[{"ddc":["580"],"date_published":"2022-10-03T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"        15","citation":{"ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>"},"status":"public","external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"volume":15,"date_created":"2023-01-16T09:51:49Z","file_date_updated":"2023-01-30T07:46:51Z","page":"1533-1542","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"date_updated":"2023-08-04T09:39:24Z","oa_version":"Published Version","type":"journal_article","month":"10","_id":"12239","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","year":"2022","doi":"10.1016/j.molp.2022.09.003","quality_controlled":"1","publication_identifier":{"issn":["1674-2052"]},"isi":1,"keyword":["Plant Science","Molecular Biology"],"language":[{"iso":"eng"}],"issue":"10","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","author":[{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","last_name":"Costanzo","first_name":"Tommaso"},{"last_name":"Dahhan","first_name":"Dana A.","full_name":"Dahhan, Dana A."},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"file":[{"file_name":"2022_MolecularPlant_Johnson.pdf","success":1,"creator":"dernst","file_size":2307251,"relation":"main_file","content_type":"application/pdf","checksum":"04d5c12490052d03e4dc4412338a43dd","file_id":"12435","date_updated":"2023-01-30T07:46:51Z","access_level":"open_access","date_created":"2023-01-30T07:46:51Z"}],"day":"03","publication":"Molecular Plant","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}]},{"author":[{"first_name":"Ximena","last_name":"Soto","full_name":"Soto, Ximena"},{"last_name":"Burton","first_name":"Joshua","full_name":"Burton, Joshua"},{"first_name":"Cerys S.","last_name":"Manning","full_name":"Manning, Cerys S."},{"full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","first_name":"Thomas"},{"last_name":"Lea","first_name":"Robert","full_name":"Lea, Robert"},{"full_name":"Lee, Jessica","last_name":"Lee","first_name":"Jessica"},{"last_name":"Kursawe","first_name":"Jochen","full_name":"Kursawe, Jochen"},{"last_name":"Rattray","first_name":"Magnus","full_name":"Rattray, Magnus"},{"last_name":"Papalopulu","first_name":"Nancy","full_name":"Papalopulu, Nancy"}],"file":[{"success":1,"file_name":"2022_Development_Soto.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":9348839,"checksum":"d7c29b74e9e4032308228cc704a30e88","date_updated":"2023-01-30T08:35:44Z","file_id":"12438","access_level":"open_access","date_created":"2023-01-30T08:35:44Z"}],"day":"01","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","article_number":"dev200474","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"The Company of Biologists","pmid":1,"department":[{"_id":"AnKi"}],"publication":"Development","article_processing_charge":"No","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"doi":"10.1242/dev.200474","quality_controlled":"1","isi":1,"keyword":["Developmental Biology","Molecular Biology"],"language":[{"iso":"eng"}],"issue":"19","date_updated":"2023-08-04T09:41:08Z","abstract":[{"text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","month":"10","volume":149,"file_date_updated":"2023-01-30T08:35:44Z","date_created":"2023-01-16T09:53:17Z","acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","year":"2022","_id":"12245","publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2022-10-01T00:00:00Z","status":"public","external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"intvolume":"       149","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"citation":{"ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company of Biologists, 2022.","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022)."}},{"author":[{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","first_name":"Andreas","last_name":"Angermayr"},{"first_name":"Tin Yau","last_name":"Pang","full_name":"Pang, Tin Yau"},{"first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume"},{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","last_name":"Mitosch","first_name":"Karin"},{"first_name":"Martin J","last_name":"Lercher","full_name":"Lercher, Martin J"},{"last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"8b1d8f5ea20c8408acf466435fb6ae01","date_updated":"2023-01-30T09:49:55Z","file_id":"12446","access_level":"open_access","date_created":"2023-01-30T09:49:55Z","success":1,"file_name":"2022_MolecularSystemsBio_Angermayr.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":1098812}],"day":"01","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","article_number":"e10490","publisher":"Embo Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToBo"}],"publication":"Molecular Systems Biology","scopus_import":"1","article_processing_charge":"No","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1744-4292"]},"doi":"10.15252/msb.202110490","quality_controlled":"1","isi":1,"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"language":[{"iso":"eng"}],"issue":"9","abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"date_updated":"2023-08-04T09:51:49Z","oa_version":"Published Version","month":"09","type":"journal_article","volume":18,"file_date_updated":"2023-01-30T09:49:55Z","date_created":"2023-01-16T09:58:34Z","acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","year":"2022","_id":"12261","publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2022-09-01T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"M-Shop"}],"status":"public","external_id":{"isi":["000856482800001"]},"intvolume":"        18","citation":{"ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” <i>Molecular Systems Biology</i>, vol. 18, no. 9. Embo Press, 2022.","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. 2022;18(9). doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>, vol. 18, no. 9, e10490, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>.","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &#38; Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>"}},{"_id":"12262","year":"2022","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","date_created":"2023-01-16T09:59:06Z","file_date_updated":"2023-01-30T10:00:04Z","volume":29,"abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"date_updated":"2023-08-04T09:52:20Z","type":"journal_article","month":"09","oa_version":"Published Version","page":"942-953","citation":{"apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural &#38; Molecular Biology 29 (2022) 942–953.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022."},"intvolume":"        29","status":"public","external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["570"],"date_published":"2022-09-12T00:00:00Z","has_accepted_license":"1","publication_status":"published","oa":1,"article_processing_charge":"No","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Nature Structural & Molecular Biology","pmid":1,"department":[{"_id":"EM-Fac"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","day":"12","file":[{"file_size":9935057,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","success":1,"date_created":"2023-01-30T10:00:04Z","access_level":"open_access","file_id":"12447","date_updated":"2023-01-30T10:00:04Z","checksum":"2d5c3ec01718fefd7553052b0b8a0793"}],"author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"full_name":"Sailer, Carolin","last_name":"Sailer","first_name":"Carolin"},{"full_name":"Kargas, Vasileios","first_name":"Vasileios","last_name":"Kargas"},{"first_name":"Mathias","last_name":"Loibl","full_name":"Loibl, Mathias"},{"last_name":"Gerhalter","first_name":"Magdalena","full_name":"Gerhalter, Magdalena"},{"full_name":"Kofler, Lisa","last_name":"Kofler","first_name":"Lisa"},{"full_name":"Warren, Alan J.","first_name":"Alan J.","last_name":"Warren"},{"full_name":"Stengel, Florian","first_name":"Florian","last_name":"Stengel"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"language":[{"iso":"eng"}],"issue":"9","isi":1,"keyword":["Molecular Biology","Structural Biology"],"quality_controlled":"1","doi":"10.1038/s41594-022-00832-5","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]}},{"intvolume":"        23","citation":{"short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>.","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” <i>EMBO Reports</i>, vol. 23, no. 7. Embo Press, 2022.","apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., &#38; Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163.","mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>, vol. 23, no. 7, e54163, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>.","ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. 2022;23(7). doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>"},"status":"public","external_id":{"isi":["000797302700001"],"pmid":["35586945"]},"date_published":"2022-07-05T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15252/embr.202154163"}],"publication_status":"published","oa":1,"has_accepted_license":"1","_id":"12275","acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship","year":"2022","volume":23,"date_created":"2023-01-16T10:01:44Z","oa_version":"Published Version","month":"07","type":"journal_article","abstract":[{"lang":"eng","text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system."}],"date_updated":"2023-10-03T11:25:54Z","keyword":["Genetics","Molecular Biology","Biochemistry"],"isi":1,"issue":"7","language":[{"iso":"eng"}],"doi":"10.15252/embr.202154163","quality_controlled":"1","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication":"EMBO Reports","article_type":"original","article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Embo Press","department":[{"_id":"MaDe"}],"pmid":1,"article_number":"e54163","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","author":[{"last_name":"Rahman","first_name":"Maisha","full_name":"Rahman, Maisha"},{"id":"39831956-E4FE-11E9-85DE-0DC7E5697425","full_name":"Ramirez, Nelson","last_name":"Ramirez","first_name":"Nelson"},{"first_name":"Carlos A","last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A"},{"full_name":"Bülow, Hannes E","first_name":"Hannes E","last_name":"Bülow"}],"day":"05"},{"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","_id":"12280","month":"06","oa_version":"Published Version","type":"journal_article","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."}],"date_updated":"2025-07-14T09:09:49Z","volume":18,"file_date_updated":"2023-01-30T11:28:13Z","date_created":"2023-01-16T10:02:51Z","status":"public","external_id":{"isi":["000843626800031"],"pmid":["35700167"]},"intvolume":"        18","citation":{"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>","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>.","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.","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>.","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.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022)."},"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2022-06-14T00:00:00Z","ddc":["000","570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"pmid":1,"publication":"PLOS Computational Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"author":[{"first_name":"Laura","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"file":[{"date_created":"2023-01-30T11:28:13Z","access_level":"open_access","file_id":"12460","date_updated":"2023-01-30T11:28:13Z","checksum":"31b6b311b6731f1658277a9dfff6632c","file_size":3143222,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2022_PlosCompBio_Schmid.pdf","success":1}],"day":"14","article_number":"e1010149","title":"Direct reciprocity between individuals that use different strategy spaces","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"isi":1,"issue":"6","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1010149","quality_controlled":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"publication":"eLife","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","article_number":"79848","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","day":"15","file":[{"creator":"dernst","file_size":8506811,"relation":"main_file","content_type":"application/pdf","file_name":"2022_eLife_Sumser.pdf","success":1,"access_level":"open_access","date_created":"2023-01-30T11:50:53Z","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","file_id":"12463","date_updated":"2023-01-30T11:50:53Z"}],"author":[{"last_name":"Sumser","first_name":"Anton L","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87","full_name":"Sumser, Anton L"},{"first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"},{"first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"}],"language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"isi":1,"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"quality_controlled":"1","doi":"10.7554/elife.79848","publication_identifier":{"eissn":["2050-084X"]},"_id":"12288","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).","file_date_updated":"2023-01-30T11:50:53Z","date_created":"2023-01-16T10:04:15Z","volume":11,"oa_version":"Published Version","type":"journal_article","month":"09","date_updated":"2023-08-04T10:29:48Z","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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>","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.","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>.","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>.","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.","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022)."},"intvolume":"        11","status":"public","external_id":{"isi":["000892204300001"],"pmid":["36040301"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_published":"2022-09-15T00:00:00Z","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa":1},{"day":"07","author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi"}],"title":"DNA methylation dynamics during germline development","department":[{"_id":"XiFe"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","article_type":"review","scopus_import":"1","article_processing_charge":"No","publication":"Journal of Integrative Plant Biology","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"quality_controlled":"1","doi":"10.1111/jipb.13422","issue":"12","language":[{"iso":"eng"}],"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"month":"12","type":"journal_article","oa_version":"Published Version","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"}],"date_updated":"2023-05-08T10:59:00Z","page":"2240-2251","date_created":"2023-02-23T09:15:57Z","volume":64,"year":"2022","_id":"12670","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jipb.13422","open_access":"1"}],"date_published":"2022-12-07T00:00:00Z","external_id":{"pmid":["36478632"]},"status":"public","citation":{"chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>."},"extern":"1","intvolume":"        64"},{"oa_version":"Preprint","month":"05","type":"journal_article","abstract":[{"text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.","lang":"eng"}],"date_updated":"2023-08-17T07:01:14Z","page":"2051-2064.e8","date_created":"2022-03-08T07:51:04Z","volume":31,"year":"2021","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","_id":"10834","oa":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.03.24.005835"}],"date_published":"2021-05-24T00:00:00Z","status":"public","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"citation":{"chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>.","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8."},"intvolume":"        31","day":"24","author":[{"first_name":"Stephanie","last_name":"Stahnke","full_name":"Stahnke, Stephanie"},{"full_name":"Döring, Hermann","last_name":"Döring","first_name":"Hermann"},{"first_name":"Charly","last_name":"Kusch","full_name":"Kusch, Charly"},{"full_name":"de Gorter, David J.J.","first_name":"David J.J.","last_name":"de Gorter"},{"full_name":"Dütting, Sebastian","last_name":"Dütting","first_name":"Sebastian"},{"first_name":"Aleks","last_name":"Guledani","full_name":"Guledani, Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"full_name":"Schnoor, Michael","first_name":"Michael","last_name":"Schnoor"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Geffers, Robert","first_name":"Robert","last_name":"Geffers"},{"last_name":"Rohde","first_name":"Manfred","full_name":"Rohde, Manfred"},{"full_name":"Müsken, Mathias","last_name":"Müsken","first_name":"Mathias"},{"full_name":"Kage, Frieda","first_name":"Frieda","last_name":"Kage"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"first_name":"Bernhard","last_name":"Nieswandt","full_name":"Nieswandt, Bernhard"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"last_name":"Stradal","first_name":"Theresia E.B.","full_name":"Stradal, Theresia E.B."}],"title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","department":[{"_id":"MiSi"}],"pmid":1,"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Current Biology","publication_identifier":{"issn":["0960-9822"]},"quality_controlled":"1","doi":"10.1016/j.cub.2021.02.043","issue":"10","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"isi":1},{"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"issue":"21","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2021.10.008","quality_controlled":"1","publication_identifier":{"issn":["1534-5807"]},"publication":"Developmental Cell","article_type":"original","scopus_import":"1","article_processing_charge":"No","publisher":"Elsevier","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","pmid":1,"title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain","author":[{"last_name":"Krishna","first_name":"Shefali","full_name":"Krishna, Shefali"},{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"full_name":"Capitanio, Juliana S.","first_name":"Juliana S.","last_name":"Capitanio"},{"last_name":"Ramachandra","first_name":"Ranjan","full_name":"Ramachandra, Ranjan"},{"full_name":"Ellisman, Mark","first_name":"Mark","last_name":"Ellisman"},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W"}],"day":"08","extern":"1","intvolume":"        56","citation":{"ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.","chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>.","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>"},"external_id":{"pmid":["34715012"]},"status":"public","date_published":"2021-11-08T00:00:00Z","publication_status":"published","_id":"11052","year":"2021","volume":56,"date_created":"2022-04-07T07:43:14Z","page":"P2952-2965.e9","month":"11","oa_version":"None","type":"journal_article","abstract":[{"text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.","lang":"eng"}],"date_updated":"2022-07-18T08:26:38Z"},{"page":"71-81","date_updated":"2023-08-07T13:30:01Z","abstract":[{"lang":"eng","text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process."}],"oa_version":"Published Version","month":"06","type":"journal_article","volume":474,"date_created":"2020-12-22T09:53:34Z","file_date_updated":"2021-08-11T10:28:06Z","acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","year":"2021","_id":"8966","oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2021-06-01T00:00:00Z","status":"public","external_id":{"isi":["000639461800008"]},"related_material":{"record":[{"status":"public","id":"12891","relation":"dissertation_contains"}]},"intvolume":"       474","citation":{"ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81."},"author":[{"last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"file":[{"success":1,"file_name":"2021_DevBiology_Schauer.pdf","creator":"kschuh","content_type":"application/pdf","relation":"main_file","file_size":1440321,"checksum":"fa2a5731fd16ab171b029f32f031c440","date_updated":"2021-08-11T10:28:06Z","file_id":"9880","access_level":"open_access","date_created":"2021-08-11T10:28:06Z"}],"day":"01","title":"Reassembling gastrulation","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaHe"}],"publication":"Developmental Biology","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","publication_identifier":{"issn":["0012-1606"]},"doi":"10.1016/j.ydbio.2020.12.014","quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"isi":1,"keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"language":[{"iso":"eng"}]},{"department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"Yes","publication":"PLOS Computational Biology","day":"07","file":[{"success":1,"file_name":"2021_PlosComBio_Kavcic.pdf","content_type":"application/pdf","relation":"main_file","file_size":3690053,"creator":"dernst","date_updated":"2021-02-04T12:30:48Z","file_id":"9092","checksum":"e29f2b42651bef8e034781de8781ffac","date_created":"2021-02-04T12:30:48Z","access_level":"open_access"}],"author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Tobias"}],"article_number":"e1008529","title":"Minimal biophysical model of combined antibiotic action","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"}],"language":[{"iso":"eng"}],"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"isi":1,"publication_identifier":{"issn":["1553-7358"]},"quality_controlled":"1","doi":"10.1371/journal.pcbi.1008529","year":"2021","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","_id":"8997","month":"01","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"date_updated":"2024-02-21T12:41:41Z","file_date_updated":"2021-02-04T12:30:48Z","date_created":"2021-01-08T07:16:18Z","volume":17,"external_id":{"isi":["000608045000010"]},"status":"public","citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>."},"intvolume":"        17","related_material":{"record":[{"id":"7673","status":"public","relation":"earlier_version"},{"id":"8930","status":"public","relation":"research_data"}]},"has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2021-01-07T00:00:00Z","ddc":["570"]},{"author":[{"first_name":"Tong","last_name":"Bian","full_name":"Bian, Tong"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"day":"01","title":"Morphology control in crystalline nanoparticle–polymer aggregates","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","pmid":1,"publication":"Annals of the New York Academy of Sciences","scopus_import":"1","article_processing_charge":"No","article_type":"original","publication_identifier":{"issn":["0077-8923"],"eissn":["1749-6632"]},"doi":"10.1111/nyas.14674","quality_controlled":"1","keyword":["History and Philosophy of Science","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"language":[{"iso":"eng"}],"issue":"1","page":"191-201","abstract":[{"text":"Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.","lang":"eng"}],"date_updated":"2023-08-07T10:01:10Z","month":"12","type":"journal_article","oa_version":"Published Version","volume":1505,"date_created":"2023-08-01T09:33:39Z","year":"2021","_id":"13356","oa":1,"publication_status":"published","date_published":"2021-12-01T00:00:00Z","ddc":["540"],"main_file_link":[{"url":"https://doi.org/10.1111/nyas.14674","open_access":"1"}],"status":"public","external_id":{"pmid":["34427923"]},"extern":"1","intvolume":"      1505","citation":{"short":"T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021) 191–201.","chicago":"Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” <i>Annals of the New York Academy of Sciences</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nyas.14674\">https://doi.org/10.1111/nyas.14674</a>.","ieee":"T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer aggregates,” <i>Annals of the New York Academy of Sciences</i>, vol. 1505, no. 1. Wiley, pp. 191–201, 2021.","apa":"Bian, T., &#38; Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer aggregates. <i>Annals of the New York Academy of Sciences</i>. Wiley. <a href=\"https://doi.org/10.1111/nyas.14674\">https://doi.org/10.1111/nyas.14674</a>","ista":"Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.","mla":"Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer Aggregates.” <i>Annals of the New York Academy of Sciences</i>, vol. 1505, no. 1, Wiley, 2021, pp. 191–201, doi:<a href=\"https://doi.org/10.1111/nyas.14674\">10.1111/nyas.14674</a>.","ama":"Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates. <i>Annals of the New York Academy of Sciences</i>. 2021;1505(1):191-201. doi:<a href=\"https://doi.org/10.1111/nyas.14674\">10.1111/nyas.14674</a>"}},{"_id":"9283","year":"2021","acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","file_date_updated":"2021-03-23T10:12:58Z","date_created":"2021-03-23T10:11:46Z","volume":10,"oa_version":"Published Version","month":"03","type":"journal_article","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.","lang":"eng"}],"date_updated":"2024-02-21T12:41:57Z","citation":{"ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &#38; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>, vol. 10, e65993, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>.","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>.","ieee":"A. A. Nagy-Staron <i>et al.</i>, “Local genetic context shapes the function of a gene regulatory network,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021)."},"intvolume":"        10","related_material":{"record":[{"status":"public","id":"8951","relation":"research_data"}]},"status":"public","external_id":{"isi":["000631050900001"]},"ddc":["570"],"date_published":"2021-03-08T00:00:00Z","has_accepted_license":"1","publication_status":"published","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","ec_funded":1,"article_processing_charge":"Yes","publication":"eLife","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","article_number":"e65993","title":"Local genetic context shapes the function of a gene regulatory network","day":"08","file":[{"file_name":"elife-65993-v2.pdf","success":1,"file_size":1390469,"content_type":"application/pdf","relation":"main_file","creator":"bkavcic","file_id":"9284","date_updated":"2021-03-23T10:12:58Z","checksum":"3c2f44058c2dd45a5a1027f09d263f8e","date_created":"2021-03-23T10:12:58Z","access_level":"open_access"}],"author":[{"first_name":"Anna A","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377"},{"first_name":"Kathrin","last_name":"Tomasek","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"full_name":"Caruso Carter, Caroline","last_name":"Caruso Carter","first_name":"Caroline"},{"last_name":"Sonnleitner","first_name":"Elisabeth","full_name":"Sonnleitner, Elisabeth"},{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","last_name":"Kavcic"},{"last_name":"Paixão","first_name":"Tiago","full_name":"Paixão, Tiago"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"}],"language":[{"iso":"eng"}],"keyword":["Genetics and Molecular Biology"],"isi":1,"project":[{"grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","call_identifier":"FP7","_id":"2517526A-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03901","_id":"268BFA92-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks"}],"quality_controlled":"1","doi":"10.7554/elife.65993","publication_identifier":{"issn":["2050-084X"]}},{"publication_status":"published","oa":1,"date_published":"2021-04-24T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"status":"public","external_id":{"isi":["000659161500002"]},"intvolume":"       524","citation":{"chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier , 2021.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729."},"date_updated":"2023-08-08T13:32:40Z","abstract":[{"lang":"eng","text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift."}],"type":"journal_article","month":"04","oa_version":"Preprint","volume":524,"date_created":"2021-05-12T05:58:42Z","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","year":"2021","_id":"9387","publication_identifier":{"issn":["0022-5193"]},"doi":"10.1016/j.jtbi.2021.110729","quality_controlled":"1","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"language":[{"iso":"eng"}],"author":[{"first_name":"Kseniia","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"},{"first_name":"Tatiana Yu.","last_name":"Neretina","full_name":"Neretina, Tatiana Yu."},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."}],"day":"24","title":"Two linked loci under mutation-selection balance and Muller’s ratchet","article_number":"110729","publisher":"Elsevier ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"}],"publication":"Journal of Theoretical Biology","article_processing_charge":"No","article_type":"original"},{"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication":"Nature Communications","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","ec_funded":1,"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"last_name":"Schwarz","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"last_name":"Basilico","first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"last_name":"Dimchev","first_name":"Georgi A","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter"},{"last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"first_name":"Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"file":[{"date_created":"2021-05-28T12:39:43Z","access_level":"open_access","date_updated":"2021-05-28T12:39:43Z","file_id":"9430","checksum":"337e0f7959c35ec959984cacdcb472ba","relation":"main_file","content_type":"application/pdf","file_size":9358599,"creator":"kschuh","success":1,"file_name":"2021_NatureCommunications_Morandell.pdf"}],"day":"24","article_number":"3058","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"isi":1,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-23123-x","quality_controlled":"1","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","year":"2021","_id":"9429","month":"05","type":"journal_article","oa_version":"Published Version","date_updated":"2024-09-10T12:04:26Z","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"volume":12,"file_date_updated":"2021-05-28T12:39:43Z","date_created":"2021-05-28T11:49:46Z","external_id":{"isi":["000658769900010"]},"status":"public","intvolume":"        12","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"relation":"dissertation_contains","id":"12401","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"citation":{"chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["572"],"date_published":"2021-05-24T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"}]},{"month":"05","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"date_updated":"2023-08-08T13:53:53Z","volume":12,"file_date_updated":"2021-06-09T15:21:14Z","date_created":"2021-05-28T14:25:50Z","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","year":"2021","_id":"9431","oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2021-05-28T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"status":"public","external_id":{"isi":["000659145000011"]},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","description":"News on IST Homepage","relation":"press_release"}]},"intvolume":"        12","citation":{"ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021)."},"author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Obr"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"full_name":"Nikulin, Nadia","first_name":"Nadia","last_name":"Nikulin"},{"last_name":"Feathers","first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R."},{"last_name":"Klanschnig","first_name":"Marco","full_name":"Klanschnig, Marco"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","last_name":"Thader","first_name":"Andreas"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"file":[{"access_level":"open_access","date_created":"2021-06-09T15:21:14Z","checksum":"53ccc53d09a9111143839dbe7784e663","file_id":"9538","date_updated":"2021-06-09T15:21:14Z","creator":"kschuh","file_size":6166295,"content_type":"application/pdf","relation":"main_file","file_name":"2021_NatureCommunications_Obr.pdf","success":1}],"day":"28","article_number":"3226","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Nature Research","department":[{"_id":"FlSc"}],"publication":"Nature Communications","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-23506-0","quality_controlled":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"isi":1,"issue":"1","language":[{"iso":"eng"}]},{"date_created":"2021-06-10T14:57:45Z","file_date_updated":"2021-06-15T18:55:59Z","volume":12,"date_updated":"2023-08-08T14:05:26Z","abstract":[{"text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","month":"06","_id":"9540","year":"2021","acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["570"],"date_published":"2021-06-09T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021)."},"intvolume":"        12","external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"status":"public","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","article_number":"3483","day":"09","file":[{"access_level":"open_access","date_created":"2021-06-15T18:55:59Z","checksum":"40fc24c1310930990b52a8ad1142ee97","date_updated":"2021-06-15T18:55:59Z","file_id":"9556","creator":"cziletti","relation":"main_file","content_type":"application/pdf","file_size":3397292,"success":1,"file_name":"2021_NatureComm_Prattes.pdf"}],"author":[{"last_name":"Prattes","first_name":"Michael","full_name":"Prattes, Michael"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Rössler, Ingrid","first_name":"Ingrid","last_name":"Rössler"},{"last_name":"Klein","first_name":"Isabella","full_name":"Klein, Isabella"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"last_name":"Zisser","first_name":"Gertrude","full_name":"Zisser, Gertrude"},{"last_name":"Gruber","first_name":"Christian C.","full_name":"Gruber, Christian C."},{"last_name":"Gruber","first_name":"Karl","full_name":"Gruber, Karl"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"article_processing_charge":"No","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Nature Communications","pmid":1,"department":[{"_id":"EM-Fac"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","doi":"10.1038/s41467-021-23854-x","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"issue":"1","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"CaBe"}],"publication":"Nature Communications","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","author":[{"last_name":"Appel","first_name":"Lisa-Marie","full_name":"Appel, Lisa-Marie"},{"last_name":"Franke","first_name":"Vedran","full_name":"Franke, Vedran"},{"full_name":"Bruno, Melania","first_name":"Melania","last_name":"Bruno"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"last_name":"Kasiliauskaite","first_name":"Aiste","full_name":"Kasiliauskaite, Aiste"},{"full_name":"Kaufmann, Tanja","first_name":"Tanja","last_name":"Kaufmann"},{"full_name":"Schoeberl, Ursula E.","first_name":"Ursula E.","last_name":"Schoeberl"},{"full_name":"Puchinger, Martin G.","last_name":"Puchinger","first_name":"Martin G."},{"full_name":"Kostrhon, Sebastian","last_name":"Kostrhon","first_name":"Sebastian"},{"first_name":"Carmen","last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"first_name":"Etienne","last_name":"Beltzung","full_name":"Beltzung, Etienne"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"first_name":"Gen","last_name":"Lin","full_name":"Lin, Gen"},{"last_name":"Vlasova","first_name":"Anna","full_name":"Vlasova, Anna"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"},{"last_name":"Pavri","first_name":"Rushad","full_name":"Pavri, Rushad"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"}],"day":"19","file":[{"file_id":"10169","date_updated":"2021-10-21T13:51:49Z","checksum":"d99fcd51aebde19c21314e3de0148007","date_created":"2021-10-21T13:51:49Z","access_level":"open_access","file_name":"2021_NatComm_Appel.pdf","success":1,"file_size":5111706,"relation":"main_file","content_type":"application/pdf","creator":"cchlebak"}],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","article_number":"6078","isi":1,"keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"language":[{"iso":"eng"}],"issue":"1","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-26360-2","quality_controlled":"1","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","year":"2021","_id":"10163","date_updated":"2023-08-14T08:02:31Z","abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"month":"10","oa_version":"Published Version","type":"journal_article","volume":12,"date_created":"2021-10-20T14:40:32Z","file_date_updated":"2021-10-21T13:51:49Z","external_id":{"isi":["000709050300001"]},"status":"public","related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","description":"Preprint "}]},"intvolume":"        12","citation":{"apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>.","ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["610"],"date_published":"2021-10-19T00:00:00Z"},{"doi":"10.7554/elife.71575","quality_controlled":"1","publication_identifier":{"issn":["2050-084X"]},"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"isi":1,"language":[{"iso":"eng"}],"article_number":"e71575","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"full_name":"Dey, Partha N","last_name":"Dey","first_name":"Partha N"},{"first_name":"Óscar","last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar"},{"first_name":"Luis E","last_name":"Garcia Rabaneda","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E"},{"last_name":"García-Lira","first_name":"Carmen","full_name":"García-Lira, Carmen"},{"full_name":"Grand, Teddy","first_name":"Teddy","last_name":"Grand"},{"full_name":"Briz, Victor","last_name":"Briz","first_name":"Victor"},{"last_name":"Velasco","first_name":"Eric R","full_name":"Velasco, Eric R"},{"full_name":"Andero Galí, Raül","last_name":"Andero Galí","first_name":"Raül"},{"full_name":"Niñerola, Sergio","first_name":"Sergio","last_name":"Niñerola"},{"full_name":"Barco, Angel","last_name":"Barco","first_name":"Angel"},{"full_name":"Paoletti, Pierre","last_name":"Paoletti","first_name":"Pierre"},{"last_name":"Wesseling","first_name":"John F","full_name":"Wesseling, John F"},{"last_name":"Gardoni","first_name":"Fabrizio","full_name":"Gardoni, Fabrizio"},{"last_name":"Tavalin","first_name":"Steven J","full_name":"Tavalin, Steven J"},{"last_name":"Perez-Otaño","first_name":"Isabel","full_name":"Perez-Otaño, Isabel"}],"day":"17","file":[{"checksum":"59318e9e41507cec83c2f4070e6ad540","date_updated":"2021-11-18T07:02:02Z","file_id":"10302","access_level":"open_access","date_created":"2021-11-18T07:02:02Z","success":1,"file_name":"elife-71575-v1.pdf","creator":"lgarciar","relation":"main_file","content_type":"application/pdf","file_size":2477302}],"publication":"eLife","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"}],"ddc":["570"],"date_published":"2021-11-17T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"        10","citation":{"chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>.","ieee":"M. J. Conde-Dusman <i>et al.</i>, “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>, vol. 10, e71575, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>.","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575."},"status":"public","external_id":{"isi":["000720945900001"]},"volume":10,"file_date_updated":"2021-11-18T07:02:02Z","date_created":"2021-11-18T06:59:45Z","oa_version":"Published Version","type":"journal_article","month":"11","date_updated":"2023-08-14T11:50:50Z","abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"_id":"10301","acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","year":"2021"}]