["570"],"isi":1,"oa_version":"Published Version","date_updated":"2023-08-03T06:25:23Z","publisher":"Elsevier","has_accepted_license":"1","citation":{"chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>."},"article_processing_charge":"Yes (via OA deal)","type":"journal_article","volume":214,"author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Obr"},{"last_name":"Hagen","first_name":"Wim J.H.","full_name":"Hagen, Wim J.H."},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"full_name":"Yu, Lingbo","first_name":"Lingbo","last_name":"Yu"},{"first_name":"Abhay","full_name":"Kotecha, Abhay","last_name":"Kotecha"},{"last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"intvolume":"       214","date_published":"2022-06-01T00:00:00Z","_id":"11155","issue":"2","quality_controlled":"1","file_date_updated":"2022-08-02T11:07:58Z","abstract":[{"lang":"eng","text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes."}],"publication_status":"published","external_id":{"pmid":["35351542"],"isi":["000790733600001"]},"date_created":"2022-04-15T07:10:26Z","scopus_import":"1","day":"01","publication":"Journal of Structural Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.jsb.2022.107852","publication_identifier":{"issn":["1047-8477"]},"language":[{"iso":"eng"}],"oa":1,"keyword":["Structural Biology"],"article_type":"original","article_number":"107852","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"pmid":1,"department":[{"_id":"FlSc"}],"year":"2022","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. 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). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF"}],"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"year":"2022","department":[{"_id":"JoDa"},{"_id":"GaNo"}],"project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"call_identifier":"FWF","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","publication":"Cell Reports","day":"05","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.celrep.2022.110615","publication_identifier":{"issn":["2211-1247"]},"language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"oa":1,"ec_funded":1,"article_type":"original","article_number":"110615","intvolume":"        39","date_published":"2022-04-05T00:00:00Z","volume":39,"author":[{"last_name":"Villa","first_name":"Carlo Emanuele","full_name":"Villa, Carlo Emanuele"},{"full_name":"Cheroni, Cristina","first_name":"Cristina","last_name":"Cheroni"},{"first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter"},{"full_name":"López-Tóbon, Alejandro","first_name":"Alejandro","last_name":"López-Tóbon"},{"last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara","first_name":"Bárbara"},{"last_name":"Sacco","full_name":"Sacco, Roberto","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87","full_name":"Yahya, Aysan Çerağ","last_name":"Yahya"},{"last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","first_name":"Jasmin"},{"full_name":"Gabriele, Michele","first_name":"Michele","last_name":"Gabriele"},{"last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"full_name":"Gabitto, Mariano","first_name":"Mariano","last_name":"Gabitto"},{"first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"last_name":"Testa","first_name":"Giuseppe","full_name":"Testa, Giuseppe"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"_id":"11160","issue":"1","quality_controlled":"1","file_date_updated":"2022-04-15T09:06:25Z","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"date_created":"2022-04-15T09:03:10Z","external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","id":"12364","relation":"dissertation_contains"}]},"file":[{"relation":"main_file","file_name":"2022_CellReports_Villa.pdf","success":1,"file_size":"7808644","content_type":"application/pdf","date_updated":"2022-04-15T09:06:25Z","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","creator":"dernst","date_created":"2022-04-15T09:06:25Z","access_level":"open_access","file_id":"11164"}],"isi":1,"ddc":["570"],"month":"04","status":"public","date_updated":"2024-03-25T23:30:25Z","oa_version":"Published Version","citation":{"chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022.","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>."},"has_accepted_license":"1","publisher":"Elsevier","article_processing_charge":"Yes","type":"journal_article"},{"article_type":"original","article_number":"102350","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-440X"]},"oa":1,"keyword":["Molecular Biology","Structural Biology"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.sbi.2022.102350","day":"01","publication":"Current Opinion in Structural Biology","title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","department":[{"_id":"LeSa"}],"year":"2022","pmid":1,"type":"journal_article","has_accepted_license":"1","publisher":"Elsevier","citation":{"ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>"},"article_processing_charge":"Yes (via OA deal)","month":"06","status":"public","isi":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2023-08-03T06:31:06Z","file":[{"checksum":"72bdde48853643a32d42b75f54965c44","creator":"dernst","date_created":"2022-08-05T05:56:03Z","access_level":"open_access","file_id":"11725","relation":"main_file","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","success":1,"file_size":815607,"content_type":"application/pdf","date_updated":"2022-08-05T05:56:03Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","file_date_updated":"2022-08-05T05:56:03Z","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"publication_status":"published","date_created":"2022-04-15T09:32:35Z","_id":"11167","quality_controlled":"1","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"volume":74,"date_published":"2022-06-01T00:00:00Z","intvolume":"        74"},{"pmid":1,"project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","year":"2022","department":[{"_id":"FlSc"}],"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","publication":"Current Biology","day":"06","doi":"10.1016/j.cub.2022.04.024","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"article_type":"original","date_published":"2022-06-06T00:00:00Z","intvolume":"        32","volume":32,"page":"P2375-2389","author":[{"last_name":"Nicolas","full_name":"Nicolas, William J.","first_name":"William J."},{"last_name":"Fäßler","full_name":"Fäßler, Florian","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dutka, Przemysław","first_name":"Przemysław","last_name":"Dutka"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"last_name":"Meyerowitz","first_name":"Elliot","full_name":"Meyerowitz, Elliot"}],"issue":"11","quality_controlled":"1","_id":"11351","external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"publication_status":"published","date_created":"2022-05-04T06:22:06Z","file_date_updated":"2022-08-05T06:29:18Z","abstract":[{"lang":"eng","text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall."}],"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"11730","date_created":"2022-08-05T06:29:18Z","access_level":"open_access","creator":"dernst","checksum":"af3f24d97c016d844df237abef987639","success":1,"file_size":12827717,"date_updated":"2022-08-05T06:29:18Z","content_type":"application/pdf","file_name":"2022_CurrentBiology_Nicolas.pdf","relation":"main_file"}],"date_updated":"2023-08-03T07:05:36Z","oa_version":"Published Version","isi":1,"ddc":["570"],"status":"public","month":"06","article_processing_charge":"No","citation":{"chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389."},"has_accepted_license":"1","publisher":"Elsevier","type":"journal_article"},{"title":"In vitro reconstitution of Escherichia coli divisome activation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","year":"2022","department":[{"_id":"MaLo"}],"oa":1,"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"article_number":"2635","article_type":"original","ec_funded":1,"publication":"Nature Communications","day":"12","doi":"10.1038/s41467-022-30301-y","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-05-13T09:06:28Z","external_id":{"isi":["000795171100037"]},"publication_status":"published","file_date_updated":"2022-05-13T09:10:51Z","abstract":[{"lang":"eng","text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ."}],"scopus_import":"1","date_published":"2022-05-12T00:00:00Z","intvolume":"        13","author":[{"last_name":"Radler","full_name":"Radler, Philipp","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova"},{"last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David","last_name":"Michalik"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"}],"volume":13,"quality_controlled":"1","_id":"11373","article_processing_charge":"No","citation":{"apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>"},"has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"14280","status":"public"},{"status":"public","relation":"research_data","id":"10934"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"11374","access_level":"open_access","date_created":"2022-05-13T09:10:51Z","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","creator":"dernst","content_type":"application/pdf","date_updated":"2022-05-13T09:10:51Z","file_size":6945191,"success":1,"file_name":"2022_NatureCommunications_Radler.pdf","relation":"main_file"}],"date_updated":"2024-02-21T12:35:18Z","oa_version":"Published Version","isi":1,"ddc":["570"],"month":"05","status":"public"},{"date_created":"2022-06-17T16:16:15Z","external_id":{"isi":["000812509800001"]},"publication_status":"published","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"}],"file_date_updated":"2022-06-20T07:51:32Z","scopus_import":"1","intvolume":"        84","date_published":"2022-06-17T00:00:00Z","author":[{"last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"}],"volume":84,"quality_controlled":"1","issue":"8","_id":"11447","article_processing_charge":"Yes (via OA deal)","citation":{"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>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (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>","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.","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>","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.","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>."},"publisher":"Springer Nature","has_accepted_license":"1","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"file":[{"file_id":"11455","creator":"dernst","checksum":"05a1fe7d10914a00c2bca9b447993a65","access_level":"open_access","date_created":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","content_type":"application/pdf","date_updated":"2022-06-20T07:51:32Z","file_size":463025,"success":1,"relation":"main_file"}],"date_updated":"2023-08-03T07:20:53Z","oa_version":"Published Version","ddc":["510","570"],"isi":1,"month":"06","status":"public","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"},{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"}],"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"}],"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"],"oa":1,"publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"language":[{"iso":"eng"}],"article_number":"74","ec_funded":1,"article_type":"original","publication":"Bulletin of Mathematical Biology","day":"17","doi":"10.1007/s11538-022-01029-z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-03T07:20:15Z","oa_version":"Published Version","ddc":["570"],"isi":1,"month":"05","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"11454","creator":"dernst","checksum":"7573c28f44028ab0cc81faef30039e44","date_created":"2022-06-20T07:44:19Z","access_level":"open_access","file_name":"2022_eLife_Somermeyer.pdf","success":1,"file_size":5297213,"date_updated":"2022-06-20T07:44:19Z","content_type":"application/pdf","relation":"main_file"}],"type":"journal_article","article_processing_charge":"No","citation":{"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>.","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.","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>","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.","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>","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>."},"has_accepted_license":"1","publisher":"eLife Sciences Publications","quality_controlled":"1","_id":"11448","date_published":"2022-05-05T00:00:00Z","intvolume":"        11","volume":11,"author":[{"orcid":"0000-0001-9139-5383","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer"},{"first_name":"Aubin","full_name":"Fleiss, Aubin","last_name":"Fleiss"},{"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"},{"first_name":"Jens","full_name":"Meiler, Jens","last_name":"Meiler"},{"last_name":"Alaball Pujol","first_name":"Maria-Elisenda","full_name":"Alaball Pujol, Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"first_name":"Karen S","full_name":"Sarkisyan, Karen S","last_name":"Sarkisyan"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"}],"scopus_import":"1","publication_status":"published","date_created":"2022-06-18T09:06:59Z","external_id":{"isi":["000799197200001"]},"file_date_updated":"2022-06-20T07:44:19Z","abstract":[{"text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.","lang":"eng"}],"doi":"10.7554/elife.75842","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"eLife","day":"05","article_number":"75842","ec_funded":1,"article_type":"original","oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"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.","year":"2022","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design"},{"isi":1,"ddc":["570"],"status":"public","month":"06","date_updated":"2023-08-03T07:21:32Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"url":"https://doi.org/10.1186/s13229-023-00539-4","relation":"erratum"}]},"file":[{"relation":"main_file","file_name":"2022_MolecularAutism_Schaaf.pdf","date_updated":"2022-06-24T08:22:59Z","content_type":"application/pdf","file_size":7552298,"success":1,"checksum":"525d2618e855139089bbfc3e3d49d1b2","creator":"dernst","access_level":"open_access","date_created":"2022-06-24T08:22:59Z","file_id":"11461"}],"type":"journal_article","citation":{"chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>."},"has_accepted_license":"1","publisher":"Springer Nature","article_processing_charge":"No","_id":"11460","quality_controlled":"1","date_published":"2022-06-22T00:00:00Z","intvolume":"        13","author":[{"first_name":"Zachary A.","full_name":"Schaaf, Zachary A.","last_name":"Schaaf"},{"full_name":"Tat, Lyvin","first_name":"Lyvin","last_name":"Tat"},{"last_name":"Cannizzaro","first_name":"Noemi","full_name":"Cannizzaro, Noemi"},{"full_name":"Green, Ralph","first_name":"Ralph","last_name":"Green"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S."}],"volume":13,"abstract":[{"lang":"eng","text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life."}],"file_date_updated":"2022-06-24T08:22:59Z","publication_status":"published","external_id":{"isi":["000814641400001"]},"date_created":"2022-06-23T14:28:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1186/s13229-022-00508-3","publication":"Molecular Autism","day":"22","article_type":"original","article_number":"27","publication_identifier":{"issn":["2040-2392"]},"language":[{"iso":"eng"}],"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"oa":1,"year":"2022","department":[{"_id":"SiHi"}],"acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons"},{"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"title":"Inversions and parallel evolution","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1098/rstb.2021.0203","day":"01","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","article_type":"original","article_number":"20210203","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"oa":1,"_id":"11546","quality_controlled":"1","issue":"1856","author":[{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"volume":377,"intvolume":"       377","date_published":"2022-08-01T00:00:00Z","scopus_import":"1","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."}],"file_date_updated":"2023-02-02T08:20:29Z","external_id":{"isi":["000812317300005"]},"publication_status":"published","date_created":"2022-07-08T11:41:56Z","month":"08","status":"public","isi":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2023-08-03T11:55:42Z","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-02-02T08:20:29Z","file_size":920304,"success":1,"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","access_level":"open_access","date_created":"2023-02-02T08:20:29Z","creator":"dernst","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_id":"12479"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","publisher":"Royal Society of London","has_accepted_license":"1","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>"},"article_processing_charge":"Yes (via OA deal)"},{"doi":"10.1093/jmicro/dfac037","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","publication":"Microscopy","article_type":"original","oa":1,"keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"language":[{"iso":"eng"}],"acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","department":[{"_id":"LeSa"}],"year":"2022","pmid":1,"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","oa_version":"Published Version","date_updated":"2023-08-03T12:13:37Z","month":"10","status":"public","isi":1,"ddc":["570"],"file":[{"relation":"main_file","file_name":"2022_Microscopy_Gerle.pdf","date_updated":"2023-02-03T08:34:48Z","content_type":"application/pdf","file_size":7812696,"success":1,"checksum":"23b51c163636bf9313f7f0818312e67e","creator":"dernst","access_level":"open_access","date_created":"2023-02-03T08:34:48Z","file_id":"12498"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","article_processing_charge":"No","has_accepted_license":"1","publisher":"Oxford University Press","citation":{"apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>"},"quality_controlled":"1","issue":"5","_id":"11648","page":"249-261","volume":71,"author":[{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"last_name":"Kishikawa","first_name":"Jun-ichi","full_name":"Kishikawa, Jun-ichi"},{"first_name":"Tomoko","full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi"},{"first_name":"Atsuko","full_name":"Nakanishi, Atsuko","last_name":"Nakanishi"},{"last_name":"Çoruh","first_name":"Mehmet Orkun","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022"},{"first_name":"Fumiaki","full_name":"Makino, Fumiaki","last_name":"Makino"},{"full_name":"Miyata, Tomoko","first_name":"Tomoko","last_name":"Miyata"},{"last_name":"Kawamoto","full_name":"Kawamoto, Akihiro","first_name":"Akihiro"},{"full_name":"Yokoyama, Ken","first_name":"Ken","last_name":"Yokoyama"},{"full_name":"Namba, Keiichi","first_name":"Keiichi","last_name":"Namba"},{"full_name":"Kurisu, Genji","first_name":"Genji","last_name":"Kurisu"},{"first_name":"Takayuki","full_name":"Kato, Takayuki","last_name":"Kato"}],"date_published":"2022-10-01T00:00:00Z","intvolume":"        71","scopus_import":"1","date_created":"2022-07-25T10:04:58Z","external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"publication_status":"published","abstract":[{"text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica.","lang":"eng"}],"file_date_updated":"2023-02-03T08:34:48Z"},{"scopus_import":"1","file_date_updated":"2022-08-01T09:24:42Z","abstract":[{"lang":"eng","text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes."}],"external_id":{"pmid":["35562780"]},"publication_status":"published","date_created":"2022-08-01T09:04:27Z","_id":"11713","quality_controlled":"1","intvolume":"        15","date_published":"2022-05-13T00:00:00Z","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","first_name":"Nela","last_name":"Nikolic"},{"full_name":"Sauert, Martina","first_name":"Martina","last_name":"Sauert"},{"full_name":"Albanese, Tanino G.","first_name":"Tanino G.","last_name":"Albanese"},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}],"volume":15,"type":"journal_article","citation":{"ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","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>","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","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>","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."},"publisher":"Springer Nature","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"month":"05","status":"public","date_updated":"2022-08-01T09:27:40Z","oa_version":"Published Version","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"11714","access_level":"open_access","date_created":"2022-08-01T09:24:42Z","checksum":"008156e5340e9789f0f6d82bde4d347a","creator":"dernst","content_type":"application/pdf","date_updated":"2022-08-01T09:24:42Z","file_size":1545310,"success":1,"file_name":"2022_BMCResearchNotes_Nikolic.pdf","relation":"main_file"}],"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","year":"2022","department":[{"_id":"CaGu"}],"project":[{"call_identifier":"FWF","grant_number":"V00738","_id":"26956E74-B435-11E9-9278-68D0E5697425","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms"}],"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.","pmid":1,"article_type":"letter_note","article_number":"173","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1756-0500"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1186/s13104-022-06061-9","publication":"BMC Research Notes","day":"13"},{"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"article_number":"4826","ec_funded":1,"article_type":"original","day":"16","publication":"Nature Communications","doi":"10.1038/s41467-022-32559-8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"}],"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.).","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"department":[{"_id":"JoCs"},{"_id":"PeJo"},{"_id":"JoDa"}],"year":"2022","article_processing_charge":"No","has_accepted_license":"1","publisher":"Springer Nature","citation":{"chicago":"Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>.","apa":"Ben Simon, Y., Käfer, K., Velicky, P., Csicsvari, J. L., Danzl, J. G., &#38; Jonas, P. M. (2022). A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32559-8\">https://doi.org/10.1038/s41467-022-32559-8</a>","ieee":"Y. Ben Simon, K. Käfer, P. Velicky, J. L. Csicsvari, J. G. Danzl, and P. M. Jonas, “A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>","ista":"Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. 2022. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. Nature Communications. 13, 4826.","mla":"Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer 6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” <i>Nature Communications</i>, vol. 13, 4826, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32559-8\">10.1038/s41467-022-32559-8</a>.","short":"Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas, Nature Communications 13 (2022)."},"type":"journal_article","file":[{"file_id":"11990","creator":"dernst","checksum":"405936d9e4d33625d80c093c9713a91f","date_created":"2022-08-26T11:51:40Z","access_level":"open_access","file_name":"2022_NatureCommunications_BenSimon.pdf","file_size":5910357,"success":1,"date_updated":"2022-08-26T11:51:40Z","content_type":"application/pdf","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-08-03T13:01:19Z","month":"08","status":"public","isi":1,"ddc":["570"],"publication_status":"published","date_created":"2022-08-24T08:25:50Z","external_id":{"isi":["000841396400008"]},"abstract":[{"text":"The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.","lang":"eng"}],"file_date_updated":"2022-08-26T11:51:40Z","author":[{"last_name":"Ben Simon","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav"},{"last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"volume":13,"intvolume":"        13","date_published":"2022-08-16T00:00:00Z","quality_controlled":"1","_id":"11951"},{"file":[{"file_id":"12062","access_level":"open_access","date_created":"2022-09-08T06:41:14Z","checksum":"4201d876a3e5e8b65e319d03300014ad","creator":"dernst","date_updated":"2022-09-08T06:41:14Z","content_type":"application/pdf","file_size":3183129,"success":1,"file_name":"2022_LifeScienceAlliance_Daiss.pdf","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-08-03T13:39:36Z","month":"09","status":"public","ddc":["570"],"isi":1,"article_processing_charge":"No","publisher":"Life Science Alliance","has_accepted_license":"1","citation":{"short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022).","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>.","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568.","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>."},"type":"journal_article","volume":5,"author":[{"full_name":"Daiß, Julia L","first_name":"Julia L","last_name":"Daiß"},{"first_name":"Michael","full_name":"Pilsl, Michael","last_name":"Pilsl"},{"last_name":"Straub","full_name":"Straub, Kristina","first_name":"Kristina"},{"last_name":"Bleckmann","first_name":"Andrea","full_name":"Bleckmann, Andrea"},{"last_name":"Höcherl","full_name":"Höcherl, Mona","first_name":"Mona"},{"last_name":"Heiss","full_name":"Heiss, Florian B","first_name":"Florian B"},{"full_name":"Abascal-Palacios, Guillermo","first_name":"Guillermo","last_name":"Abascal-Palacios"},{"last_name":"Ramsay","first_name":"Ewan P","full_name":"Ramsay, Ewan P"},{"last_name":"Tluckova","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"full_name":"Mars, Jean-Clement","first_name":"Jean-Clement","last_name":"Mars"},{"last_name":"Fürtges","first_name":"Torben","full_name":"Fürtges, Torben"},{"full_name":"Bruckmann, Astrid","first_name":"Astrid","last_name":"Bruckmann"},{"full_name":"Rudack, Till","first_name":"Till","last_name":"Rudack"},{"first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"},{"full_name":"Lamour, Valérie","first_name":"Valérie","last_name":"Lamour"},{"full_name":"Panov, Konstantin","first_name":"Konstantin","last_name":"Panov"},{"first_name":"Alessandro","full_name":"Vannini, Alessandro","last_name":"Vannini"},{"first_name":"Tom","full_name":"Moss, Tom","last_name":"Moss"},{"full_name":"Engel, Christoph","first_name":"Christoph","last_name":"Engel"}],"intvolume":"         5","date_published":"2022-09-01T00:00:00Z","issue":"11","quality_controlled":"1","_id":"12051","publication_status":"published","date_created":"2022-09-06T18:45:23Z","external_id":{"isi":["000972702600001"]},"file_date_updated":"2022-09-08T06:41:14Z","abstract":[{"lang":"eng","text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble."}],"day":"01","publication":"Life Science Alliance","doi":"10.26508/lsa.202201568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2575-1077"]},"article_number":"e202201568","article_type":"original","acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","department":[{"_id":"CaBe"}],"year":"2022","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans"},{"date_published":"2022-12-16T00:00:00Z","intvolume":"         3","volume":3,"author":[{"full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","last_name":"Hübschmann"},{"first_name":"Medina","full_name":"Korkut, Medina","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","last_name":"Korkut"},{"first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"}],"_id":"12117","quality_controlled":"1","issue":"4","file_date_updated":"2023-01-23T09:50:51Z","abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"date_created":"2023-01-12T11:56:38Z","publication_status":"published","scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"related_material":{"record":[{"relation":"other","id":"11478","status":"public"}]},"file":[{"file_id":"12340","date_created":"2023-01-23T09:50:51Z","access_level":"open_access","creator":"dernst","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_size":6251945,"success":1,"content_type":"application/pdf","date_updated":"2023-01-23T09:50:51Z","file_name":"2022_STARProtocols_Huebschmann.pdf","relation":"main_file"}],"ddc":["570"],"month":"12","status":"public","date_updated":"2023-11-02T12:21:32Z","oa_version":"Published Version","citation":{"mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","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>","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.","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>","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>."},"publisher":"Elsevier","has_accepted_license":"1","article_processing_charge":"No","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"}],"year":"2022","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020"},{"grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"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.","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","publication":"STAR Protocols","day":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.xpro.2022.101866","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2666-1667"]},"oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"ec_funded":1,"article_type":"letter_note","article_number":"101866"}]