[{"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","ec_funded":1,"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).","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>","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>","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>.","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.","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>."},"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Davaatseren","first_name":"Amarbayasgalan","full_name":"Davaatseren, Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen"},{"id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag","full_name":"Sonntag, Johanna","first_name":"Johanna"},{"first_name":"Lill","full_name":"Andersen, Lill","last_name":"Andersen"},{"last_name":"Bernthaler","first_name":"Tina","full_name":"Bernthaler, Tina"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher"},{"full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena","last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Randy L.","first_name":"Randy L.","last_name":"Johnson"},{"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","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"22","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.","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release"}]},"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","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"doi":"10.1016/j.celrep.2021.109274","language":[{"iso":"eng"}],"date_created":"2021-06-27T22:01:48Z","month":"06","isi":1,"publisher":"Cell Press","intvolume":"        35","status":"public","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"quality_controlled":"1","publication":"Cell Reports","year":"2021","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["22111247"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_updated":"2023-08-10T13:55:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000664463600016"]},"issue":"12","article_processing_charge":"No","_id":"9603","abstract":[{"lang":"eng","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."}],"date_published":"2021-06-22T00:00:00Z","file":[{"creator":"asandaue","file_size":7653149,"file_name":"2021_CellReports_Contreras.pdf","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","access_level":"open_access","date_updated":"2021-06-28T14:06:24Z","file_id":"9613","relation":"main_file","content_type":"application/pdf","date_created":"2021-06-28T14:06:24Z","success":1}],"article_number":"109274","oa":1,"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":35,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2021-06-28T14:06:24Z"},{"article_type":"original","oa_version":"Published Version","year":"2021","has_accepted_license":"1","date_updated":"2023-08-10T13:36:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"scopus_import":"1","publication_identifier":{"eissn":["2050084X"]},"file":[{"success":1,"date_created":"2021-06-28T11:35:30Z","content_type":"application/pdf","relation":"main_file","file_id":"9609","date_updated":"2021-06-28T11:35:30Z","access_level":"open_access","checksum":"885b746051a7a6b6e24e3d2781a48fde","file_name":"2021_ELife_Bespalov.pdf","file_size":2500720,"creator":"asandaue"}],"_id":"9607","date_published":"2021-05-24T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","file_date_updated":"2021-06-28T11:35:30Z","volume":10,"tmp":{"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","short":"CC BY (4.0)"},"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","oa":1,"day":"24","author":[{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"first_name":"René","full_name":"Bernard, René","last_name":"Bernard"},{"full_name":"Gilis, Anja","first_name":"Anja","last_name":"Gilis"},{"first_name":"Björn","full_name":"Gerlach, Björn","last_name":"Gerlach"},{"last_name":"Guillén","full_name":"Guillén, Javier","first_name":"Javier"},{"last_name":"Castagné","full_name":"Castagné, Vincent","first_name":"Vincent"},{"full_name":"Lefevre, Isabel A.","first_name":"Isabel A.","last_name":"Lefevre"},{"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"},{"last_name":"Altevogt","first_name":"Bruce","full_name":"Altevogt, Bruce"},{"last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María","first_name":"María"},{"first_name":"Lior","full_name":"Bikovski, Lior","last_name":"Bikovski"},{"full_name":"De Bruin, Natasja","first_name":"Natasja","last_name":"De Bruin"},{"first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez"},{"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"},{"full_name":"Ferland-Beckham, Chantelle","first_name":"Chantelle","last_name":"Ferland-Beckham"},{"first_name":"Christelle","full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux"},{"last_name":"Gailus-Durner","first_name":"Valerie","full_name":"Gailus-Durner, Valerie"},{"full_name":"Hölter, Sabine M.","first_name":"Sabine M.","last_name":"Hölter"},{"last_name":"Hofmann","first_name":"Martine Cj","full_name":"Hofmann, Martine Cj"},{"last_name":"Kabitzke","full_name":"Kabitzke, Patricia","first_name":"Patricia"},{"first_name":"Martien Jh","full_name":"Kas, Martien Jh","last_name":"Kas"},{"last_name":"Kurreck","first_name":"Claudia","full_name":"Kurreck, Claudia"},{"last_name":"Moser","first_name":"Paul","full_name":"Moser, Paul"},{"last_name":"Pietraszek","first_name":"Malgorzata","full_name":"Pietraszek, Malgorzata"},{"first_name":"Piotr","full_name":"Popik, Piotr","last_name":"Popik"},{"first_name":"Heidrun","full_name":"Potschka, Heidrun","last_name":"Potschka"},{"first_name":"Ernesto","full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca"},{"last_name":"Restivo","first_name":"Leonardo","full_name":"Restivo, Leonardo"},{"first_name":"Gernot","full_name":"Riedel, Gernot","last_name":"Riedel"},{"first_name":"Merel","full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga"},{"last_name":"Samardzic","full_name":"Samardzic, Janko","first_name":"Janko"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","last_name":"Schunn","full_name":"Schunn, Michael","first_name":"Michael"},{"full_name":"Stöger, Claudia","first_name":"Claudia","last_name":"Stöger"},{"last_name":"Voikar","first_name":"Vootele","full_name":"Voikar, Vootele"},{"last_name":"Vollert","full_name":"Vollert, Jan","first_name":"Jan"},{"full_name":"Wever, Kimberley E.","first_name":"Kimberley E.","last_name":"Wever"},{"last_name":"Wuyts","full_name":"Wuyts, Kathleen","first_name":"Kathleen"},{"last_name":"Macleod","first_name":"Malcolm R.","full_name":"Macleod, Malcolm R."},{"full_name":"Dirnagl, Ulrich","first_name":"Ulrich","last_name":"Dirnagl"},{"full_name":"Steckler, Thomas","first_name":"Thomas","last_name":"Steckler"}],"type":"journal_article","citation":{"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>.","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.","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>","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>","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)."},"title":"Introduction to the EQIPD quality system","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.7554/eLife.63294","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).","pmid":1,"month":"05","date_created":"2021-06-27T22:01:49Z","department":[{"_id":"PreCl"}],"quality_controlled":"1","publication":"eLife","status":"public","intvolume":"        10","publisher":"eLife Sciences Publications","isi":1},{"status":"public","publication":"Research Square","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_created":"2021-10-06T08:56:22Z","month":"09","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"_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"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"},{"relation":"later_version","id":"10223","status":"public"}]},"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.","doi":"10.21203/rs.3.rs-266395/v3","language":[{"iso":"eng"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","citation":{"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>","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>. .","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.","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>.","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>."},"ec_funded":1,"type":"preprint","author":[{"last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"last_name":"Ren","full_name":"Ren, Hong","first_name":"Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"day":"09","oa":1,"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"publication_status":"accepted","tmp":{"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","short":"CC BY (4.0)"},"article_processing_charge":"No","_id":"10095","date_published":"2021-09-09T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_number":"266395","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["2693-5015"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-29T10:22:44Z","oa_version":"Preprint","year":"2021"},{"date_updated":"2024-03-25T23:30:07Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/AT:ISTA:10110","ddc":["005"],"related_material":{"record":[{"id":"10816","relation":"used_for_analysis_in","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage"}]},"day":"16","author":[{"orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","first_name":"José","last_name":"Guzmán"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl"},{"orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","last_name":"Espinoza Martinez"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin"},{"first_name":"Benjamin","full_name":"Suter, Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M"}],"type":"software","year":"2021","has_accepted_license":"1","citation":{"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>","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>","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","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>.","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>.","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.","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>."},"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","file_date_updated":"2021-10-08T08:46:04Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"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"},"status":"public","publisher":"IST Austria","license":"https://opensource.org/licenses/GPL-3.0","oa":1,"month":"12","file":[{"file_name":"patternseparation-main (1).zip","creator":"cchlebak","file_size":332990101,"date_updated":"2021-10-08T08:46:04Z","access_level":"open_access","checksum":"f92f8931cad0aa7e411c1715337bf408","content_type":"application/x-zip-compressed","relation":"main_file","file_id":"10114","success":1,"date_created":"2021-10-08T08:46:04Z"}],"date_created":"2021-10-08T06:44:22Z","_id":"10110","abstract":[{"lang":"eng","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."}],"date_published":"2021-12-16T00:00:00Z"},{"file":[{"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","date_updated":"2021-10-11T12:20:58Z","access_level":"open_access","file_name":"2021_JBC_Artan.pdf","creator":"cchlebak","file_size":1680010,"date_created":"2021-10-11T12:20:58Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"10121"}],"article_number":"101094","_id":"10117","date_published":"2021-09-01T00:00:00Z","abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"article_processing_charge":"Yes","issue":"3","file_date_updated":"2021-10-11T12:20:58Z","tmp":{"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","short":"CC BY (4.0)"},"volume":297,"publication_status":"published","oa":1,"article_type":"original","year":"2021","has_accepted_license":"1","oa_version":"Published Version","external_id":{"isi":["000706409200006"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T07:24:09Z","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"month":"09","date_created":"2021-10-10T22:01:23Z","publication":"Journal of Biological Chemistry","quality_controlled":"1","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"status":"public","intvolume":"       297","publisher":"Elsevier","isi":1,"day":"01","type":"journal_article","author":[{"first_name":"Murat","full_name":"Artan, Murat","last_name":"Artan","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"last_name":"Barratt","first_name":"Stephen","full_name":"Barratt, Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677"},{"full_name":"Flynn, Sean M.","first_name":"Sean M.","last_name":"Flynn"},{"first_name":"Farida","full_name":"Begum, Farida","last_name":"Begum"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","full_name":"Nicolas, Armel","first_name":"Armel"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono"}],"citation":{"mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>.","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>.","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021)."},"ec_funded":1,"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","language":[{"iso":"eng"}],"doi":"10.1016/J.JBC.2021.101094","ddc":["612"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna)."},{"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T07:25:27Z","year":"2021","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","oa":1,"publication_status":"published","tmp":{"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","short":"CC BY (4.0)"},"volume":33,"file_date_updated":"2022-02-03T13:16:14Z","article_processing_charge":"Yes (via OA deal)","issue":"52","_id":"10123","date_published":"2021-12-29T00:00:00Z","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"}],"article_number":"2106858","file":[{"relation":"main_file","file_id":"10720","content_type":"application/pdf","date_created":"2022-02-03T13:16:14Z","success":1,"file_size":5595666,"creator":"cchlebak","file_name":"2021_AdvancedMaterials_Liu.pdf","checksum":"990bccc527c64d85cf1c97885110b5f4","access_level":"open_access","date_updated":"2022-02-03T13:16:14Z"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12885"}]},"pmid":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"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.","ddc":["620"],"doi":"10.1002/adma.202106858","keyword":["mechanical engineering","mechanics of materials","general materials science"],"language":[{"iso":"eng"}],"title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","citation":{"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>.","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>.","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.","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.","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>","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)."},"ec_funded":1,"type":"journal_article","author":[{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","first_name":"Mariano","last_name":"Calcabrini"},{"last_name":"Yu","first_name":"Yuan","full_name":"Yu, Yuan"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"last_name":"Chang","full_name":"Chang, Cheng","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo"},{"last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"last_name":"Lee","full_name":"Lee, Seungho","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"last_name":"Llorca","full_name":"Llorca, Jordi","first_name":"Jordi"},{"full_name":"Cojocaru‐Mirédin, Oana","first_name":"Oana","last_name":"Cojocaru‐Mirédin"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria"}],"day":"29","isi":1,"publisher":"Wiley","status":"public","intvolume":"        33","publication":"Advanced Materials","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"quality_controlled":"1","date_created":"2021-10-11T20:07:24Z","month":"12"},{"month":"10","date_created":"2021-10-24T22:01:33Z","publisher":"American Association for the Advancement of Science","isi":1,"publication":"Science Advances","department":[{"_id":"NanoFab"}],"quality_controlled":"1","status":"public","intvolume":"         7","citation":{"apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. 2021;7(41). doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>.","ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","ieee":"J. Martín-Sánchez <i>et al.</i>, “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” <i>Science Advances</i>, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>."},"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","day":"08","author":[{"first_name":"Javier","full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"last_name":"Voronin","full_name":"Voronin, Kirill V.","first_name":"Kirill V."},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"first_name":"Weiliang","full_name":"Ma, Weiliang","last_name":"Ma"},{"last_name":"Bao","full_name":"Bao, Qiaoliang","first_name":"Qiaoliang"},{"first_name":"Valentyn S.","full_name":"Volkov, Valentyn S.","last_name":"Volkov"},{"full_name":"Hillenbrand, Rainer","first_name":"Rainer","last_name":"Hillenbrand"},{"first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y.","last_name":"Nikitin"},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"type":"journal_article","acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","ddc":["530"],"arxiv":1,"article_processing_charge":"Yes","issue":"41","article_number":"abj0127","file":[{"file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","creator":"cziletti","file_size":2441163,"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","date_updated":"2021-10-27T14:16:06Z","access_level":"open_access","content_type":"application/pdf","file_id":"10189","relation":"main_file","date_created":"2021-10-27T14:16:06Z","success":1}],"_id":"10177","date_published":"2021-10-08T00:00:00Z","abstract":[{"text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","oa":1,"file_date_updated":"2021-10-27T14:16:06Z","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"volume":7,"article_type":"original","year":"2021","has_accepted_license":"1","oa_version":"Published Version","external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"scopus_import":"1","date_updated":"2023-08-14T08:04:42Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["23752548"]}},{"pmid":1,"acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","language":[{"iso":"eng"}],"doi":"10.15252/embj.2021108714","ddc":["610"],"citation":{"ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>.","ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714."},"title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","day":"18","author":[{"full_name":"Bajaj, Sunanjay","first_name":"Sunanjay","last_name":"Bajaj"},{"first_name":"Joshua A.","full_name":"Bagley, Joshua A.","last_name":"Bagley"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"last_name":"Vertesy","first_name":"Abel","full_name":"Vertesy, Abel"},{"last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako","first_name":"Sakurako"},{"last_name":"Krenn","first_name":"Veronica","full_name":"Krenn, Veronica"},{"last_name":"Lévi-Strauss","first_name":"Julie","full_name":"Lévi-Strauss, Julie"},{"last_name":"Knoblich","full_name":"Knoblich, Juergen A.","first_name":"Juergen A."}],"type":"journal_article","publisher":"Embo Press","isi":1,"publication":"EMBO Journal","department":[{"_id":"Bio"}],"quality_controlled":"1","status":"public","intvolume":"        40","month":"10","date_created":"2021-10-24T22:01:34Z","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T08:05:23Z","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"article_type":"original","has_accepted_license":"1","year":"2021","oa_version":"Published Version","publication_status":"published","oa":1,"file_date_updated":"2021-12-13T14:54:14Z","tmp":{"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","short":"CC BY (4.0)"},"volume":40,"article_processing_charge":"Yes (in subscription journal)","issue":"23","article_number":"e108714","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"10541","success":1,"date_created":"2021-12-13T14:54:14Z","file_name":"2021_EMBO_Bajaj.pdf","creator":"alisjak","file_size":7819881,"date_updated":"2021-12-13T14:54:14Z","access_level":"open_access","checksum":"78d2d02e775322297e774f72810a41a4"}],"_id":"10179","abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"date_published":"2021-10-18T00:00:00Z"},{"year":"2021","oa_version":"Preprint","article_type":"original","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-10-29T10:22:45Z","article_processing_charge":"No","issue":"7884","_id":"10223","date_published":"2021-11-11T00:00:00Z","abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend 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 phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. 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 alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"oa":1,"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"publication_status":"published","volume":599,"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","citation":{"ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</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, Nature 599 (2021) 273–277.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>.","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<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</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. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021."},"ec_funded":1,"author":[{"last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","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","first_name":"Wouter","full_name":"Smet, Wouter"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","full_name":"Gray, William M.","last_name":"Gray"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"type":"journal_article","day":"11","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"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"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage"}],"record":[{"status":"public","id":"10095","relation":"earlier_version"}]},"pmid":1,"acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the 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) under 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), 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 Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","doi":"10.1038/s41586-021-04037-6","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"page":"273-277","date_created":"2021-11-07T23:01:25Z","month":"11","isi":1,"publisher":"Springer Nature","status":"public","intvolume":"       599","publication":"Nature","quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"NanoFab"}]},{"oa":1,"publication_status":"published","volume":22,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2022-05-16T07:07:41Z","article_processing_charge":"Yes (in subscription journal)","_id":"10283","abstract":[{"text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.","lang":"eng"}],"date_published":"2021-11-04T00:00:00Z","article_number":"e53824","file":[{"checksum":"74743baa6ef431ef60c3de3bc4da045a","date_updated":"2022-05-16T07:07:41Z","access_level":"open_access","file_name":"2021_EmboReports_Restivo.pdf","creator":"dernst","file_size":488583,"date_created":"2022-05-16T07:07:41Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11381"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"date_updated":"2023-08-14T11:47:35Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000714350000001"]},"scopus_import":"1","has_accepted_license":"1","year":"2021","oa_version":"Published Version","article_type":"original","isi":1,"publisher":"EMBO Press","status":"public","intvolume":"        22","department":[{"_id":"PreCl"}],"quality_controlled":"1","publication":"EMBO Reports","date_created":"2021-11-14T23:01:24Z","month":"11","acknowledgement":"This EQIPD 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 program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","doi":"10.15252/embr.202153824","ddc":["570"],"language":[{"iso":"eng"}],"title":"Towards best practices in research: Role of academic core facilities","citation":{"ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. 2021;22. doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021).","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>, vol. 22, e53824, EMBO Press, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>.","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>. EMBO Press, 2021. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>.","ieee":"L. Restivo <i>et al.</i>, “Towards best practices in research: Role of academic core facilities,” <i>EMBO Reports</i>, vol. 22. EMBO Press, 2021.","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824."},"author":[{"full_name":"Restivo, Leonardo","first_name":"Leonardo","last_name":"Restivo"},{"last_name":"Gerlach","first_name":"Björn","full_name":"Gerlach, Björn"},{"first_name":"Michael","full_name":"Tsoory, Michael","last_name":"Tsoory"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"full_name":"Badurek, Sylvia","first_name":"Sylvia","last_name":"Badurek"},{"first_name":"Claudia","full_name":"Pitzer, Claudia","last_name":"Pitzer"},{"last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C.","first_name":"Isabelle C."},{"last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj","full_name":"Mausset-Bonnefont, Anne Laure Mj"},{"first_name":"Jonathan","full_name":"Ward, Jonathan","last_name":"Ward"},{"last_name":"Schunn","full_name":"Schunn, Michael","first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300"},{"last_name":"Noldus","first_name":"Lucas P.J.J.","full_name":"Noldus, Lucas P.J.J."},{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"first_name":"Vootele","full_name":"Voikar, Vootele","last_name":"Voikar"}],"type":"journal_article","day":"04"},{"oa":1,"publication_status":"published","tmp":{"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","short":"CC BY (4.0)"},"volume":91,"file_date_updated":"2022-01-10T13:41:40Z","article_processing_charge":"No","_id":"10607","date_published":"2021-10-01T00:00:00Z","abstract":[{"text":"The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders.","lang":"eng"}],"file":[{"date_updated":"2022-01-10T13:41:40Z","access_level":"open_access","checksum":"360681585acb51e80d17c6b213c56b55","file_name":"2021_Parkinsonism_Venezia.pdf","file_size":6848513,"creator":"alisjak","success":1,"date_created":"2022-01-10T13:41:40Z","content_type":"application/pdf","relation":"main_file","file_id":"10612"}],"publication_identifier":{"eissn":["1873-5126"],"issn":["1353-8020"]},"external_id":{"pmid":["34530328"],"isi":["000701142900012"]},"scopus_import":"1","date_updated":"2023-08-17T06:36:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","year":"2021","has_accepted_license":"1","article_type":"original","isi":1,"publisher":"Elsevier","intvolume":"        91","status":"public","publication":"Parkinsonism & Related Disorders","department":[{"_id":"EM-Fac"}],"quality_controlled":"1","page":"59-65","date_created":"2022-01-09T23:01:26Z","month":"10","pmid":1,"acknowledgement":"This study was supported by grants of the Austrian Science Fund (FWF) F4414 and W1206-08. Electron microscopy was performed at the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron Microscopy Facility.","ddc":["610"],"doi":"10.1016/j.parkreldis.2021.09.007","language":[{"iso":"eng"}],"title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","citation":{"ama":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. 2021;91:59-65. doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>","apa":"Venezia, S., Kaufmann, W., Wenning, G. K., &#38; Stefanova, N. (2021). Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. <i>Parkinsonism &#38; Related Disorders</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism &#38; Related Disorders 91 (2021) 59–65.","mla":"Venezia, Serena, et al. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91, Elsevier, 2021, pp. 59–65, doi:<a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">10.1016/j.parkreldis.2021.09.007</a>.","chicago":"Venezia, Serena, Walter Kaufmann, Gregor K. Wenning, and Nadia Stefanova. “Toll-like Receptor 4 Deficiency Facilitates α-Synuclein Propagation and Neurodegeneration in a Mouse Model of Prodromal Parkinson’s Disease.” <i>Parkinsonism &#38; Related Disorders</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.parkreldis.2021.09.007\">https://doi.org/10.1016/j.parkreldis.2021.09.007</a>.","ista":"Venezia S, Kaufmann W, Wenning GK, Stefanova N. 2021. Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease. Parkinsonism &#38; Related Disorders. 91, 59–65.","ieee":"S. Venezia, W. Kaufmann, G. K. Wenning, and N. Stefanova, “Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson’s disease,” <i>Parkinsonism &#38; Related Disorders</i>, vol. 91. Elsevier, pp. 59–65, 2021."},"type":"journal_article","author":[{"first_name":"Serena","full_name":"Venezia, Serena","last_name":"Venezia"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"full_name":"Wenning, Gregor K.","first_name":"Gregor K.","last_name":"Wenning"},{"full_name":"Stefanova, Nadia","first_name":"Nadia","last_name":"Stefanova"}],"day":"01"},{"citation":{"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>.","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.","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.","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>.","short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 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>","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>"},"title":"Managing software on a heterogenous HPC cluster","conference":{"location":"Virtual","name":"ASHPC - Austrian-Slovenian HPC Meeting","end_date":"2021-06-02","start_date":"2021-05-31"},"day":"02","author":[{"last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","full_name":"Elefante, Stefano","first_name":"Stefano"},{"id":"77129392-B450-11EA-8745-D4653DDC885E","full_name":"Hornoiu, Andrei","first_name":"Andrei","last_name":"Hornoiu"},{"last_name":"Stadlbauer","first_name":"Stephan","full_name":"Stadlbauer, Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"}],"type":"conference_abstract","oa_version":"Published Version","year":"2021","has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2023-05-16T07:43:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"doi":"10.3359/2021hpc","ddc":["000"],"page":"5","article_processing_charge":"No","month":"06","file":[{"file_id":"12971","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-16T07:36:34Z","success":1,"file_size":422761,"creator":"dernst","file_name":"2021_ASHPC_Schloegl.pdf","checksum":"ba73f85858fb9d5737ebc7724646dd45","access_level":"open_access","date_updated":"2023-05-16T07:36:34Z"}],"_id":"12909","date_published":"2021-06-02T00:00:00Z","date_created":"2023-05-05T13:17:36Z","publisher":"University of Ljubljana","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:36:34Z","status":"public"},{"_id":"9756","date_published":"2021-07-27T00:00:00Z","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"}],"article_processing_charge":"No","volume":169,"publication_status":"published","year":"2021","oa_version":"None","has_accepted_license":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2024-03-25T23:30:16Z","publication_identifier":{"isbn":["9781071615218"],"eisbn":["9781071615225"]},"place":"New York","month":"07","series_title":"Neuromethods","date_created":"2021-07-30T09:34:56Z","page":"267-283","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":" Receptor and Ion Channel Detection in the Brain","status":"public","intvolume":"       169","publisher":"Humana","day":"27","alternative_title":["Neuromethods"],"author":[{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harada","full_name":"Harada, Harumi","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"type":"book_chapter","ec_funded":1,"citation":{"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, 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.","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, 2021, pp. 267–283.","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, 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>.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:,  Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 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; 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>","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. <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>"},"title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","language":[{"iso":"eng"}],"keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"doi":"10.1007/978-1-0716-1522-5_19","ddc":["573"],"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":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}]},{"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.","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"pmid":1,"doi":"10.1021/acsami.1c09850","ddc":["620","570"],"language":[{"iso":"eng"}],"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","ec_funded":1,"citation":{"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.","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>","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>","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>.","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>."},"author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Balles","full_name":"Balles, Miriam","first_name":"Miriam"},{"last_name":"Kretschmer","full_name":"Kretschmer, Maibritt","first_name":"Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","first_name":"Maria","full_name":"Nemethova, Maria"},{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","first_name":"Remy P","last_name":"Chait"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"first_name":"Janina","full_name":"Lange, Janina","last_name":"Lange"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zahler, Stefan","first_name":"Stefan","last_name":"Zahler"}],"type":"journal_article","day":"04","isi":1,"publisher":"American Chemical Society","intvolume":"        13","status":"public","quality_controlled":"1","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"publication":"ACS Applied Materials and Interfaces","page":"35545–35560","date_created":"2021-08-08T22:01:28Z","month":"08","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"date_updated":"2023-08-10T14:22:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34283577"],"isi":["000683741400026"]},"scopus_import":"1","has_accepted_license":"1","year":"2021","oa_version":"Published Version","article_type":"original","oa":1,"publication_status":"published","volume":13,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2021-08-09T09:44:03Z","issue":"30","article_processing_charge":"Yes (in subscription journal)","_id":"9822","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"}],"date_published":"2021-08-04T00:00:00Z","file":[{"checksum":"b043a91d9f9200e467b970b692687ed3","access_level":"open_access","date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"creator":"asandaue","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","date_created":"2021-08-09T09:44:03Z","success":1,"file_id":"9833","relation":"main_file","content_type":"application/pdf"}]},{"quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication":"Proceedings of the National Academy of Sciences","status":"public","intvolume":"       118","publisher":"National Academy of Sciences","isi":1,"month":"12","date_created":"2021-08-11T14:11:43Z","language":[{"iso":"eng"}],"ddc":["580"],"doi":"10.1073/pnas.2113046118","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.).","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"related_material":{"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14510"},{"id":"14988","relation":"research_data","status":"public"}]},"pmid":1,"day":"14","author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann"},{"orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","full_name":"Costanzo, Tommaso","last_name":"Costanzo"},{"last_name":"Mahou","full_name":"Mahou, Pierre","first_name":"Pierre"},{"first_name":"Mónika","full_name":"Hrtyan, Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","first_name":"Jie","full_name":"Wang, Jie"},{"last_name":"Aguilera Servin","first_name":"Juan L","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniël","full_name":"van Damme, Daniël","last_name":"van Damme"},{"full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel","last_name":"Beaurepaire"},{"last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y","last_name":"Bednarek"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"type":"journal_article","citation":{"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 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</i>. National Academy of Sciences. <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</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","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</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","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. 118(51), e2113046118.","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</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","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</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>."},"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","file_date_updated":"2021-12-15T08:59:40Z","volume":118,"tmp":{"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","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"e2113046118","file":[{"date_created":"2021-12-15T08:59:40Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"10546","checksum":"8d01e72e22c4fb1584e72d8601947069","date_updated":"2021-12-15T08:59:40Z","access_level":"open_access","file_name":"2021_PNAS_Johnson.pdf","creator":"cchlebak","file_size":2757340}],"abstract":[{"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.","lang":"eng"}],"_id":"9887","date_published":"2021-12-14T00:00:00Z","issue":"51","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-02-19T11:06:09Z","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1091-6490"]},"article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2021"},{"page":"56-73","date_created":"2021-08-15T22:01:29Z","month":"08","isi":1,"publisher":"Wiley","intvolume":"       284","status":"public","publication":"Journal of Microscopy","quality_controlled":"1","department":[{"_id":"Bio"}],"title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","citation":{"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.","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>","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.","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.","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>.","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>."},"type":"journal_article","author":[{"first_name":"Glyn","full_name":"Nelson, Glyn","last_name":"Nelson"},{"last_name":"Boehm","first_name":"Ulrike","full_name":"Boehm, Ulrike"},{"last_name":"Bagley","first_name":"Steve","full_name":"Bagley, Steve"},{"last_name":"Bajcsy","full_name":"Bajcsy, Peter","first_name":"Peter"},{"full_name":"Bischof, Johanna","first_name":"Johanna","last_name":"Bischof"},{"last_name":"Brown","first_name":"Claire M.","full_name":"Brown, Claire M."},{"last_name":"Dauphin","first_name":"Aurélien","full_name":"Dauphin, Aurélien"},{"first_name":"Ian M.","full_name":"Dobbie, Ian M.","last_name":"Dobbie"},{"last_name":"Eriksson","full_name":"Eriksson, John E.","first_name":"John E."},{"last_name":"Faklaris","full_name":"Faklaris, Orestis","first_name":"Orestis"},{"last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia","first_name":"Julia"},{"last_name":"Ferrand","full_name":"Ferrand, Alexia","first_name":"Alexia"},{"last_name":"Gelman","first_name":"Laurent","full_name":"Gelman, Laurent"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"first_name":"Hella","full_name":"Hartmann, Hella","last_name":"Hartmann"},{"last_name":"Kukat","first_name":"Christian","full_name":"Kukat, Christian"},{"last_name":"Laude","first_name":"Alex","full_name":"Laude, Alex"},{"first_name":"Miso","full_name":"Mitkovski, Miso","last_name":"Mitkovski"},{"first_name":"Sebastian","full_name":"Munck, Sebastian","last_name":"Munck"},{"full_name":"North, Alison J.","first_name":"Alison J.","last_name":"North"},{"last_name":"Rasse","first_name":"Tobias M.","full_name":"Rasse, Tobias M."},{"first_name":"Ute","full_name":"Resch-Genger, Ute","last_name":"Resch-Genger"},{"last_name":"Schuetz","first_name":"Lucas C.","full_name":"Schuetz, Lucas C."},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina"},{"first_name":"Jason R.","full_name":"Swedlow, Jason R.","last_name":"Swedlow"},{"first_name":"Ioannis","full_name":"Alexopoulos, Ioannis","last_name":"Alexopoulos"},{"last_name":"Aumayr","first_name":"Karin","full_name":"Aumayr, Karin"},{"full_name":"Avilov, Sergiy","first_name":"Sergiy","last_name":"Avilov"},{"last_name":"Bakker","full_name":"Bakker, Gert Jan","first_name":"Gert Jan"},{"last_name":"Bammann","full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R."},{"last_name":"Bassi","full_name":"Bassi, Andrea","first_name":"Andrea"},{"last_name":"Beckert","first_name":"Hannes","full_name":"Beckert, Hannes"},{"first_name":"Sebastian","full_name":"Beer, Sebastian","last_name":"Beer"},{"full_name":"Belyaev, Yury","first_name":"Yury","last_name":"Belyaev"},{"last_name":"Bierwagen","first_name":"Jakob","full_name":"Bierwagen, Jakob"},{"first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A.","last_name":"Birngruber"},{"last_name":"Bosch","full_name":"Bosch, Manel","first_name":"Manel"},{"last_name":"Breitlow","first_name":"Juergen","full_name":"Breitlow, Juergen"},{"full_name":"Cameron, Lisa A.","first_name":"Lisa A.","last_name":"Cameron"},{"first_name":"Joe","full_name":"Chalfoun, Joe","last_name":"Chalfoun"},{"first_name":"James J.","full_name":"Chambers, James J.","last_name":"Chambers"},{"first_name":"Chieh Li","full_name":"Chen, Chieh Li","last_name":"Chen"},{"full_name":"Conde-Sousa, Eduardo","first_name":"Eduardo","last_name":"Conde-Sousa"},{"last_name":"Corbett","first_name":"Alexander D.","full_name":"Corbett, Alexander D."},{"last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P."},{"full_name":"Nery, Elaine Del","first_name":"Elaine Del","last_name":"Nery"},{"first_name":"Ralf","full_name":"Dietzel, Ralf","last_name":"Dietzel"},{"full_name":"Eismann, Frank","first_name":"Frank","last_name":"Eismann"},{"last_name":"Fazeli","first_name":"Elnaz","full_name":"Fazeli, Elnaz"},{"full_name":"Felscher, Andreas","first_name":"Andreas","last_name":"Felscher"},{"full_name":"Fried, Hans","first_name":"Hans","last_name":"Fried"},{"last_name":"Gaudreault","first_name":"Nathalie","full_name":"Gaudreault, Nathalie"},{"last_name":"Goh","full_name":"Goh, Wah Ing","first_name":"Wah Ing"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"full_name":"Hadleigh, Roland","first_name":"Roland","last_name":"Hadleigh"},{"full_name":"Hemmerich, Peter","first_name":"Peter","last_name":"Hemmerich"},{"last_name":"Holst","full_name":"Holst, Gerhard A.","first_name":"Gerhard A."},{"full_name":"Itano, Michelle S.","first_name":"Michelle S.","last_name":"Itano"},{"last_name":"Jaffe","first_name":"Claudia B.","full_name":"Jaffe, Claudia B."},{"last_name":"Jambor","full_name":"Jambor, Helena K.","first_name":"Helena K."},{"full_name":"Jarvis, Stuart C.","first_name":"Stuart C.","last_name":"Jarvis"},{"last_name":"Keppler","full_name":"Keppler, Antje","first_name":"Antje"},{"last_name":"Kirchenbuechler","first_name":"David","full_name":"Kirchenbuechler, David"},{"full_name":"Kirchner, Marcel","first_name":"Marcel","last_name":"Kirchner"},{"first_name":"Norio","full_name":"Kobayashi, Norio","last_name":"Kobayashi"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"full_name":"Lacoste, Judith","first_name":"Judith","last_name":"Lacoste"},{"first_name":"Marco","full_name":"Marcello, Marco","last_name":"Marcello"},{"last_name":"Martins","first_name":"Gabriel G.","full_name":"Martins, Gabriel G."},{"first_name":"Daniel J.","full_name":"Metcalf, Daniel J.","last_name":"Metcalf"},{"first_name":"Claire A.","full_name":"Mitchell, Claire A.","last_name":"Mitchell"},{"last_name":"Moore","first_name":"Joshua","full_name":"Moore, Joshua"},{"last_name":"Mueller","full_name":"Mueller, Tobias","first_name":"Tobias"},{"first_name":"Michael S.","full_name":"Nelson, 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."},{"first_name":"Perrine","full_name":"Paul-Gilloteaux, Perrine","last_name":"Paul-Gilloteaux"},{"last_name":"Pimentel","full_name":"Pimentel, Jaime A.","first_name":"Jaime A."},{"last_name":"Plantard","full_name":"Plantard, Laure","first_name":"Laure"},{"last_name":"Podder","full_name":"Podder, Santosh","first_name":"Santosh"},{"first_name":"Elton","full_name":"Rexhepaj, Elton","last_name":"Rexhepaj"},{"full_name":"Royon, Arnaud","first_name":"Arnaud","last_name":"Royon"},{"last_name":"Saari","full_name":"Saari, Markku A.","first_name":"Markku A."},{"first_name":"Damien","full_name":"Schapman, Damien","last_name":"Schapman"},{"full_name":"Schoonderwoert, Vincent","first_name":"Vincent","last_name":"Schoonderwoert"},{"last_name":"Schroth-Diez","first_name":"Britta","full_name":"Schroth-Diez, Britta"},{"last_name":"Schwartz","first_name":"Stanley","full_name":"Schwartz, Stanley"},{"last_name":"Shaw","full_name":"Shaw, Michael","first_name":"Michael"},{"first_name":"Martin","full_name":"Spitaler, Martin","last_name":"Spitaler"},{"last_name":"Stoeckl","first_name":"Martin T.","full_name":"Stoeckl, Martin T."},{"last_name":"Sudar","full_name":"Sudar, Damir","first_name":"Damir"},{"first_name":"Jeremie","full_name":"Teillon, Jeremie","last_name":"Teillon"},{"first_name":"Stefan","full_name":"Terjung, Stefan","last_name":"Terjung"},{"full_name":"Thuenauer, Roland","first_name":"Roland","last_name":"Thuenauer"},{"last_name":"Wilms","first_name":"Christian D.","full_name":"Wilms, Christian D."},{"last_name":"Wright","first_name":"Graham D.","full_name":"Wright, Graham D."},{"last_name":"Nitschke","first_name":"Roland","full_name":"Nitschke, Roland"}],"day":"11","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.","doi":"10.1111/jmi.13041","language":[{"iso":"eng"}],"article_processing_charge":"Yes","issue":"1","_id":"9911","abstract":[{"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.","lang":"eng"}],"date_published":"2021-08-11T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1111/jmi.13041","open_access":"1"}],"oa":1,"publication_status":"published","volume":284,"year":"2021","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"external_id":{"isi":["000683702700001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-11T10:30:40Z"},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_identifier":{"eissn":["2691-3399"]},"date_updated":"2023-09-07T13:31:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"oa_version":"Published Version","has_accepted_license":"1","year":"2021","article_type":"original","volume":2,"tmp":{"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","short":"CC BY (4.0)"},"file_date_updated":"2022-01-18T11:29:33Z","oa":1,"publication_status":"published","_id":"9928","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"}],"date_published":"2021-11-24T00:00:00Z","file":[{"date_updated":"2022-01-18T11:29:33Z","access_level":"open_access","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","file_name":"2021_PRXQuantum_Peruzzo.pdf","creator":"cchlebak","file_size":4247422,"success":1,"date_created":"2022-01-18T11:29:33Z","content_type":"application/pdf","relation":"main_file","file_id":"10641"}],"issue":"4","article_processing_charge":"No","arxiv":1,"doi":"10.1103/PRXQuantum.2.040341","ddc":["530"],"language":[{"iso":"eng"}],"keyword":["quantum physics","mesoscale and nanoscale physics"],"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.","related_material":{"record":[{"id":"13057","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"9920"}]},"project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"type":"journal_article","author":[{"full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid"},{"first_name":"Gregory","full_name":"Szep, Gregory","last_name":"Szep"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"day":"24","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","ec_funded":1,"citation":{"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.","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.","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>.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 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>","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>"},"intvolume":"         2","status":"public","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"quality_controlled":"1","publication":"PRX Quantum","isi":1,"publisher":"American Physical Society","date_created":"2021-08-17T08:14:18Z","month":"11","page":"040341"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T12:05:58Z","scopus_import":"1","external_id":{"pmid":["32530634"],"isi":["000548893200082"],"arxiv":["2004.14599"]},"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"article_type":"original","year":"2020","oa_version":"Preprint","volume":20,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2004.14599","open_access":"1"}],"oa":1,"_id":"10866","date_published":"2020-07-01T00:00:00Z","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"}],"arxiv":1,"issue":"7","article_processing_charge":"No","language":[{"iso":"eng"}],"keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"doi":"10.1021/acs.nanolett.0c01673","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.","pmid":1,"day":"01","type":"journal_article","author":[{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"first_name":"Nathaniel","full_name":"Capote-Robayna, Nathaniel","last_name":"Capote-Robayna"},{"last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier"},{"last_name":"Álvarez-Pérez","first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan"},{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"citation":{"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>.","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.","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.","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>.","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>","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>","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."},"title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","quality_controlled":"1","department":[{"_id":"NanoFab"}],"publication":"Nano Letters","status":"public","intvolume":"        20","publisher":"American Chemical Society","isi":1,"month":"07","date_created":"2022-03-18T11:37:38Z","page":"5323-5329"},{"article_processing_charge":"No","_id":"7792","date_published":"2020-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"Phonon polaritons—light coupled to lattice vibrations—in polar van der Waals crystals are promising candidates for controlling the flow of energy on the nanoscale due to their strong field confinement, anisotropic propagation and ultra-long lifetime in the picosecond range1,2,3,4,5. However, the lack of tunability of their narrow and material-specific spectral range—the Reststrahlen band—severely limits their technological implementation. Here, we demonstrate that intercalation of Na atoms in the van der Waals semiconductor α-V2O5 enables a broad spectral shift of Reststrahlen bands, and that the phonon polaritons excited show ultra-low losses (lifetime of 4 ± 1 ps), similar to phonon polaritons in a non-intercalated crystal (lifetime of 6 ± 1 ps). We expect our intercalation method to be applicable to other van der Waals crystals, opening the door for the use of phonon polaritons in broad spectral bands in the mid-infrared domain."}],"publication_status":"published","volume":19,"article_type":"original","oa_version":"None","year":"2020","scopus_import":"1","external_id":{"pmid":["32284598"],"isi":["000526218500004"]},"date_updated":"2023-08-21T06:18:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["14764660"],"issn":["14761122"]},"page":"964–968","month":"09","date_created":"2020-05-03T22:00:49Z","publisher":"Springer Nature","isi":1,"publication":"Nature Materials","quality_controlled":"1","department":[{"_id":"NanoFab"}],"intvolume":"        19","status":"public","citation":{"chicago":"Taboada-Gutiérrez, Javier, Gonzalo Álvarez-Pérez, Jiahua Duan, Weiliang Ma, Kyle Crowley, Ivan Prieto Gonzalez, Andrei Bylinkin, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” <i>Nature Materials</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41563-020-0665-0\">https://doi.org/10.1038/s41563-020-0665-0</a>.","ista":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, Ma W, Crowley K, Prieto Gonzalez I, Bylinkin A, Autore M, Volkova H, Kimura K, Kimura T, Berger MH, Li S, Bao Q, Gao XPA, Errea I, Nikitin AY, Hillenbrand R, Martín-Sánchez J, Alonso-González P. 2020. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. Nature Materials. 19, 964–968.","ieee":"J. Taboada-Gutiérrez <i>et al.</i>, “Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation,” <i>Nature Materials</i>, vol. 19. Springer Nature, pp. 964–968, 2020.","mla":"Taboada-Gutiérrez, Javier, et al. “Broad Spectral Tuning of Ultra-Low-Loss Polaritons in a van Der Waals Crystal by Intercalation.” <i>Nature Materials</i>, vol. 19, Springer Nature, 2020, pp. 964–968, doi:<a href=\"https://doi.org/10.1038/s41563-020-0665-0\">10.1038/s41563-020-0665-0</a>.","short":"J. Taboada-Gutiérrez, G. Álvarez-Pérez, J. Duan, W. Ma, K. Crowley, I. Prieto Gonzalez, A. Bylinkin, M. Autore, H. Volkova, K. Kimura, T. Kimura, M.H. Berger, S. Li, Q. Bao, X.P.A. Gao, I. Errea, A.Y. Nikitin, R. Hillenbrand, J. Martín-Sánchez, P. Alonso-González, Nature Materials 19 (2020) 964–968.","ama":"Taboada-Gutiérrez J, Álvarez-Pérez G, Duan J, et al. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. <i>Nature Materials</i>. 2020;19:964–968. doi:<a href=\"https://doi.org/10.1038/s41563-020-0665-0\">10.1038/s41563-020-0665-0</a>","apa":"Taboada-Gutiérrez, J., Álvarez-Pérez, G., Duan, J., Ma, W., Crowley, K., Prieto Gonzalez, I., … Alonso-González, P. (2020). Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-020-0665-0\">https://doi.org/10.1038/s41563-020-0665-0</a>"},"title":"Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation","day":"01","type":"journal_article","author":[{"last_name":"Taboada-Gutiérrez","first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier"},{"last_name":"Álvarez-Pérez","first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Jiahua","full_name":"Duan, Jiahua","last_name":"Duan"},{"first_name":"Weiliang","full_name":"Ma, Weiliang","last_name":"Ma"},{"last_name":"Crowley","first_name":"Kyle","full_name":"Crowley, Kyle"},{"orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez"},{"full_name":"Bylinkin, Andrei","first_name":"Andrei","last_name":"Bylinkin"},{"full_name":"Autore, Marta","first_name":"Marta","last_name":"Autore"},{"full_name":"Volkova, Halyna","first_name":"Halyna","last_name":"Volkova"},{"first_name":"Kenta","full_name":"Kimura, Kenta","last_name":"Kimura"},{"full_name":"Kimura, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Kimura"},{"full_name":"Berger, M. H.","first_name":"M. H.","last_name":"Berger"},{"full_name":"Li, Shaojuan","first_name":"Shaojuan","last_name":"Li"},{"full_name":"Bao, Qiaoliang","first_name":"Qiaoliang","last_name":"Bao"},{"last_name":"Gao","full_name":"Gao, Xuan P.A.","first_name":"Xuan P.A."},{"first_name":"Ion","full_name":"Errea, Ion","last_name":"Errea"},{"last_name":"Nikitin","first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y."},{"full_name":"Hillenbrand, Rainer","first_name":"Rainer","last_name":"Hillenbrand"},{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"first_name":"Pablo","full_name":"Alonso-González, Pablo","last_name":"Alonso-González"}],"pmid":1,"acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the Government of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA-20-PF-BP19-053, respectively). J.M.-S. acknowledges finantial support from the Clarín Programme from the Government of the Principality of Asturias and a Marie Curie-COFUND grant (PA-18-ACB17-29) and the Ramón y Cajal Program from the Government of Spain (RYC2018-026196-I). K.C., X.P.A.G., H.V. and M.H.B. acknowledge the Air Force Office of Scientific Research (AFOSR) grant no. FA 9550-18-1-0030 for funding support. I.E. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness (grant no. FIS2016-76617-P). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT2017-88358-C3-3-R) and the Basque Government (grant no. IT1164-19). Q.B. acknowledges the support from Australian Research Council (grant nos. FT150100450, IH150100006 and CE170100039). R.H. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (national project RTI2018-094830-B-100 and the Project MDM-2016-0618 of the María de Maeztu Units of Excellence Program) and the Basque Goverment (grant no. IT1164-19). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA.","language":[{"iso":"eng"}],"doi":"10.1038/s41563-020-0665-0"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2020-07-14T12:48:03Z","oa":1,"publication_status":"submitted","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages."}],"_id":"7800","date_published":"2020-01-11T00:00:00Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"7801","date_created":"2020-05-05T14:31:19Z","file_name":"2020.01.10.902064v1.full.pdf","file_size":2931370,"creator":"rsix","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"PreCl"}],"date_updated":"2024-09-10T12:04:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","oa_version":"Preprint","year":"2020","status":"public","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"publication":"bioRxiv","publisher":"Cold Spring Harbor Laboratory","date_created":"2020-05-05T14:31:33Z","month":"01","ddc":["570"],"doi":"10.1101/2020.01.10.902064 ","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8620","status":"public"},{"id":"9429","relation":"later_version","status":"public"}]},"project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwarz, Lena A","first_name":"Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico"},{"orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","full_name":"Tasciyan, Saren","last_name":"Tasciyan"},{"first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dobler","full_name":"Dobler, Zoe","first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"type":"preprint","day":"11","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>.","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>.","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">https://doi.org/10.1101/2020.01.10.902064 </a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.01.10.902064 \">https://doi.org/10.1101/2020.01.10.902064 </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>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.01.10.902064 \">10.1101/2020.01.10.902064 </a>","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.)."}}]