[{"doi":"10.7554/elife.80803","article_processing_charge":"Yes","quality_controlled":"1","dataavailabilitystatement":"The data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 6D-F', Figure 6Q, Figure 5—figure supplement 1D, Figure 6—figure supplement 2G, Figure 6—figure supplement 3E and F. All the sequencing data are available at NCBI as an SRA project PRJNA820593.","OA_type":"gold","OA_place":"publisher","acknowledgement":"This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","publisher":"eLife Sciences Publications","title":"Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator","date_published":"2024-02-07T00:00:00Z","intvolume":"        13","researchdata_availability":"yes","month":"02","author":[{"first_name":"Paul","full_name":"Knabl, Paul","last_name":"Knabl"},{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra"},{"last_name":"Pomreinke","first_name":"Autumn P","full_name":"Pomreinke, Autumn P"},{"last_name":"Zimmermann","full_name":"Zimmermann, Bob","first_name":"Bob"},{"full_name":"Rogers, Katherine W","first_name":"Katherine W","last_name":"Rogers"},{"last_name":"Čapek","full_name":"Čapek, Daniel","first_name":"Daniel"},{"first_name":"Patrick","full_name":"Müller, Patrick","last_name":"Müller"},{"last_name":"Genikhovich","first_name":"Grigory","full_name":"Genikhovich, Grigory"}],"fulldoi":"https://doi.org/10.7554/elife.80803","type":"journal_article","abstract":[{"lang":"eng","text":"BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan <jats:italic>Nematostella vectensis</jats:italic>, several of which were conserved in <jats:italic>Drosophila</jats:italic> and <jats:italic>Xenopus</jats:italic>. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in <jats:italic>Nematostella</jats:italic> are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is <jats:italic>zswim4-6</jats:italic>, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression."}],"file_date_updated":"2025-01-29T08:50:18Z","DOAJ_listed":"1","license":"https://creativecommons.org/licenses/by/4.0/","supplementarymaterial":"no","das_tickbox":"1","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"file":[{"success":1,"creator":"dernst","checksum":"24548a184215d3f4547bba535ccfd7b1","relation":"main_file","file_size":11855972,"content_type":"application/pdf","date_updated":"2025-01-29T08:50:18Z","date_created":"2025-01-29T08:50:18Z","file_name":"2024_eLife_Knabl.pdf","file_id":"18941","access_level":"open_access"}],"article_type":"original","language":[{"iso":"eng"}],"ddc":["570"],"publication":"eLife","day":"07","date_updated":"2026-10-01T08:31:50Z","_id":"18940","date_created":"2025-01-29T08:48:34Z","oa":1,"status":"public","oa_version":"Published Version","year":"2024","citation":{"short":"P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024).","ama":"Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>","chicago":"Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>.","ista":"Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13.","ieee":"P. Knabl <i>et al.</i>, “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","apa":"Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>","mla":"Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>."},"department":[{"_id":"CaHe"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":13},{"publisher":"eLife Sciences Publications","date_published":"2024-12-10T00:00:00Z","title":"A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus","intvolume":"        12","scopus_import":"1","dataavailabilitystatement":"The code for the analysis is available online as a user-friendly MATLAB script at: https://github.com/dcsabaCD225/Moran_Matlab/blob/main/moran_local.m (copy archived at Csaba, 2024). All source data relevant to figures and charts are included in source data files.","OA_type":"gold","OA_place":"publisher","acknowledgement":"This research was supported by the Wellcome Trust (ZN, LA). In addition, LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681). We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly providing microscopy support. Authors would like to express their deepest gratitude to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable discussion about analysis of spatial association, and to Krisztina Faddi for the excellent technical assistance. ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.7554/elife.89361","article_processing_charge":"Yes","quality_controlled":"1","abstract":[{"lang":"eng","text":"Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran’s <jats:italic>I</jats:italic> coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran’s method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method’s power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran’s method is a rapid, simple image segmentation method optimal for variable and high noise conditions."}],"DOAJ_listed":"1","file_date_updated":"2025-01-08T13:33:05Z","fulldoi":"https://doi.org/10.7554/elife.89361","type":"journal_article","researchdata_availability":"yes","article_number":"89361","author":[{"full_name":"Dávid, Csaba","first_name":"Csaba","last_name":"Dávid"},{"first_name":"Kristóf","full_name":"Giber, Kristóf","last_name":"Giber"},{"last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","first_name":"Margit Katalin","full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758"},{"last_name":"Köllő","full_name":"Köllő, Mihály","first_name":"Mihály"},{"last_name":"Nusser","first_name":"Zoltan","full_name":"Nusser, Zoltan"},{"first_name":"Laszlo","full_name":"Acsady, Laszlo","last_name":"Acsady"}],"month":"12","language":[{"iso":"eng"}],"article_type":"original","ddc":["570"],"file":[{"file_id":"18780","access_level":"open_access","date_created":"2025-01-08T13:33:05Z","file_name":"2024_eLife_David.pdf","date_updated":"2025-01-08T13:33:05Z","content_type":"application/pdf","checksum":"1d64265f62a3bf14550b4f5c684f1782","relation":"main_file","file_size":9992462,"creator":"dernst","success":1}],"has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"supplementarymaterial":"yes","das_tickbox":"1","publication_status":"published","citation":{"ieee":"C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","ista":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. eLife. 12, 89361.","short":"C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12 (2024).","ama":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>","chicago":"Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>.","apa":"Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., &#38; Acsady, L. (2024). A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>","mla":"Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>, vol. 12, 89361, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>."},"department":[{"_id":"GaNo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":12,"year":"2024","date_updated":"2026-10-02T09:53:20Z","oa":1,"_id":"18779","date_created":"2025-01-08T13:25:45Z","status":"public","oa_version":"Published Version","day":"10","publication":"eLife"},{"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.68993","isi":1,"file_date_updated":"2024-07-22T11:51:50Z","DOAJ_listed":"1","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"ec_funded":1,"author":[{"orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","first_name":"Ivana","full_name":"Matijevic, Ivana"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"month":"02","researchdata_availability":"yes (supplementary data)","scopus_import":"1","intvolume":"        13","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","date_published":"2024-02-21T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","corr_author":"1","article_processing_charge":"Yes","doi":"10.7554/elife.68993","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research Council Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","OA_place":"publisher","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"OA_type":"gold","dataavailabilitystatement":"All data generated or analysed during this study are included in the manuscript and supporting files. No additional source files were provided.","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"year":"2024","volume":13,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"JiFr"}],"citation":{"ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>"},"publication":"eLife","day":"21","oa_version":"Published Version","status":"public","_id":"15033","date_created":"2024-02-27T07:10:11Z","oa":1,"date_updated":"2026-10-15T08:07:21Z","external_id":{"isi":["001174278000001"],"pmid":["38381485"]},"file":[{"relation":"main_file","file_size":15675744,"checksum":"b2b2d583b433823af731842f1420113e","success":1,"creator":"dernst","access_level":"open_access","file_id":"17310","date_updated":"2024-07-22T11:51:50Z","content_type":"application/pdf","date_created":"2024-07-22T11:51:50Z","file_name":"2024_eLife_Adamowski.pdf"}],"ddc":["580"],"article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","das_tickbox":"1","supplementarymaterial":"no","publication_identifier":{"issn":["2050-084X"]},"APC_amount":"2792,52 EUR","pmid":1,"has_accepted_license":"1"},{"citation":{"apa":"Kulich, I., Schmid, J., Teplova, A., Qi, L., &#38; Friml, J. (2024). Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>","mla":"Kulich, Ivan, et al. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>, vol. 12, 91523, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>.","ama":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>","short":"I. Kulich, J. Schmid, A. Teplova, L. Qi, J. Friml, ELife 12 (2024).","chicago":"Kulich, Ivan, Julia Schmid, Anastasiia Teplova, Linlin Qi, and Jiří Friml. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>.","ista":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. 2024. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife. 12, 91523.","ieee":"I. Kulich, J. Schmid, A. Teplova, L. Qi, and J. Friml, “Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024."},"department":[{"_id":"JiFr"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":12,"year":"2024","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-10-15T08:30:04Z","_id":"15257","date_created":"2024-04-02T11:35:58Z","oa":1,"status":"public","oa_version":"Published Version","day":"05","publication":"eLife","language":[{"iso":"eng"}],"article_type":"original","ddc":["580"],"file":[{"file_name":"2024_eLife_Kulich.pdf","date_created":"2024-04-03T13:18:00Z","content_type":"application/pdf","date_updated":"2024-04-03T13:18:00Z","access_level":"open_access","file_id":"15288","creator":"dernst","success":1,"file_size":11451904,"relation":"main_file","checksum":"a73a84d3bf97a6d09d24308ca6dd0a0c"}],"external_id":{"pmid":["38441122"]},"has_accepted_license":"1","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supplementarymaterial":"yes","das_tickbox":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation."}],"file_date_updated":"2024-04-03T13:18:00Z","DOAJ_listed":"1","fulldoi":"https://doi.org/10.7554/elife.91523","type":"journal_article","researchdata_availability":"yes (supplementary data)","related_material":{"link":[{"url":"https://ista.ac.at/en/news/beneath-the-surface/","relation":"press_release","description":"News on ISTA website"}],"record":[{"id":"22984","status":"public","relation":"dissertation_contains"}]},"article_number":"91523","author":[{"full_name":"Kulich, Ivan","first_name":"Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"full_name":"Schmid, Julia","first_name":"Julia","last_name":"Schmid","id":"07cf4637-baaf-11ee-9227-e1de57d1d69b"},{"full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova"},{"orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"month":"03","ec_funded":1,"publisher":"eLife Sciences Publications","date_published":"2024-03-05T00:00:00Z","title":"Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism","intvolume":"        12","scopus_import":"1","dataavailabilitystatement":"All data generated in this study are included as a manuscript supporting files.","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F. This research was also supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria, namely Tereza Bělinová for her help with the imaging. JS was supported by FemTECH fellowship.","doi":"10.7554/elife.91523","article_processing_charge":"Yes","corr_author":"1","quality_controlled":"1"},{"publication":"eLife","day":"05","date_updated":"2026-10-02T11:21:40Z","oa":1,"_id":"11448","date_created":"2022-06-18T09:06:59Z","status":"public","oa_version":"Published Version","year":"2022","project":[{"grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":11,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","has_accepted_license":"1","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"file":[{"relation":"main_file","file_size":5297213,"checksum":"7573c28f44028ab0cc81faef30039e44","success":1,"creator":"dernst","access_level":"open_access","file_id":"11454","date_updated":"2022-06-20T07:44:19Z","content_type":"application/pdf","file_name":"2022_eLife_Somermeyer.pdf","date_created":"2022-06-20T07:44:19Z"}],"external_id":{"pmid":["35510622"],"isi":["000799197200001"]},"article_type":"original","language":[{"iso":"eng"}],"ddc":["570"],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"17850","relation":"dissertation_contains"}],"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}]},"article_number":"75842","month":"05","author":[{"orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa"},{"first_name":"Aubin","full_name":"Fleiss, Aubin","last_name":"Fleiss"},{"last_name":"Mishin","full_name":"Mishin, Alexander S","first_name":"Alexander S"},{"first_name":"Nina G","full_name":"Bozhanova, Nina G","last_name":"Bozhanova"},{"first_name":"Anna A","full_name":"Igolkina, Anna A","last_name":"Igolkina"},{"full_name":"Meiler, Jens","first_name":"Jens","last_name":"Meiler"},{"last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda","first_name":"Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S","first_name":"Karen S"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"}],"fulldoi":"https://doi.org/10.7554/elife.75842","type":"journal_article","abstract":[{"text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.","lang":"eng"}],"file_date_updated":"2022-06-20T07:44:19Z","isi":1,"doi":"10.7554/elife.75842","article_processing_charge":"No","corr_author":"1","quality_controlled":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publisher":"eLife Sciences Publications","date_published":"2022-05-05T00:00:00Z","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","intvolume":"        11"},{"publisher":"eLife Sciences Publications","intvolume":"        10","date_published":"2021-02-22T00:00:00Z","title":"Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse","article_processing_charge":"Yes","doi":"10.7554/elife.63819","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"fulldoi":"https://doi.org/10.7554/elife.63819","type":"journal_article","file_date_updated":"2024-04-09T11:13:07Z","abstract":[{"lang":"eng","text":"Synapses of glutamatergic mossy fibers (MFs) onto cerebellar unipolar brush cells (UBCs) generate slow excitatory (ON) or inhibitory (OFF) postsynaptic responses dependent on the complement of glutamate receptors expressed on the UBC’s large dendritic brush. Using mouse brain slice recording and computational modeling of synaptic transmission, we found that substantial glutamate is maintained in the UBC synaptic cleft, sufficient to modify spontaneous firing in OFF UBCs and tonically desensitize AMPARs of ON UBCs. The source of this ambient glutamate was spontaneous, spike-independent exocytosis from the MF terminal, and its level was dependent on activity of glutamate transporters EAAT1–2. Increasing levels of ambient glutamate shifted the polarity of evoked synaptic responses in ON UBCs and altered the phase of responses to in vivo-like synaptic activity. Unlike classical fast synapses, receptors at the UBC synapse are virtually always exposed to a significant level of glutamate, which varies in a graded manner during transmission."}],"article_number":"e63819","author":[{"last_name":"Balmer","first_name":"Timothy S","full_name":"Balmer, Timothy S"},{"orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurence O","full_name":"Trussell, Laurence O","last_name":"Trussell"}],"month":"02","file":[{"access_level":"open_access","file_id":"15307","date_created":"2024-04-09T11:13:07Z","file_name":"2021_eLife_Balmer.pdf","date_updated":"2024-04-09T11:13:07Z","content_type":"application/pdf","file_size":6997954,"relation":"main_file","checksum":"bbd4de2e54b7fbc11fba14f59e87fe3f","creator":"dernst","success":1}],"external_id":{"pmid":["33616036"]},"article_type":"original","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"year":"2021","department":[{"_id":"PeJo"}],"citation":{"apa":"Balmer, T. S., Borges Merjane, C., &#38; Trussell, L. O. (2021). Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.63819\">https://doi.org/10.7554/elife.63819</a>","mla":"Balmer, Timothy S., et al. “Incomplete Removal of Extracellular Glutamate Controls Synaptic Transmission and Integration at a Cerebellar Synapse.” <i>ELife</i>, vol. 10, e63819, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.63819\">10.7554/elife.63819</a>.","ieee":"T. S. Balmer, C. Borges Merjane, and L. O. Trussell, “Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"T.S. Balmer, C. Borges Merjane, L.O. Trussell, ELife 10 (2021).","ista":"Balmer TS, Borges Merjane C, Trussell LO. 2021. Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse. eLife. 10, e63819.","chicago":"Balmer, Timothy S, Carolina Borges Merjane, and Laurence O Trussell. “Incomplete Removal of Extracellular Glutamate Controls Synaptic Transmission and Integration at a Cerebellar Synapse.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.63819\">https://doi.org/10.7554/elife.63819</a>.","ama":"Balmer TS, Borges Merjane C, Trussell LO. Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.63819\">10.7554/elife.63819</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"publication":"eLife","day":"22","date_created":"2024-04-03T07:58:11Z","_id":"15273","oa":1,"date_updated":"2024-04-09T11:15:01Z","oa_version":"Published Version","status":"public"},{"ddc":["570"],"article_type":"original","language":[{"iso":"eng"}],"external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"file":[{"success":1,"creator":"dernst","checksum":"fad13c509b53bb7a2bef9c946a7ca60a","relation":"main_file","file_size":14137503,"date_updated":"2022-05-13T09:00:29Z","content_type":"application/pdf","file_name":"2021_eLife_Marconi.pdf","date_created":"2022-05-13T09:00:29Z","file_id":"11372","access_level":"open_access"}],"publication_identifier":{"issn":["2050-084X"]},"pmid":1,"has_accepted_license":"1","publication_status":"published","volume":10,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"EvBe"}],"citation":{"ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Marconi, M., Gallemi, M., Benková, E., &#38; Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>","mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>, vol. 10, 72132, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>."},"year":"2021","oa_version":"Published Version","status":"public","_id":"10270","date_created":"2021-11-11T10:05:18Z","oa":1,"date_updated":"2023-08-14T11:49:23Z","day":"01","publication":"eLife","intvolume":"        10","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","date_published":"2021-11-01T00:00:00Z","publisher":"eLife Sciences Publications","scopus_import":"1","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","article_processing_charge":"Yes","doi":"10.7554/elife.72132","isi":1,"file_date_updated":"2022-05-13T09:00:29Z","abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.72132","author":[{"last_name":"Marconi","first_name":"Marco","full_name":"Marconi, Marco"},{"first_name":"Marçal","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","orcid":"0000-0003-4675-6893"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Wabnik, Krzysztof","first_name":"Krzysztof","last_name":"Wabnik"}],"month":"11","article_number":"72132"},{"oa_version":"Published Version","status":"public","_id":"10301","oa":1,"date_created":"2021-11-18T06:59:45Z","date_updated":"2024-10-21T06:02:05Z","day":"17","publication":"eLife","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"department":[{"_id":"GaNo"}],"citation":{"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>","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.","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.","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>."},"year":"2021","publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","publication_status":"published","ddc":["570"],"language":[{"iso":"eng"}],"article_type":"original","external_id":{"isi":["000720945900001"]},"file":[{"file_id":"10302","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-11-18T07:02:02Z","date_created":"2021-11-18T07:02:02Z","file_name":"elife-71575-v1.pdf","checksum":"59318e9e41507cec83c2f4070e6ad540","relation":"main_file","file_size":2477302,"success":1,"creator":"lgarciar"}],"author":[{"last_name":"Conde-Dusman","first_name":"María J","full_name":"Conde-Dusman, María J"},{"last_name":"Dey","full_name":"Dey, Partha N","first_name":"Partha N"},{"last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar","first_name":"Óscar"},{"first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda","id":"33D1B084-F248-11E8-B48F-1D18A9856A87"},{"full_name":"García-Lira, Carmen","first_name":"Carmen","last_name":"García-Lira"},{"last_name":"Grand","first_name":"Teddy","full_name":"Grand, Teddy"},{"last_name":"Briz","first_name":"Victor","full_name":"Briz, Victor"},{"full_name":"Velasco, Eric R","first_name":"Eric R","last_name":"Velasco"},{"full_name":"Andero Galí, Raül","first_name":"Raül","last_name":"Andero Galí"},{"last_name":"Niñerola","full_name":"Niñerola, Sergio","first_name":"Sergio"},{"last_name":"Barco","first_name":"Angel","full_name":"Barco, Angel"},{"last_name":"Paoletti","full_name":"Paoletti, Pierre","first_name":"Pierre"},{"last_name":"Wesseling","first_name":"John F","full_name":"Wesseling, John F"},{"full_name":"Gardoni, Fabrizio","first_name":"Fabrizio","last_name":"Gardoni"},{"last_name":"Tavalin","first_name":"Steven J","full_name":"Tavalin, Steven J"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"month":"11","article_number":"e71575","isi":1,"file_date_updated":"2021-11-18T07:02:02Z","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"}],"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.71575","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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.7554/elife.71575","intvolume":"        10","date_published":"2021-11-17T00:00:00Z","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","publisher":"eLife Sciences Publications","scopus_import":"1"},{"day":"01","publication":"eLife","status":"public","oa_version":"Published Version","date_updated":"2025-04-14T07:57:42Z","_id":"10533","date_created":"2021-12-10T13:12:08Z","oa":1,"project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020","grant_number":"725746"}],"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"citation":{"apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>."},"department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"file":[{"checksum":"22ed4c55fb550f6da02ae55c359be651","relation":"main_file","file_size":2715200,"success":1,"creator":"dernst","file_id":"11384","access_level":"open_access","date_updated":"2022-05-16T10:42:22Z","content_type":"application/pdf","date_created":"2022-05-16T10:42:22Z","file_name":"2021_eLife_Choi.pdf"}],"ddc":["570"],"article_type":"original","language":[{"iso":"eng"}],"ec_funded":1,"author":[{"last_name":"Choi","full_name":"Choi, Jaemyung","first_name":"Jaemyung"},{"last_name":"Lyons","full_name":"Lyons, David B","first_name":"David B"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"month":"12","article_number":"e72676","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.72676","isi":1,"abstract":[{"lang":"eng","text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin."}],"file_date_updated":"2022-05-16T10:42:22Z","corr_author":"1","quality_controlled":"1","doi":"10.7554/elife.72676","article_processing_charge":"No","keyword":["genetics and molecular biology"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","scopus_import":"1","date_published":"2021-12-01T00:00:00Z","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","intvolume":"        10","publisher":"eLife Sciences Publications"},{"keyword":["Genetics and Molecular Biology"],"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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","quality_controlled":"1","doi":"10.7554/elife.65993","article_processing_charge":"Yes","date_published":"2021-03-08T00:00:00Z","title":"Local genetic context shapes the function of a gene regulatory network","intvolume":"        10","publisher":"eLife Sciences Publications","scopus_import":"1","month":"03","author":[{"full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","full_name":"Tomasek, Kathrin","first_name":"Kathrin","orcid":"0000-0003-3768-877X"},{"last_name":"Caruso Carter","first_name":"Caroline","full_name":"Caruso Carter, Caroline"},{"first_name":"Elisabeth","full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner"},{"orcid":"0000-0001-6041-254X","first_name":"Bor","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixão","first_name":"Tiago","full_name":"Paixão, Tiago"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"}],"related_material":{"record":[{"id":"8951","status":"public","relation":"research_data"}]},"article_number":"e65993","ec_funded":1,"isi":1,"abstract":[{"lang":"eng","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."}],"file_date_updated":"2021-03-23T10:12:58Z","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.65993","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","publication_status":"published","ddc":["570"],"language":[{"iso":"eng"}],"article_type":"original","external_id":{"pmid":["33683203"],"isi":["000631050900001"]},"file":[{"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","file_size":1390469,"relation":"main_file","creator":"bkavcic","success":1,"file_id":"9284","access_level":"open_access","date_created":"2021-03-23T10:12:58Z","file_name":"elife-65993-v2.pdf","date_updated":"2021-03-23T10:12:58Z","content_type":"application/pdf"}],"status":"public","oa_version":"Published Version","date_updated":"2025-06-12T06:36:17Z","date_created":"2021-03-23T10:11:46Z","_id":"9283","oa":1,"day":"08","publication":"eLife","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"citation":{"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>.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","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.","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>","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.","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>.","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>"},"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"project":[{"_id":"2517526A-B435-11E9-9278-68D0E5697425","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","grant_number":"628377","call_identifier":"FP7"},{"name":"Cybergenetic circuits to test composability of gene networks","_id":"268BFA92-B435-11E9-9278-68D0E5697425","grant_number":"I03901","call_identifier":"FWF"}],"year":"2021"},{"ddc":["570"],"language":[{"iso":"eng"}],"article_type":"original","external_id":{"pmid":["32896271"]},"file":[{"checksum":"f8b3821349a194050be02570d8fe7d4b","file_size":4399825,"relation":"main_file","creator":"dernst","success":1,"file_id":"11132","access_level":"open_access","date_created":"2022-04-08T06:53:10Z","file_name":"2020_eLife_Bersini.pdf","date_updated":"2022-04-08T06:53:10Z","content_type":"application/pdf"}],"publication_identifier":{"issn":["2050-084X"]},"pmid":1,"has_accepted_license":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":9,"citation":{"apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>","mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>.","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"year":"2020","oa_version":"Published Version","status":"public","_id":"11055","oa":1,"date_created":"2022-04-07T07:43:48Z","date_updated":"2024-10-14T11:17:02Z","day":"08","publication":"eLife","intvolume":"         9","title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","date_published":"2020-09-08T00:00:00Z","publisher":"eLife Sciences Publications","extern":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.7554/elife.54383","file_date_updated":"2022-04-08T06:53:10Z","abstract":[{"text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro.","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.54383","author":[{"last_name":"Bersini","full_name":"Bersini, Simone","first_name":"Simone"},{"full_name":"Schulte, Roberta","first_name":"Roberta","last_name":"Schulte"},{"last_name":"Huang","first_name":"Ling","full_name":"Huang, Ling"},{"last_name":"Tsai","first_name":"Hannah","full_name":"Tsai, Hannah"},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X"}],"month":"09","article_number":"e54383"},{"type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.55275","abstract":[{"text":"Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.","lang":"eng"}],"month":"02","author":[{"last_name":"Fribourgh","first_name":"Jennifer L","full_name":"Fribourgh, Jennifer L"},{"last_name":"Srivastava","first_name":"Ashutosh","full_name":"Srivastava, Ashutosh"},{"full_name":"Sandate, Colby R","first_name":"Colby R","last_name":"Sandate"},{"first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Hsu, Peter L","first_name":"Peter L","last_name":"Hsu"},{"last_name":"Rakers","full_name":"Rakers, Christin","first_name":"Christin"},{"last_name":"Nguyen","full_name":"Nguyen, Leslee T","first_name":"Leslee T"},{"first_name":"Megan R","full_name":"Torgrimson, Megan R","last_name":"Torgrimson"},{"first_name":"Gian Carlo G","full_name":"Parico, Gian Carlo G","last_name":"Parico"},{"last_name":"Tripathi","first_name":"Sarvind","full_name":"Tripathi, Sarvind"},{"full_name":"Zheng, Ning","first_name":"Ning","last_name":"Zheng"},{"first_name":"Gabriel C","full_name":"Lander, Gabriel C","last_name":"Lander"},{"last_name":"Hirota","full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi"},{"last_name":"Tama","full_name":"Tama, Florence","first_name":"Florence"},{"last_name":"Partch","full_name":"Partch, Carrie L","first_name":"Carrie L"}],"article_number":"55275","scopus_import":"1","intvolume":"         9","title":"Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing","date_published":"2020-02-26T00:00:00Z","publisher":"eLife Sciences Publications","extern":"1","quality_controlled":"1","article_processing_charge":"No","doi":"10.7554/elife.55275","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"year":"2020","volume":9,"citation":{"ieee":"J. L. Fribourgh <i>et al.</i>, “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>.","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>","mla":"Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>, vol. 9, 55275, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>."},"day":"26","publication":"eLife","oa_version":"Published Version","status":"public","date_created":"2024-03-21T07:55:12Z","_id":"15153","oa":1,"main_file_link":[{"url":"https://doi.org/10.7554/eLife.55275","open_access":"1"}],"date_updated":"2024-03-25T12:25:02Z","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]}},{"article_processing_charge":"No","doi":"10.7554/elife.51512","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","publisher":"eLife Sciences Publications","intvolume":"         9","title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","date_published":"2020-03-11T00:00:00Z","article_number":"51512","month":"03","author":[{"full_name":"Moon, Hyang Mi","first_name":"Hyang Mi","last_name":"Moon"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"first_name":"Anthony","full_name":"Wynshaw-Boris, Anthony","last_name":"Wynshaw-Boris"}],"fulldoi":"https://doi.org/10.7554/elife.51512","type":"journal_article","file_date_updated":"2020-09-24T07:03:20Z","abstract":[{"lang":"eng","text":"Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation."}],"isi":1,"publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"file":[{"relation":"main_file","file_size":15089438,"checksum":"396ceb2dd10b102ef4e699666b9342c3","success":1,"creator":"dernst","access_level":"open_access","file_id":"8567","content_type":"application/pdf","date_updated":"2020-09-24T07:03:20Z","date_created":"2020-09-24T07:03:20Z","file_name":"2020_elife_Moon.pdf"}],"external_id":{"isi":["000522835800001"],"pmid":["32159512"]},"article_type":"original","language":[{"iso":"eng"}],"ddc":["570"],"publication":"eLife","day":"11","oa":1,"_id":"7593","date_created":"2020-03-20T13:16:41Z","date_updated":"2023-08-18T07:06:31Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/751958"}],"oa_version":"Published Version","status":"public","year":"2020","department":[{"_id":"SiHi"}],"citation":{"ieee":"H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","chicago":"Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>.","ista":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 9, 51512.","ama":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>","mla":"Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>, vol. 9, 51512, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>.","apa":"Moon, H. M., Hippenmeyer, S., Luo, L., &#38; Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":9},{"publisher":"eLife Sciences Publications","intvolume":"         9","date_published":"2020-04-08T00:00:00Z","title":"Direct ETTIN-auxin interaction controls chromatin states in gynoecium development","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","doi":"10.7554/elife.51787","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"lang":"eng","text":"Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner."}],"isi":1,"fulldoi":"https://doi.org/10.7554/elife.51787","type":"journal_article","article_number":"e51787","author":[{"last_name":"Kuhn","first_name":"André","full_name":"Kuhn, André"},{"full_name":"Ramans Harborough, Sigurd","first_name":"Sigurd","last_name":"Ramans Harborough"},{"last_name":"McLaughlin","full_name":"McLaughlin, Heather M","first_name":"Heather M"},{"first_name":"Bhavani","full_name":"Natarajan, Bhavani","last_name":"Natarajan"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Kepinski, Stefan","first_name":"Stefan","last_name":"Kepinski"},{"full_name":"Østergaard, Lars","first_name":"Lars","last_name":"Østergaard"}],"month":"04","article_type":"original","language":[{"iso":"eng"}],"ddc":["580"],"file":[{"creator":"dernst","checksum":"15d740de1a741fdcc6ec128c48eed017","file_size":2893082,"relation":"main_file","date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf","date_created":"2020-05-04T09:06:43Z","file_name":"2020_eLife_Kuhn.pdf","file_id":"7794","access_level":"open_access"}],"external_id":{"pmid":["32267233"],"isi":["000527752200001"]},"has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"citation":{"ieee":"A. Kuhn <i>et al.</i>, “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020).","ista":"Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787.","chicago":"Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.51787\">https://doi.org/10.7554/elife.51787</a>.","ama":"Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.51787\">10.7554/elife.51787</a>","apa":"Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.51787\">https://doi.org/10.7554/elife.51787</a>","mla":"Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” <i>ELife</i>, vol. 9, e51787, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.51787\">10.7554/elife.51787</a>."},"volume":9,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2020","oa":1,"_id":"7793","date_created":"2020-05-04T08:50:47Z","date_updated":"2023-08-21T06:17:12Z","oa_version":"Published Version","status":"public","day":"08","publication":"eLife"},{"doi":"10.7554/elife.55190","article_processing_charge":"No","corr_author":"1","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","publisher":"eLife Sciences Publications","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","date_published":"2020-04-06T00:00:00Z","intvolume":"         9","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"article_number":"e55190","author":[{"full_name":"Schauer, Alexandra","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","orcid":"0000-0001-7659-9142"},{"last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C","first_name":"Diana C","orcid":"0000-0003-4333-7503"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"month":"04","fulldoi":"https://doi.org/10.7554/elife.55190","type":"journal_article","abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"file_date_updated":"2020-07-14T12:48:04Z","isi":1,"publication_status":"published","has_accepted_license":"1","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"file":[{"creator":"dernst","file_size":7744848,"relation":"main_file","checksum":"f6aad884cf706846ae9357fcd728f8b5","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","file_name":"2020_eLife_Schauer.pdf","date_created":"2020-05-25T15:15:43Z","access_level":"open_access","file_id":"7890"}],"external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"language":[{"iso":"eng"}],"article_type":"original","ddc":["570"],"day":"06","publication":"eLife","date_updated":"2026-11-06T23:30:11Z","_id":"7888","oa":1,"date_created":"2020-05-25T15:01:40Z","status":"public","oa_version":"Published Version","year":"2020","project":[{"grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., &#38; Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>, vol. 9, e55190, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>."},"department":[{"_id":"CaHe"},{"_id":"Bio"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":9},{"day":"10","publication":"eLife","_id":"11060","oa":1,"date_created":"2022-04-07T07:45:02Z","date_updated":"2024-10-14T12:08:36Z","oa_version":"Published Version","status":"public","year":"2019","citation":{"apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., &#38; Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>","mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>, vol. 8, e49796, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796.","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>.","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019."},"volume":8,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"file":[{"success":1,"creator":"dernst","file_size":6984654,"relation":"main_file","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","content_type":"application/pdf","date_updated":"2022-04-08T08:18:01Z","file_name":"2019_eLife_Buchwalter.pdf","date_created":"2022-04-08T08:18:01Z","access_level":"open_access","file_id":"11138"}],"external_id":{"pmid":["31599721"]},"language":[{"iso":"eng"}],"article_type":"original","ddc":["570"],"article_number":"e49796","related_material":{"record":[{"relation":"research_data","status":"public","id":"13079"}]},"month":"10","author":[{"full_name":"Buchwalter, Abigail","first_name":"Abigail","last_name":"Buchwalter"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"first_name":"Hsiao","full_name":"Tsai, Hsiao","last_name":"Tsai"},{"full_name":"Capitanio, Juliana","first_name":"Juliana","last_name":"Capitanio"},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"fulldoi":"https://doi.org/10.7554/elife.49796","type":"journal_article","file_date_updated":"2022-04-08T08:18:01Z","abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"article_processing_charge":"No","doi":"10.7554/elife.49796","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"scopus_import":"1","extern":"1","publisher":"eLife Sciences Publications","intvolume":"         8","date_published":"2019-10-10T00:00:00Z","title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress"},{"month":"05","author":[{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"}],"article_number":"42530","abstract":[{"text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.","lang":"eng"}],"file_date_updated":"2023-02-07T09:42:46Z","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.42530","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.7554/elife.42530","article_processing_charge":"No","date_published":"2019-05-28T00:00:00Z","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","intvolume":"         8","extern":"1","publisher":"eLife Sciences Publications","scopus_import":"1","status":"public","oa_version":"Published Version","date_updated":"2025-01-14T14:31:41Z","_id":"12192","oa":1,"date_created":"2023-01-16T09:17:21Z","publication":"eLife","day":"28","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":8,"citation":{"mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>, vol. 8, 42530, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>.","apa":"He, S., Vickers, M., Zhang, J., &#38; Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>.","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019."},"department":[{"_id":"XiFe"}],"year":"2019","publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","publication_status":"published","ddc":["580"],"article_type":"original","language":[{"iso":"eng"}],"external_id":{"unknown":["31135340"]},"file":[{"creator":"alisjak","success":1,"checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_size":2493837,"relation":"main_file","file_name":"2019_elife_He.pdf","date_created":"2023-02-07T09:42:46Z","date_updated":"2023-02-07T09:42:46Z","content_type":"application/pdf","file_id":"12525","access_level":"open_access"}]},{"fulldoi":"https://doi.org/10.7554/elife.44494","type":"journal_article","abstract":[{"lang":"eng","text":"Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena."}],"file_date_updated":"2020-07-14T12:47:57Z","isi":1,"article_number":"e44494","author":[{"last_name":"Dura-Bernal","first_name":"Salvador","full_name":"Dura-Bernal, Salvador"},{"orcid":"0000-0002-9885-6936","first_name":"Benjamin","full_name":"Suter, Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Padraig","full_name":"Gleeson, Padraig","last_name":"Gleeson"},{"last_name":"Cantarelli","first_name":"Matteo","full_name":"Cantarelli, Matteo"},{"full_name":"Quintana, Adrian","first_name":"Adrian","last_name":"Quintana"},{"full_name":"Rodriguez, Facundo","first_name":"Facundo","last_name":"Rodriguez"},{"last_name":"Kedziora","first_name":"David J","full_name":"Kedziora, David J"},{"full_name":"Chadderdon, George L","first_name":"George L","last_name":"Chadderdon"},{"last_name":"Kerr","full_name":"Kerr, Cliff C","first_name":"Cliff C"},{"full_name":"Neymotin, Samuel A","first_name":"Samuel A","last_name":"Neymotin"},{"last_name":"McDougal","first_name":"Robert A","full_name":"McDougal, Robert A"},{"first_name":"Michael","full_name":"Hines, Michael","last_name":"Hines"},{"last_name":"Shepherd","full_name":"Shepherd, Gordon MG","first_name":"Gordon MG"},{"first_name":"William W","full_name":"Lytton, William W","last_name":"Lytton"}],"month":"05","scopus_import":"1","publisher":"eLife Sciences Publications","title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits","date_published":"2019-05-31T00:00:00Z","intvolume":"         8","doi":"10.7554/elife.44494","article_processing_charge":"No","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","citation":{"apa":"Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>","mla":"Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>, vol. 8, e44494, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>.","ieee":"S. Dura-Bernal <i>et al.</i>, “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ama":"Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>","chicago":"Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>.","short":"S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019).","ista":"Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494."},"department":[{"_id":"PeJo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":8,"publication":"eLife","day":"31","date_updated":"2023-09-07T14:27:52Z","oa":1,"_id":"7405","date_created":"2020-01-30T09:08:01Z","status":"public","oa_version":"Published Version","file":[{"checksum":"7014189c11c10a12feeeae37f054871d","file_size":6182359,"relation":"main_file","creator":"dernst","file_id":"7444","access_level":"open_access","date_created":"2020-02-04T08:41:47Z","file_name":"2019_eLife_DuraBernal.pdf","date_updated":"2020-07-14T12:47:57Z","content_type":"application/pdf"}],"external_id":{"pmid":["31025934"],"isi":["000468968400001"]},"article_type":"original","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","has_accepted_license":"1","pmid":1,"publication_identifier":{"issn":["2050-084X"]}},{"ec_funded":1,"author":[{"orcid":"0000-0002-7926-0221","first_name":"Katarina","full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková"},{"full_name":"Biebl, Julia","first_name":"Julia","last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","orcid":"0000-0001-9588-1389"},{"first_name":"Shamsi","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","last_name":"Emtenani","orcid":"0000-0001-6981-6938"},{"last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X"},{"last_name":"Misova","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","full_name":"Misova, Michaela","first_name":"Michaela","orcid":"0000-0003-2427-6856"},{"orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh"},{"orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","full_name":"Dos Reis Rodrigues, Patricia","first_name":"Patricia"},{"last_name":"Shkarina","first_name":"Katerina","full_name":"Shkarina, Katerina"},{"full_name":"Larsen, Ida Signe Bohse","first_name":"Ida Signe Bohse","last_name":"Larsen"},{"full_name":"Vakhrushev, Sergey Y","first_name":"Sergey Y","last_name":"Vakhrushev"},{"first_name":"Henrik","full_name":"Clausen, Henrik","last_name":"Clausen"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","full_name":"Siekhaus, Daria E"}],"month":"03","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/"}],"record":[{"id":"6530","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8983","status":"public"},{"relation":"dissertation_contains","id":"6546","status":"public"}]},"article_number":"e41801","type":"journal_article","fulldoi":"https://doi.org/10.7554/elife.41801","isi":1,"abstract":[{"lang":"eng","text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis."}],"file_date_updated":"2020-07-14T12:47:23Z","quality_controlled":"1","doi":"10.7554/elife.41801","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","date_published":"2019-03-26T00:00:00Z","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","intvolume":"         8","publisher":"eLife Sciences Publications","day":"26","publication":"eLife","status":"public","oa_version":"Published Version","date_updated":"2026-11-06T23:30:55Z","_id":"6187","date_created":"2019-03-28T13:37:45Z","oa":1,"project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF"},{"name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077"},{"call_identifier":"FP7","grant_number":"329540","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","_id":"25388084-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"year":"2019","volume":8,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>","mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>, vol. 8, e41801, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>.","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Dos Reis Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Dos Reis Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019).","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>.","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>","ieee":"K. Valosková <i>et al.</i>, “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019."},"department":[{"_id":"DaSi"}],"publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"}],"publication_identifier":{"issn":["2050-084X"]},"has_accepted_license":"1","external_id":{"isi":["000462530200001"]},"file":[{"date_updated":"2020-07-14T12:47:23Z","content_type":"application/pdf","file_name":"2019_eLife_Valoskova.pdf","date_created":"2019-03-28T14:00:41Z","file_id":"6188","access_level":"open_access","creator":"dernst","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","file_size":4496017,"relation":"main_file"}],"ddc":["570"],"language":[{"iso":"eng"}]},{"oa_version":"Published Version","status":"public","oa":1,"_id":"5861","date_created":"2019-01-20T22:59:19Z","date_updated":"2025-07-10T11:53:05Z","publication":"eLife","day":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":7,"department":[{"_id":"MiSi"}],"citation":{"ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.37888\">https://doi.org/10.7554/eLife.37888</a>.","ama":"Alanko JH, Sixt MK. The cell sets the tone. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.37888\">10.7554/eLife.37888</a>","apa":"Alanko, J. H., &#38; Sixt, M. K. (2018). The cell sets the tone. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.37888\">https://doi.org/10.7554/eLife.37888</a>","mla":"Alanko, Jonna H., and Michael K. 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