[{"oa":1,"type":"journal_article","_id":"9361","day":"14","quality_controlled":"1","intvolume":"         6","month":"04","date_created":"2021-05-02T22:01:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"article_processing_charge":"No","date_published":"2021-04-14T00:00:00Z","abstract":[{"text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.","lang":"eng"}],"publication_status":"published","status":"public","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_number":"e01024-20","fulldoi":"https://doi.org/10.1128/mSphere.01024-20","file":[{"access_level":"open_access","success":1,"checksum":"310748d140c8838335c1314431095898","creator":"kschuh","relation":"main_file","file_id":"9370","date_updated":"2021-05-04T12:41:38Z","content_type":"application/pdf","file_name":"2021_mSphere_Gast.pdf","date_created":"2021-05-04T12:41:38Z","file_size":3379349}],"author":[{"last_name":"Gast","full_name":"Gast, Matthieu","first_name":"Matthieu"},{"full_name":"Kadzioch, Nicole P.","first_name":"Nicole P.","last_name":"Kadzioch"},{"full_name":"Milius, Doreen","first_name":"Doreen","last_name":"Milius","id":"384050BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Origgi","first_name":"Francesco","full_name":"Origgi, Francesco"},{"last_name":"Plattet","full_name":"Plattet, Philippe","first_name":"Philippe"}],"publication":"mSphere","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","publication_identifier":{"eissn":["2379-5042"]},"file_date_updated":"2021-05-04T12:41:38Z","issue":"2","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","ddc":["570"],"pmid":1,"external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"date_updated":"2026-04-02T13:58:38Z","doi":"10.1128/mSphere.01024-20","scopus_import":"1","citation":{"mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>.","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., &#38; Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>MSphere</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” <i>mSphere</i>, vol. 6, no. 2. American Society for Microbiology, 2021.","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>. American Society for Microbiology, 2021. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>.","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>mSphere</i>. 2021;6(2). doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20."},"year":"2021","department":[{"_id":"Bio"}],"publisher":"American Society for Microbiology","volume":6},{"oa":1,"quality_controlled":"1","_id":"9363","type":"journal_article","day":"01","date_created":"2021-05-02T22:01:29Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"04","intvolume":"        17","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","abstract":[{"text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair.","lang":"eng"}],"status":"public","has_accepted_license":"1","date_published":"2021-04-01T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","orcid":"0000-0002-5409-8571"},{"last_name":"Furthmann","first_name":"Nikolas","full_name":"Furthmann, Nikolas"},{"last_name":"Crossman","full_name":"Crossman, Samuel H.","first_name":"Samuel H."},{"last_name":"Tichy","full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine"},{"last_name":"Hoyer","full_name":"Hoyer, Nina","first_name":"Nina"},{"last_name":"Petersen","full_name":"Petersen, Meike","first_name":"Meike"},{"last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"last_name":"Bicher","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Bicher, Julia"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"},{"last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila"},{"last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","first_name":"Daria E","orcid":"0000-0001-8323-8353"},{"full_name":"Soba, Peter","first_name":"Peter","last_name":"Soba"},{"last_name":"Winklhofer","first_name":"Konstanze F.","full_name":"Winklhofer, Konstanze F."},{"full_name":"Janovjak, Harald L","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"}],"publication":"PLoS genetics","file":[{"file_size":3072764,"date_created":"2021-05-04T09:05:27Z","file_name":"2021_PLOS_Ingles-Prieto.pdf","checksum":"82a74668f863e8dfb22fdd4f845c92ce","success":1,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","date_updated":"2021-05-04T09:05:27Z","file_id":"9369","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1371/journal.pgen.1009479","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","page":"e1009479","publication_identifier":{"eissn":["1553-7404"]},"acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","ddc":["570"],"issue":"4","file_date_updated":"2021-05-04T09:05:27Z","scopus_import":"1","doi":"10.1371/journal.pgen.1009479","date_updated":"2026-04-02T14:07:10Z","external_id":{"isi":["000640606700001"],"pmid":["33857132"]},"pmid":1,"publisher":"Public Library of Science","volume":17,"department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"citation":{"mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>.","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS genetics</i>. 2021;17(4):e1009479. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>","ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","ieee":"Á. Inglés Prieto <i>et al.</i>, “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” <i>PLoS genetics</i>, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021."},"year":"2021"},{"status":"public","abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"has_accepted_license":"1","publication_status":"published","date_published":"2021-06-09T00:00:00Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"}],"isi":1,"oa_version":"Published Version","article_number":"3483","article_type":"original","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","type":"journal_article","_id":"9540","day":"09","date_created":"2021-06-10T14:57:45Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"month":"06","intvolume":"        12","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","doi":"10.1038/s41467-021-23854-x","date_updated":"2024-10-21T06:02:01Z","pmid":1,"external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"publisher":"Springer Nature","volume":12,"department":[{"_id":"EM-Fac"}],"year":"2021","citation":{"ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>."},"author":[{"first_name":"Michael","full_name":"Prattes, Michael","last_name":"Prattes"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Rössler","first_name":"Ingrid","full_name":"Rössler, Ingrid"},{"last_name":"Klein","first_name":"Isabella","full_name":"Klein, Isabella"},{"full_name":"Hetzmannseder, Christina","first_name":"Christina","last_name":"Hetzmannseder"},{"last_name":"Zisser","full_name":"Zisser, Gertrude","first_name":"Gertrude"},{"last_name":"Gruber","full_name":"Gruber, Christian C.","first_name":"Christian C."},{"last_name":"Gruber","first_name":"Karl","full_name":"Gruber, Karl"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"publication":"Nature Communications","file":[{"file_size":3397292,"file_name":"2021_NatureComm_Prattes.pdf","date_created":"2021-06-15T18:55:59Z","checksum":"40fc24c1310930990b52a8ad1142ee97","success":1,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","date_updated":"2021-06-15T18:55:59Z","file_id":"9556","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1038/s41467-021-23854-x","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","ddc":["570"],"file_date_updated":"2021-06-15T18:55:59Z","issue":"1"},{"oa_version":"Published Version","abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","date_published":"2021-06-22T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"article_number":"109274","article_type":"original","language":[{"iso":"eng"}],"quality_controlled":"1","day":"22","_id":"9603","type":"journal_article","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_created":"2021-06-27T22:01:48Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","intvolume":"        35","scopus_import":"1","date_updated":"2026-04-02T14:04:28Z","doi":"10.1016/j.celrep.2021.109274","external_id":{"pmid":["34161767"],"isi":["000664463600016"]},"pmid":1,"ec_funded":1,"publisher":"Cell Press","volume":35,"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"year":"2021","citation":{"short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>, vol. 35, no. 12, 109274, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>.","ieee":"X. Contreras <i>et al.</i>, “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” <i>Cell Reports</i>, vol. 35, no. 12. Cell Press, 2021.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. 2021;35(12). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>."},"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","author":[{"full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras"},{"full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan","first_name":"Amarbayasgalan"},{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johanna","full_name":"Sonntag, Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag"},{"first_name":"Lill","full_name":"Andersen, Lill","last_name":"Andersen"},{"last_name":"Bernthaler","full_name":"Bernthaler, Tina","first_name":"Tina"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","full_name":"Heger, Anna-Magdalena"},{"last_name":"Johnson","first_name":"Randy L.","full_name":"Johnson, Randy L."},{"first_name":"Lindsay A.","full_name":"Schwarz, Lindsay A.","last_name":"Schwarz"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"publication":"Cell Reports","file":[{"file_name":"2021_CellReports_Contreras.pdf","date_created":"2021-06-28T14:06:24Z","file_size":7653149,"access_level":"open_access","file_id":"9613","date_updated":"2021-06-28T14:06:24Z","relation":"main_file","creator":"asandaue","content_type":"application/pdf","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77"}],"fulldoi":"https://doi.org/10.1016/j.celrep.2021.109274","project":[{"name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","ddc":["570"],"issue":"12","file_date_updated":"2021-06-28T14:06:24Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release","description":"News on IST Homepage"}]},"publication_identifier":{"eissn":["2211-1247"]}},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"month":"05","intvolume":"        10","date_created":"2021-06-27T22:01:49Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9607","type":"journal_article","day":"24","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","article_processing_charge":"No","isi":1,"abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"status":"public","publication_status":"published","has_accepted_license":"1","date_published":"2021-05-24T00:00:00Z","file_date_updated":"2021-06-28T11:35:30Z","ddc":["570"],"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","publication_identifier":{"eissn":["2050-084X"]},"title":"Introduction to the EQIPD quality system","file":[{"file_size":2500720,"file_name":"2021_ELife_Bespalov.pdf","date_created":"2021-06-28T11:35:30Z","file_id":"9609","creator":"asandaue","relation":"main_file","date_updated":"2021-06-28T11:35:30Z","content_type":"application/pdf","success":1,"checksum":"885b746051a7a6b6e24e3d2781a48fde","access_level":"open_access"}],"fulldoi":"https://doi.org/10.7554/eLife.63294","publication":"eLife","author":[{"last_name":"Bespalov","first_name":"Anton","full_name":"Bespalov, Anton"},{"last_name":"Bernard","full_name":"Bernard, René","first_name":"René"},{"full_name":"Gilis, Anja","first_name":"Anja","last_name":"Gilis"},{"last_name":"Gerlach","full_name":"Gerlach, Björn","first_name":"Björn"},{"last_name":"Guillén","first_name":"Javier","full_name":"Guillén, Javier"},{"last_name":"Castagné","first_name":"Vincent","full_name":"Castagné, Vincent"},{"last_name":"Lefevre","first_name":"Isabel A.","full_name":"Lefevre, Isabel A."},{"last_name":"Ducrey","full_name":"Ducrey, Fiona","first_name":"Fiona"},{"last_name":"Monk","full_name":"Monk, Lee","first_name":"Lee"},{"first_name":"Sandrine","full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni"},{"first_name":"Bruce","full_name":"Altevogt, Bruce","last_name":"Altevogt"},{"last_name":"Arroyo-Araujo","first_name":"María","full_name":"Arroyo-Araujo, María"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"first_name":"Natasja","full_name":"De Bruin, Natasja","last_name":"De Bruin"},{"last_name":"Castaños-Vélez","full_name":"Castaños-Vélez, Esmeralda","first_name":"Esmeralda"},{"first_name":"Alexander","full_name":"Dityatev, Alexander","last_name":"Dityatev"},{"first_name":"Christoph H.","full_name":"Emmerich, Christoph H.","last_name":"Emmerich"},{"first_name":"Raafat","full_name":"Fares, Raafat","last_name":"Fares"},{"last_name":"Ferland-Beckham","full_name":"Ferland-Beckham, Chantelle","first_name":"Chantelle"},{"full_name":"Froger-Colléaux, Christelle","first_name":"Christelle","last_name":"Froger-Colléaux"},{"last_name":"Gailus-Durner","first_name":"Valerie","full_name":"Gailus-Durner, Valerie"},{"first_name":"Sabine M.","full_name":"Hölter, Sabine M.","last_name":"Hölter"},{"full_name":"Hofmann, Martine Cj","first_name":"Martine Cj","last_name":"Hofmann"},{"first_name":"Patricia","full_name":"Kabitzke, Patricia","last_name":"Kabitzke"},{"full_name":"Kas, Martien Jh","first_name":"Martien Jh","last_name":"Kas"},{"last_name":"Kurreck","full_name":"Kurreck, Claudia","first_name":"Claudia"},{"last_name":"Moser","full_name":"Moser, Paul","first_name":"Paul"},{"last_name":"Pietraszek","first_name":"Malgorzata","full_name":"Pietraszek, Malgorzata"},{"first_name":"Piotr","full_name":"Popik, Piotr","last_name":"Popik"},{"last_name":"Potschka","full_name":"Potschka, Heidrun","first_name":"Heidrun"},{"last_name":"Prado Montes De Oca","first_name":"Ernesto","full_name":"Prado Montes De Oca, Ernesto"},{"first_name":"Leonardo","full_name":"Restivo, Leonardo","last_name":"Restivo"},{"last_name":"Riedel","full_name":"Riedel, Gernot","first_name":"Gernot"},{"last_name":"Ritskes-Hoitinga","first_name":"Merel","full_name":"Ritskes-Hoitinga, Merel"},{"full_name":"Samardzic, Janko","first_name":"Janko","last_name":"Samardzic"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","last_name":"Schunn","first_name":"Michael","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael"},{"last_name":"Stöger","full_name":"Stöger, Claudia","first_name":"Claudia"},{"full_name":"Voikar, Vootele","first_name":"Vootele","last_name":"Voikar"},{"last_name":"Vollert","first_name":"Jan","full_name":"Vollert, Jan"},{"first_name":"Kimberley E.","full_name":"Wever, Kimberley E.","last_name":"Wever"},{"last_name":"Wuyts","first_name":"Kathleen","full_name":"Wuyts, Kathleen"},{"last_name":"Macleod","full_name":"Macleod, Malcolm R.","first_name":"Malcolm R."},{"last_name":"Dirnagl","first_name":"Ulrich","full_name":"Dirnagl, Ulrich"},{"first_name":"Thomas","full_name":"Steckler, Thomas","last_name":"Steckler"}],"department":[{"_id":"PreCl"}],"year":"2021","citation":{"short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>, vol. 10, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>.","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>.","ieee":"A. Bespalov <i>et al.</i>, “Introduction to the EQIPD quality system,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"volume":10,"publisher":"eLife Sciences Publications","doi":"10.7554/eLife.63294","date_updated":"2026-04-02T13:55:57Z","pmid":1,"external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"scopus_import":"1"},{"language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","isi":1,"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"publication_status":"published","status":"public","has_accepted_license":"1","date_published":"2021-08-04T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"month":"08","intvolume":"        13","date_created":"2021-08-08T22:01:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"04","_id":"9822","type":"journal_article","quality_controlled":"1","corr_author":"1","oa":1,"department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"citation":{"chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. 2021;13(30):35545–35560. doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ieee":"T. Zisis <i>et al.</i>, “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>"},"year":"2021","publisher":"American Chemical Society","volume":13,"doi":"10.1021/acsami.1c09850","date_updated":"2025-07-10T12:02:02Z","pmid":1,"external_id":{"pmid":["34283577"],"isi":["000683741400026"]},"scopus_import":"1","ec_funded":1,"issue":"30","file_date_updated":"2021-08-09T09:44:03Z","acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","ddc":["620","570"],"publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","page":"35545–35560","file":[{"date_updated":"2021-08-09T09:44:03Z","creator":"asandaue","file_id":"9833","relation":"main_file","content_type":"application/pdf","success":1,"checksum":"b043a91d9f9200e467b970b692687ed3","access_level":"open_access","file_size":7123293,"file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","date_created":"2021-08-09T09:44:03Z"}],"fulldoi":"https://doi.org/10.1021/acsami.1c09850","project":[{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"first_name":"Jan","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"full_name":"Balles, Miriam","first_name":"Miriam","last_name":"Balles"},{"first_name":"Maibritt","full_name":"Kretschmer, Maibritt","last_name":"Kretschmer"},{"last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","first_name":"Maria"},{"last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","first_name":"Remy P"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Lange","full_name":"Lange, Janina","first_name":"Janina"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"publication":"ACS Applied Materials and Interfaces"},{"publication_identifier":{"issn":["0022-2720"],"eissn":["1365-2818"]},"issue":"1","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","ddc":["600"],"fulldoi":"https://doi.org/10.1111/jmi.13041","author":[{"first_name":"Glyn","full_name":"Nelson, Glyn","last_name":"Nelson"},{"full_name":"Boehm, Ulrike","first_name":"Ulrike","last_name":"Boehm"},{"last_name":"Bagley","full_name":"Bagley, Steve","first_name":"Steve"},{"last_name":"Bajcsy","full_name":"Bajcsy, Peter","first_name":"Peter"},{"first_name":"Johanna","full_name":"Bischof, Johanna","last_name":"Bischof"},{"first_name":"Claire M.","full_name":"Brown, Claire M.","last_name":"Brown"},{"last_name":"Dauphin","full_name":"Dauphin, Aurélien","first_name":"Aurélien"},{"last_name":"Dobbie","full_name":"Dobbie, Ian M.","first_name":"Ian M."},{"last_name":"Eriksson","first_name":"John E.","full_name":"Eriksson, John E."},{"first_name":"Orestis","full_name":"Faklaris, Orestis","last_name":"Faklaris"},{"last_name":"Fernandez-Rodriguez","first_name":"Julia","full_name":"Fernandez-Rodriguez, Julia"},{"last_name":"Ferrand","first_name":"Alexia","full_name":"Ferrand, Alexia"},{"last_name":"Gelman","full_name":"Gelman, Laurent","first_name":"Laurent"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"last_name":"Hartmann","full_name":"Hartmann, Hella","first_name":"Hella"},{"first_name":"Christian","full_name":"Kukat, Christian","last_name":"Kukat"},{"last_name":"Laude","first_name":"Alex","full_name":"Laude, Alex"},{"full_name":"Mitkovski, Miso","first_name":"Miso","last_name":"Mitkovski"},{"full_name":"Munck, Sebastian","first_name":"Sebastian","last_name":"Munck"},{"full_name":"North, Alison J.","first_name":"Alison J.","last_name":"North"},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"first_name":"Ute","full_name":"Resch-Genger, Ute","last_name":"Resch-Genger"},{"first_name":"Lucas C.","full_name":"Schuetz, Lucas C.","last_name":"Schuetz"},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"last_name":"Strambio-De-Castillia","first_name":"Caterina","full_name":"Strambio-De-Castillia, Caterina"},{"last_name":"Swedlow","first_name":"Jason R.","full_name":"Swedlow, Jason R."},{"last_name":"Alexopoulos","full_name":"Alexopoulos, Ioannis","first_name":"Ioannis"},{"last_name":"Aumayr","full_name":"Aumayr, Karin","first_name":"Karin"},{"first_name":"Sergiy","full_name":"Avilov, Sergiy","last_name":"Avilov"},{"full_name":"Bakker, Gert Jan","first_name":"Gert Jan","last_name":"Bakker"},{"first_name":"Rodrigo R.","full_name":"Bammann, Rodrigo R.","last_name":"Bammann"},{"full_name":"Bassi, Andrea","first_name":"Andrea","last_name":"Bassi"},{"last_name":"Beckert","first_name":"Hannes","full_name":"Beckert, Hannes"},{"full_name":"Beer, Sebastian","first_name":"Sebastian","last_name":"Beer"},{"full_name":"Belyaev, Yury","first_name":"Yury","last_name":"Belyaev"},{"first_name":"Jakob","full_name":"Bierwagen, Jakob","last_name":"Bierwagen"},{"first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A.","last_name":"Birngruber"},{"last_name":"Bosch","first_name":"Manel","full_name":"Bosch, Manel"},{"full_name":"Breitlow, Juergen","first_name":"Juergen","last_name":"Breitlow"},{"first_name":"Lisa A.","full_name":"Cameron, Lisa A.","last_name":"Cameron"},{"full_name":"Chalfoun, Joe","first_name":"Joe","last_name":"Chalfoun"},{"first_name":"James J.","full_name":"Chambers, James J.","last_name":"Chambers"},{"last_name":"Chen","first_name":"Chieh Li","full_name":"Chen, Chieh Li"},{"last_name":"Conde-Sousa","first_name":"Eduardo","full_name":"Conde-Sousa, Eduardo"},{"last_name":"Corbett","full_name":"Corbett, Alexander D.","first_name":"Alexander D."},{"first_name":"Fabrice P.","full_name":"Cordelieres, Fabrice P.","last_name":"Cordelieres"},{"full_name":"Nery, Elaine Del","first_name":"Elaine Del","last_name":"Nery"},{"last_name":"Dietzel","full_name":"Dietzel, Ralf","first_name":"Ralf"},{"last_name":"Eismann","full_name":"Eismann, Frank","first_name":"Frank"},{"last_name":"Fazeli","first_name":"Elnaz","full_name":"Fazeli, Elnaz"},{"last_name":"Felscher","first_name":"Andreas","full_name":"Felscher, Andreas"},{"last_name":"Fried","first_name":"Hans","full_name":"Fried, Hans"},{"first_name":"Nathalie","full_name":"Gaudreault, Nathalie","last_name":"Gaudreault"},{"first_name":"Wah Ing","full_name":"Goh, Wah Ing","last_name":"Goh"},{"full_name":"Guilbert, Thomas","first_name":"Thomas","last_name":"Guilbert"},{"first_name":"Roland","full_name":"Hadleigh, Roland","last_name":"Hadleigh"},{"last_name":"Hemmerich","first_name":"Peter","full_name":"Hemmerich, Peter"},{"first_name":"Gerhard A.","full_name":"Holst, Gerhard A.","last_name":"Holst"},{"last_name":"Itano","full_name":"Itano, Michelle S.","first_name":"Michelle S."},{"first_name":"Claudia B.","full_name":"Jaffe, Claudia B.","last_name":"Jaffe"},{"last_name":"Jambor","first_name":"Helena K.","full_name":"Jambor, Helena K."},{"first_name":"Stuart C.","full_name":"Jarvis, Stuart C.","last_name":"Jarvis"},{"full_name":"Keppler, Antje","first_name":"Antje","last_name":"Keppler"},{"first_name":"David","full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler"},{"last_name":"Kirchner","first_name":"Marcel","full_name":"Kirchner, Marcel"},{"full_name":"Kobayashi, Norio","first_name":"Norio","last_name":"Kobayashi"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"first_name":"Judith","full_name":"Lacoste, Judith","last_name":"Lacoste"},{"last_name":"Marcello","first_name":"Marco","full_name":"Marcello, Marco"},{"full_name":"Martins, Gabriel G.","first_name":"Gabriel G.","last_name":"Martins"},{"last_name":"Metcalf","full_name":"Metcalf, Daniel J.","first_name":"Daniel J."},{"full_name":"Mitchell, Claire A.","first_name":"Claire A.","last_name":"Mitchell"},{"full_name":"Moore, Joshua","first_name":"Joshua","last_name":"Moore"},{"first_name":"Tobias","full_name":"Mueller, Tobias","last_name":"Mueller"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"first_name":"Stephen","full_name":"Ogg, Stephen","last_name":"Ogg"},{"last_name":"Onami","first_name":"Shuichi","full_name":"Onami, Shuichi"},{"last_name":"Palmer","full_name":"Palmer, Alexandra L.","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","first_name":"Perrine","full_name":"Paul-Gilloteaux, Perrine"},{"last_name":"Pimentel","first_name":"Jaime A.","full_name":"Pimentel, Jaime A."},{"first_name":"Laure","full_name":"Plantard, Laure","last_name":"Plantard"},{"last_name":"Podder","first_name":"Santosh","full_name":"Podder, Santosh"},{"first_name":"Elton","full_name":"Rexhepaj, Elton","last_name":"Rexhepaj"},{"last_name":"Royon","first_name":"Arnaud","full_name":"Royon, Arnaud"},{"last_name":"Saari","first_name":"Markku A.","full_name":"Saari, Markku A."},{"last_name":"Schapman","full_name":"Schapman, Damien","first_name":"Damien"},{"full_name":"Schoonderwoert, Vincent","first_name":"Vincent","last_name":"Schoonderwoert"},{"first_name":"Britta","full_name":"Schroth-Diez, Britta","last_name":"Schroth-Diez"},{"last_name":"Schwartz","first_name":"Stanley","full_name":"Schwartz, Stanley"},{"full_name":"Shaw, Michael","first_name":"Michael","last_name":"Shaw"},{"full_name":"Spitaler, Martin","first_name":"Martin","last_name":"Spitaler"},{"first_name":"Martin T.","full_name":"Stoeckl, Martin T.","last_name":"Stoeckl"},{"last_name":"Sudar","first_name":"Damir","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","first_name":"Jeremie","last_name":"Teillon"},{"last_name":"Terjung","full_name":"Terjung, Stefan","first_name":"Stefan"},{"first_name":"Roland","full_name":"Thuenauer, Roland","last_name":"Thuenauer"},{"last_name":"Wilms","full_name":"Wilms, Christian D.","first_name":"Christian D."},{"last_name":"Wright","full_name":"Wright, Graham D.","first_name":"Graham D."},{"last_name":"Nitschke","full_name":"Nitschke, Roland","first_name":"Roland"}],"publication":"Journal of Microscopy","page":"56-73","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","year":"2021","citation":{"chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73."},"department":[{"_id":"Bio"}],"volume":284,"publisher":"Wiley","pmid":1,"external_id":{"isi":["000683702700001"],"pmid":["34214188"]},"doi":"10.1111/jmi.13041","date_updated":"2026-06-18T19:59:18Z","scopus_import":"1","intvolume":"       284","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-08-15T22:01:29Z","oa":1,"type":"journal_article","_id":"9911","day":"11","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","isi":1,"article_processing_charge":"Yes","date_published":"2021-08-11T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics."}],"oa_version":"Published Version"},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"isi":1,"article_processing_charge":"Yes (via OA deal)","date_published":"2021-12-29T00:00:00Z","status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials.","lang":"eng"}],"language":[{"iso":"eng"}],"article_type":"original","article_number":"2106858","_id":"10123","type":"journal_article","day":"29","corr_author":"1","quality_controlled":"1","oa":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"intvolume":"        33","month":"12","keyword":["mechanical engineering","mechanics of materials","general materials science"],"date_created":"2021-10-11T20:07:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000709899300001"],"pmid":["34626034"]},"pmid":1,"date_updated":"2026-07-06T13:07:38Z","doi":"10.1002/adma.202106858","scopus_import":"1","ec_funded":1,"citation":{"apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>, vol. 33, no. 52, 2106858, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>.","ieee":"Y. Liu <i>et al.</i>, “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” <i>Advanced Materials</i>, vol. 33, no. 52. Wiley, 2021.","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. 2021;33(52). doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>."},"year":"2021","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"publisher":"Wiley","volume":33,"title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","fulldoi":"https://doi.org/10.1002/adma.202106858","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"file":[{"file_size":5595666,"date_created":"2022-02-03T13:16:14Z","file_name":"2021_AdvancedMaterials_Liu.pdf","file_id":"10720","creator":"cchlebak","relation":"main_file","date_updated":"2022-02-03T13:16:14Z","content_type":"application/pdf","success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","access_level":"open_access"}],"author":[{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu","full_name":"Liu, Yu"},{"last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","full_name":"Calcabrini, Mariano"},{"last_name":"Yu","first_name":"Yuan","full_name":"Yu, Yuan"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"orcid":"0000-0002-9515-4277","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Costanzo, Tommaso","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo"},{"last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","orcid":"0000-0003-1537-7436","first_name":"Tobias"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Cojocaru‐Mirédin, Oana","first_name":"Oana","last_name":"Cojocaru‐Mirédin"},{"full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"publication":"Advanced Materials","issue":"52","file_date_updated":"2022-02-03T13:16:14Z","ddc":["620"],"acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"12885","status":"public"},{"relation":"later_version","id":"17062","status":"public"}]}},{"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.29363/nanoge.incnc.2021.050"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-04-03T08:28:26Z","ddc":["530"],"oa":1,"fulldoi":"https://doi.org/10.29363/nanoge.incnc.2021.050","conference":{"name":"iNCNC: Internet nanoGe Conference on Nanocrystals","end_date":"2021-07-02","start_date":"2021-06-28","location":"Virtual"},"publication":"Proceedings of the Internet NanoGe Conference on Nanocrystals","author":[{"first_name":"Daniel","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Cimada da Silva, Jessica","first_name":"Jessica","last_name":"Cimada da Silva"},{"first_name":"Tyler","full_name":"Dunbar, Tyler","last_name":"Dunbar"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843"},{"last_name":"Hanrath","full_name":"Hanrath, Tobias","first_name":"Tobias"}],"_id":"15280","day":"08","type":"conference_abstract","quality_controlled":"1","corr_author":"1","title":"Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics","citation":{"mla":"Balazs, Daniel, et al. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, 050, Fundació de la comunitat valenciana SCITO, 2021, doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>.","apa":"Balazs, D., Cimada da Silva, J., Dunbar, T., Ibáñez, M., &#38; Hanrath, T. (2021). Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Virtual: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>","short":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, T. Hanrath, in:, Proceedings of the Internet NanoGe Conference on Nanocrystals, Fundació de la comunitat valenciana SCITO, 2021.","ieee":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, and T. Hanrath, “Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics,” in <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, Virtual, 2021.","chicago":"Balazs, Daniel, Jessica Cimada da Silva, Tyler Dunbar, Maria Ibáñez, and Tobias Hanrath. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació de la comunitat valenciana SCITO, 2021. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>.","ista":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. 2021. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. Proceedings of the Internet NanoGe Conference on Nanocrystals. iNCNC: Internet nanoGe Conference on Nanocrystals, 050.","ama":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In: <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació de la comunitat valenciana SCITO; 2021. doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>"},"year":"2021","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publisher":"Fundació de la comunitat valenciana SCITO","language":[{"iso":"eng"}],"article_number":"050","article_processing_charge":"No","date_published":"2021-06-08T00:00:00Z","status":"public","publication_status":"published","date_updated":"2026-07-06T13:07:52Z","doi":"10.29363/nanoge.incnc.2021.050","oa_version":"Published Version"},{"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2021-11-24T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-08-17T08:14:18Z","keyword":["quantum physics","mesoscale and nanoscale physics"],"month":"11","intvolume":"         2","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"arxiv":1,"oa":1,"corr_author":"1","quality_controlled":"1","day":"24","_id":"9928","type":"journal_article","publisher":"American Physical Society","volume":2,"department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"year":"2021","citation":{"ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. 2021;2(4):040341. doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>.","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” <i>PRX Quantum</i>, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., &#38; Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>."},"ec_funded":1,"scopus_import":"1","date_updated":"2026-10-02T11:28:16Z","doi":"10.1103/PRXQuantum.2.040341","external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"related_material":{"record":[{"status":"public","id":"13057","relation":"research_data"},{"relation":"dissertation_contains","id":"9920","status":"public"},{"status":"public","id":"17133","relation":"dissertation_contains"}]},"publication_identifier":{"eissn":["2691-3399"]},"ddc":["530"],"acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","file_date_updated":"2022-01-18T11:29:33Z","issue":"4","publication":"PRX Quantum","author":[{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo"},{"full_name":"Hassani, Farid","first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gregory","full_name":"Szep, Gregory","last_name":"Szep"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea"},{"last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Redchenko, Elena"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","orcid":"0009-0005-0878-3032","first_name":"Martin","full_name":"Zemlicka, Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"file":[{"access_level":"open_access","success":1,"checksum":"36eb41ea43d8ca22b0efab12419e4eb2","creator":"cchlebak","file_id":"10641","relation":"main_file","date_updated":"2022-01-18T11:29:33Z","content_type":"application/pdf","file_name":"2021_PRXQuantum_Peruzzo.pdf","date_created":"2022-01-18T11:29:33Z","file_size":4247422}],"fulldoi":"https://doi.org/10.1103/PRXQuantum.2.040341","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","page":"040341"},{"publisher":"University of Ljubljana","department":[{"_id":"ScienComp"}],"year":"2021","citation":{"short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5.","apa":"Schlögl, A., Elefante, S., Hornoiu, A., &#38; Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i> (p. 5). Virtual: University of Ljubljana. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>","mla":"Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, University of Ljubljana, 2021, p. 5, doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>.","ieee":"A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software on a heterogenous HPC cluster,” in <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, Virtual, 2021, p. 5.","ama":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>. University of Ljubljana; 2021:5. doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>","ista":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC: Austrian-Slovenian HPC Meeting, 5.","chicago":"Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer. “Managing Software on a Heterogenous HPC Cluster.” In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, 5. University of Ljubljana, 2021. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>."},"doi":"10.3359/2021hpc","date_updated":"2026-10-14T09:47:31Z","ddc":["000"],"file_date_updated":"2023-05-16T07:36:34Z","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"title":"Managing software on a heterogenous HPC cluster","page":"5","publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","author":[{"first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano"},{"full_name":"Hornoiu, Andrei","first_name":"Andrei","last_name":"Hornoiu","id":"77129392-B450-11EA-8745-D4653DDC885E"},{"full_name":"Stadlbauer, Stephan","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","last_name":"Stadlbauer"}],"file":[{"access_level":"open_access","checksum":"ba73f85858fb9d5737ebc7724646dd45","success":1,"content_type":"application/pdf","relation":"main_file","creator":"dernst","date_updated":"2023-05-16T07:36:34Z","file_id":"12971","date_created":"2023-05-16T07:36:34Z","file_name":"2021_ASHPC_Schloegl.pdf","file_size":422761}],"fulldoi":"https://doi.org/10.3359/2021hpc","conference":{"end_date":"2021-06-02","name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2021-05-31","location":"Virtual"},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2021-06-02T00:00:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-05T13:17:36Z","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"month":"06","corr_author":"1","_id":"12909","type":"conference_abstract","day":"02","oa":1},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-05-28T11:49:46Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"month":"05","intvolume":"        12","quality_controlled":"1","corr_author":"1","_id":"9429","type":"journal_article","day":"24","oa":1,"article_number":"3058","language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2021-05-24T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"PreCl"}],"ddc":["572"],"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","file_date_updated":"2021-05-28T12:39:43Z","issue":"1","related_material":{"record":[{"relation":"earlier_version","id":"7800","status":"public"},{"id":"19557","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"12401"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"publication_identifier":{"eissn":["2041-1723"]},"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"full_name":"Morandell, Jasmin","first_name":"Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","full_name":"Schwarz, Lena A"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","full_name":"Basilico, Bernadette","first_name":"Bernadette","orcid":"0000-0003-1843-3173"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","first_name":"Saren"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","first_name":"Christoph","orcid":"0000-0002-9033-9096"},{"first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"},{"last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe","first_name":"Zoe"},{"last_name":"Cacci","full_name":"Cacci, Emanuele","first_name":"Emanuele"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"publication":"Nature Communications","file":[{"checksum":"337e0f7959c35ec959984cacdcb472ba","success":1,"content_type":"application/pdf","date_updated":"2021-05-28T12:39:43Z","file_id":"9430","creator":"kschuh","relation":"main_file","access_level":"open_access","file_size":9358599,"file_name":"2021_NatureCommunications_Morandell.pdf","date_created":"2021-05-28T12:39:43Z"}],"fulldoi":"https://doi.org/10.1038/s41467-021-23123-x","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232"},{"grant_number":"F7807","name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"}],"publisher":"Springer Nature","volume":12,"department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"year":"2021","citation":{"ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021)."},"scopus_import":"1","doi":"10.1038/s41467-021-23123-x","date_updated":"2026-10-25T23:30:14Z","external_id":{"isi":["000658769900010"]},"ec_funded":1},{"volume":20,"publisher":"Springer Nature","year":"2021","citation":{"ieee":"D. Jirovec <i>et al.</i>, “A singlet triplet hole spin qubit in planar Ge,” <i>Nature Materials</i>, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. 2021;20(8):1106–1112. doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” <i>Nature Materials</i>, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:<a href=\"https://doi.org/10.1038/s41563-021-01022-2\">10.1038/s41563-021-01022-2</a>.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-021-01022-2\">https://doi.org/10.1038/s41563-021-01022-2</a>"},"department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"ec_funded":1,"scopus_import":"1","external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"],"pmid":["34083775"]},"pmid":1,"doi":"10.1038/s41563-021-01022-2","date_updated":"2026-10-25T23:30:41Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9323"},{"relation":"dissertation_contains","status":"public","id":"10058"}],"link":[{"url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","relation":"press_release","description":"News on IST Homepage"}]},"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","issue":"8","author":[{"orcid":"0000-0002-7197-4801","first_name":"Daniel","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec"},{"first_name":"Andrea C","full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"last_name":"Mutter","full_name":"Mutter, Philipp M.","first_name":"Philipp M."},{"first_name":"Giulio","full_name":"Tavani, Giulio","last_name":"Tavani"},{"last_name":"Botifoll","full_name":"Botifoll, Marc","first_name":"Marc"},{"id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","last_name":"Crippa","full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","first_name":"Alessandro"},{"last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip"},{"full_name":"Sagi, Oliver","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi"},{"full_name":"Martins, Frederico","first_name":"Frederico","orcid":"0000-0003-2668-2401","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","last_name":"Martins"},{"first_name":"Jaime","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"orcid":"0000-0002-7370-5357","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Borovkov","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","first_name":"Maksim","full_name":"Borovkov, Maksim"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"publication":"Nature Materials","fulldoi":"https://doi.org/10.1038/s41563-021-01022-2","project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"page":"1106–1112","title":"A singlet triplet hole spin qubit in planar Ge","language":[{"iso":"eng"}],"article_type":"original","date_published":"2021-08-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"isi":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"No","oa_version":"Preprint","date_created":"2020-12-02T10:50:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        20","main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"month":"08","arxiv":1,"oa":1,"corr_author":"1","quality_controlled":"1","type":"journal_article","_id":"8909","day":"01"},{"date_published":"2021-02-01T00:00:00Z","abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"status":"public","publication_status":"published","has_accepted_license":"1","isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","article_number":"110750","language":[{"iso":"eng"}],"article_type":"original","oa":1,"quality_controlled":"1","corr_author":"1","type":"journal_article","_id":"8931","day":"01","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"date_created":"2020-12-09T14:48:28Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       303","month":"02","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ec_funded":1,"scopus_import":"1","pmid":1,"external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"doi":"10.1016/j.plantsci.2020.110750","date_updated":"2026-10-25T23:30:42Z","publisher":"Elsevier","volume":303,"citation":{"ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>."},"year":"2021","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publication":"Plant Science","author":[{"last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","first_name":"Zuzana","orcid":"0000-0003-4783-1752"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei"},{"first_name":"Markéta","full_name":"Pernisová, Markéta","last_name":"Pernisová"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Michalko, Jaroslav","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko"},{"last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata","first_name":"Zlata"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","full_name":"Verstraeten, Inge"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"last_name":"Čovanová","first_name":"Milada","full_name":"Čovanová, Milada"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"first_name":"Lukas","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","first_name":"Matyas"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","first_name":"Teva","last_name":"Vernoux"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"fulldoi":"https://doi.org/10.1016/j.plantsci.2020.110750","file":[{"file_id":"9083","relation":"main_file","creator":"dernst","date_updated":"2021-02-04T07:49:25Z","content_type":"application/pdf","success":1,"checksum":"a7f2562bdca62d67dfa88e271b62a629","access_level":"open_access","file_size":12563728,"file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z"}],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0168-9452"]},"ddc":["580"],"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","file_date_updated":"2021-02-04T07:49:25Z"},{"doi":"10.21203/rs.3.rs-266395/v3","date_updated":"2026-10-25T23:30:43Z","ec_funded":1,"citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>"},"year":"2021","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin","orcid":"0000-0002-5607-272X"},{"last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"first_name":"Lana","full_name":"Shabala, Lana","last_name":"Shabala"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publication":"Research Square","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.21203/rs.3.rs-266395/v3","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","related_material":{"record":[{"status":"public","id":"10223","relation":"later_version"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["2693-5015"]},"oa_version":"Preprint","date_published":"2021-09-09T00:00:00Z","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"status":"public","publication_status":"draft","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"article_processing_charge":"No","article_number":"266395","language":[{"iso":"eng"}],"corr_author":"1","type":"preprint","_id":"10095","day":"09","oa":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2021-10-06T08:56:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"09"},{"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","file":[{"file_name":"2021_PNAS_Johnson.pdf","date_created":"2021-12-15T08:59:40Z","file_size":2757340,"access_level":"open_access","checksum":"8d01e72e22c4fb1584e72d8601947069","success":1,"content_type":"application/pdf","creator":"cchlebak","file_id":"10546","date_updated":"2021-12-15T08:59:40Z","relation":"main_file"}],"fulldoi":"https://doi.org/10.1073/pnas.2113046118","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"first_name":"Dana A","full_name":"Dahhan, Dana A","last_name":"Dahhan"},{"orcid":"0000-0002-2198-0509","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","first_name":"Vanessa","orcid":"0000-0002-9438-4783"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"full_name":"Mahou, Pierre","first_name":"Pierre","last_name":"Mahou"},{"last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","full_name":"Hrtyan, Mónika"},{"last_name":"Wang","full_name":"Wang, Jie","first_name":"Jie"},{"orcid":"0000-0002-2862-8372","first_name":"Juan L","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire"},{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y","last_name":"Bednarek"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2021-12-15T08:59:40Z","issue":"51","ddc":["580"],"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","publication_identifier":{"eissn":["1091-6490"]},"related_material":{"record":[{"id":"14988","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"14510","status":"public"}],"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}]},"doi":"10.1073/pnas.2113046118","date_updated":"2026-10-25T23:30:49Z","pmid":1,"external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"citation":{"ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>"},"year":"2021","publisher":"National Academy of Sciences","volume":118,"type":"journal_article","_id":"9887","day":"14","corr_author":"1","quality_controlled":"1","oa":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"month":"12","intvolume":"       118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-08-11T14:11:43Z","oa_version":"Published Version","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"isi":1,"status":"public","publication_status":"published","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"date_published":"2021-12-14T00:00:00Z","language":[{"iso":"eng"}],"article_type":"original","article_number":"e2113046118"},{"year":"2021","citation":{"ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>."},"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"IST Austria","date_published":"2021-12-16T00:00:00Z","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"has_accepted_license":"1","status":"public","doi":"10.15479/AT:ISTA:10110","date_updated":"2026-10-25T23:30:54Z","month":"12","date_created":"2021-10-08T06:44:22Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage"}],"record":[{"status":"public","id":"10816","relation":"used_for_analysis_in"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","license":"https://opensource.org/licenses/GPL-3.0","file_date_updated":"2021-10-08T08:46:04Z","ddc":["005"],"tmp":{"short":"GPL 3.0","name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html"},"oa":1,"fulldoi":"https://doi.org/10.15479/AT:ISTA:10110","file":[{"access_level":"open_access","checksum":"f92f8931cad0aa7e411c1715337bf408","success":1,"content_type":"application/x-zip-compressed","file_id":"10114","creator":"cchlebak","date_updated":"2021-10-08T08:46:04Z","relation":"main_file","file_name":"patternseparation-main (1).zip","date_created":"2021-10-08T08:46:04Z","file_size":332990101}],"author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José"},{"first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","first_name":"Claudia "},{"first_name":"Xiaomin","orcid":"0000-0003-0256-6529","full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","first_name":"Benjamin","full_name":"Suter, Benjamin"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"_id":"10110","day":"16","type":"software","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network"},{"oa_version":"None","publication_status":"published","has_accepted_license":"1","status":"public","abstract":[{"text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.","lang":"eng"}],"date_published":"2021-07-27T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"alternative_title":["Neuromethods"],"corr_author":"1","quality_controlled":"1","type":"book_chapter","_id":"9756","day":"27","series_title":"Neuromethods","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-07-30T09:34:56Z","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"month":"07","intvolume":"       169","scopus_import":"1","doi":"10.1007/978-1-0716-1522-5_19","date_updated":"2026-10-25T23:31:03Z","ec_funded":1,"volume":169,"publisher":"Humana Press","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"citation":{"ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana Press, 2021, pp. 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana Press; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana Press, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana Press, New York, 2021, pp. 267–283."},"year":"2021","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","page":"267-283","publication":"Receptor and Ion Channel Detection in the Brain","author":[{"orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David"},{"first_name":"Harumi","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-1522-5_19","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"ddc":["573"],"place":"New York","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","related_material":{"record":[{"status":"public","id":"9562","relation":"dissertation_contains"}]},"das_tickbox":"1","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]}},{"year":"2020","citation":{"chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. 2020;20(7):5323-5329. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","ieee":"J. Duan <i>et al.</i>, “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>.","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329.","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>"},"department":[{"_id":"NanoFab"}],"volume":20,"publisher":"American Chemical Society","pmid":1,"external_id":{"isi":["000548893200082"],"arxiv":["2004.14599"],"pmid":["32530634"]},"doi":"10.1021/acs.nanolett.0c01673","date_updated":"2023-09-05T12:05:58Z","scopus_import":"1","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"issue":"7","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","fulldoi":"https://doi.org/10.1021/acs.nanolett.0c01673","publication":"Nano Letters","author":[{"first_name":"Jiahua","full_name":"Duan, Jiahua","last_name":"Duan"},{"full_name":"Capote-Robayna, Nathaniel","first_name":"Nathaniel","last_name":"Capote-Robayna"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"last_name":"Álvarez-Pérez","first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"last_name":"Nikitin","first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y."},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"page":"5323-5329","title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","article_type":"original","language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"No","date_published":"2020-07-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.","lang":"eng"}],"oa_version":"Preprint","intvolume":"        20","main_file_link":[{"url":"https://arxiv.org/abs/2004.14599","open_access":"1"}],"month":"07","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2022-03-18T11:37:38Z","arxiv":1,"oa":1,"day":"01","_id":"10866","type":"journal_article","quality_controlled":"1"},{"publication_identifier":{"issn":["1431-9276"],"eissn":["1435-8115"]},"issue":"S2","fulldoi":"https://doi.org/10.1017/s1431927620021881","author":[{"first_name":"Florian","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin"},{"full_name":"Zens, Bettina","first_name":"Bettina","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens"},{"first_name":"Christoph","full_name":"Möhl, Christoph","last_name":"Möhl"},{"first_name":"Frank","full_name":"Bradke, Frank","last_name":"Bradke"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"publication":"Microscopy and Microanalysis","page":"2518-2519","title":"Cryo-electron tomography workflows for quantitative analysis of actin networks involved in cell migration","citation":{"mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Workflows for Quantitative Analysis of Actin Networks Involved in Cell Migration.” <i>Microscopy and Microanalysis</i>, vol. 26, no. S2, Oxford University Press, 2020, pp. 2518–19, doi:<a href=\"https://doi.org/10.1017/s1431927620021881\">10.1017/s1431927620021881</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, B. Zens, C. Möhl, F. Bradke, F.K. Schur, Microscopy and Microanalysis 26 (2020) 2518–2519.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Zens, B., Möhl, C., Bradke, F., &#38; Schur, F. K. (2020). Cryo-electron tomography workflows for quantitative analysis of actin networks involved in cell migration. <i>Microscopy and Microanalysis</i>. Oxford University Press. <a href=\"https://doi.org/10.1017/s1431927620021881\">https://doi.org/10.1017/s1431927620021881</a>","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, Bettina Zens, Christoph Möhl, Frank Bradke, and Florian KM Schur. “Cryo-Electron Tomography Workflows for Quantitative Analysis of Actin Networks Involved in Cell Migration.” <i>Microscopy and Microanalysis</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1017/s1431927620021881\">https://doi.org/10.1017/s1431927620021881</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, et al. Cryo-electron tomography workflows for quantitative analysis of actin networks involved in cell migration. <i>Microscopy and Microanalysis</i>. 2020;26(S2):2518-2519. doi:<a href=\"https://doi.org/10.1017/s1431927620021881\">10.1017/s1431927620021881</a>","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Zens B, Möhl C, Bradke F, Schur FK. 2020. Cryo-electron tomography workflows for quantitative analysis of actin networks involved in cell migration. Microscopy and Microanalysis. 26(S2), 2518–2519.","ieee":"F. Fäßler <i>et al.</i>, “Cryo-electron tomography workflows for quantitative analysis of actin networks involved in cell migration,” <i>Microscopy and Microanalysis</i>, vol. 26, no. S2. Oxford University Press, pp. 2518–2519, 2020."},"year":"2020","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"volume":26,"publisher":"Oxford University Press","date_updated":"2024-10-09T21:08:43Z","doi":"10.1017/s1431927620021881","intvolume":"        26","month":"08","keyword":["Instrumentation"],"date_created":"2024-04-03T09:40:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15286","day":"01","type":"journal_article","corr_author":"1","quality_controlled":"1","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2020-08-01T00:00:00Z","status":"public","publication_status":"published","oa_version":"None"}]