[{"external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"article_type":"original","oa_version":"Published Version","type":"journal_article","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"date_published":"2023-09-01T00:00:00Z","volume":8,"month":"09","quality_controlled":"1","oa":1,"article_number":"adc9584","article_processing_charge":"No","doi":"10.1126/sciimmunol.adc9584","date_updated":"2023-12-21T14:30:01Z","publisher":"American Association for the Advancement of Science","publication":"Science Immunology","date_created":"2023-09-06T08:07:51Z","day":"01","publication_status":"published","keyword":["General Medicine","Immunology"],"author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","full_name":"Alanko, Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061"},{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"orcid":"0000-0002-8518-5926","last_name":"Canigova","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","full_name":"Canigova, Nikola"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","full_name":"Stopp, Julian A","last_name":"Stopp"},{"full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"related_material":{"record":[{"id":"14279","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"14697"}]},"year":"2023","language":[{"iso":"eng"}],"intvolume":"         8","citation":{"chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584."},"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"status":"public","ec_funded":1,"pmid":1,"acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","_id":"14274","publication_identifier":{"issn":["2470-9468"]},"issue":"87","scopus_import":"1","isi":1},{"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"year":"2023","ddc":["530","570"],"date_created":"2023-09-24T22:01:10Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"day":"13","publication_status":"published","author":[{"orcid":"0000-0003-4844-6311","last_name":"Riedl","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mayer","full_name":"Mayer, Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"month":"09","oa":1,"quality_controlled":"1","file":[{"relation":"main_file","creator":"dernst","content_type":"application/pdf","file_id":"14366","date_created":"2023-09-25T08:32:37Z","date_updated":"2023-09-25T08:32:37Z","file_size":2317272,"file_name":"2023_NatureComm_Riedl.pdf","access_level":"open_access","success":1,"checksum":"82d2d4ad736cc8493db8ce45cd313f7b"}],"article_number":"5633","article_processing_charge":"Yes","date_updated":"2023-12-13T12:29:41Z","doi":"10.1038/s41467-023-41432-1","publisher":"Springer Nature","publication":"Nature Communications","external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"article_type":"original","oa_version":"Published Version","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"date_published":"2023-09-13T00:00:00Z","type":"journal_article","volume":14,"file_date_updated":"2023-09-25T08:32:37Z","scopus_import":"1","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"title":"Synchronization in collectively moving inanimate and living active matter","_id":"14361","citation":{"chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633."},"intvolume":"        14","has_accepted_license":"1","status":"public","ec_funded":1},{"issue":"6665","publication_identifier":{"eissn":["1095-9203"]},"scopus_import":"1","status":"public","intvolume":"       381","citation":{"mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. <i>Science</i>. 2023;381(6665):1413-1414. doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>.","apa":"Balazs, D., &#38; Ibáñez, M. (2023). Widening the use of 3D printing. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” <i>Science</i>, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414."},"abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14404","title":"Widening the use of 3D printing","pmid":1,"acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","author":[{"orcid":"0000-0001-7597-043X","last_name":"Balazs","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"page":"1413-1414","date_created":"2023-10-08T22:01:16Z","publication_status":"published","day":"29","year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"volume":381,"date_published":"2023-09-29T00:00:00Z","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"type":"journal_article","oa_version":"None","external_id":{"pmid":["37769110"]},"article_type":"letter_note","article_processing_charge":"No","publication":"Science","doi":"10.1126/science.adk3070","publisher":"AAAS","date_updated":"2023-10-09T07:32:58Z","month":"09","quality_controlled":"1"},{"day":"25","publication_status":"published","date_created":"2023-10-22T22:01:16Z","author":[{"last_name":"D’Elia","first_name":"Domenica","full_name":"D’Elia, Domenica"},{"last_name":"Truu","full_name":"Truu, Jaak","first_name":"Jaak"},{"first_name":"Leo","full_name":"Lahti, Leo","last_name":"Lahti"},{"full_name":"Berland, Magali","first_name":"Magali","last_name":"Berland"},{"full_name":"Papoutsoglou, Georgios","first_name":"Georgios","last_name":"Papoutsoglou"},{"last_name":"Ceci","full_name":"Ceci, Michelangelo","first_name":"Michelangelo"},{"first_name":"Aldert","full_name":"Zomer, Aldert","last_name":"Zomer"},{"first_name":"Marta B.","full_name":"Lopes, Marta B.","last_name":"Lopes"},{"last_name":"Ibrahimi","full_name":"Ibrahimi, Eliana","first_name":"Eliana"},{"first_name":"Aleksandra","full_name":"Gruca, Aleksandra","last_name":"Gruca"},{"first_name":"Alina","full_name":"Nechyporenko, Alina","last_name":"Nechyporenko"},{"first_name":"Marcus","full_name":"Frohme, Marcus","last_name":"Frohme"},{"first_name":"Thomas","full_name":"Klammsteiner, Thomas","last_name":"Klammsteiner"},{"full_name":"Pau, Enrique Carrillo De Santa","first_name":"Enrique Carrillo De Santa","last_name":"Pau"},{"first_name":"Laura Judith","full_name":"Marcos-Zambrano, Laura Judith","last_name":"Marcos-Zambrano"},{"full_name":"Hron, Karel","first_name":"Karel","last_name":"Hron"},{"last_name":"Pio","full_name":"Pio, Gianvito","first_name":"Gianvito"},{"full_name":"Simeon, Andrea","first_name":"Andrea","last_name":"Simeon"},{"full_name":"Suharoschi, Ramona","first_name":"Ramona","last_name":"Suharoschi"},{"full_name":"Moreno-Indias, Isabel","first_name":"Isabel","last_name":"Moreno-Indias"},{"first_name":"Andriy","full_name":"Temko, Andriy","last_name":"Temko"},{"first_name":"Miroslava","full_name":"Nedyalkova, Miroslava","last_name":"Nedyalkova"},{"last_name":"Apostol","first_name":"Elena Simona","full_name":"Apostol, Elena Simona"},{"full_name":"Truică, Ciprian Octavian","first_name":"Ciprian Octavian","last_name":"Truică"},{"full_name":"Shigdel, Rajesh","first_name":"Rajesh","last_name":"Shigdel"},{"full_name":"Telalović, Jasminka Hasić","first_name":"Jasminka Hasić","last_name":"Telalović"},{"full_name":"Bongcam-Rudloff, Erik","first_name":"Erik","last_name":"Bongcam-Rudloff"},{"last_name":"Przymus","first_name":"Piotr","full_name":"Przymus, Piotr"},{"last_name":"Jordamović","full_name":"Jordamović, Naida Babić","first_name":"Naida Babić"},{"last_name":"Falquet","full_name":"Falquet, Laurent","first_name":"Laurent"},{"last_name":"Tarazona","full_name":"Tarazona, Sonia","first_name":"Sonia"},{"first_name":"Alexia","full_name":"Sampri, Alexia","last_name":"Sampri"},{"last_name":"Isola","full_name":"Isola, Gaetano","first_name":"Gaetano"},{"last_name":"Pérez-Serrano","first_name":"David","full_name":"Pérez-Serrano, David"},{"last_name":"Trajkovik","first_name":"Vladimir","full_name":"Trajkovik, Vladimir"},{"full_name":"Klucar, Lubos","first_name":"Lubos","last_name":"Klucar"},{"last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana","first_name":"Tatjana"},{"last_name":"Havulinna","first_name":"Aki S.","full_name":"Havulinna, Aki S."},{"full_name":"Jansen, Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2","first_name":"Christian","last_name":"Jansen"},{"full_name":"Bertelsen, Randi J.","first_name":"Randi J.","last_name":"Bertelsen"},{"full_name":"Claesson, Marcus Joakim","first_name":"Marcus Joakim","last_name":"Claesson"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"ScienComp"}],"year":"2023","ddc":["000"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_type":"original","external_id":{"isi":["001080536000001"],"pmid":["37808321"]},"date_published":"2023-09-25T00:00:00Z","type":"journal_article","volume":14,"oa":1,"quality_controlled":"1","file":[{"content_type":"application/pdf","file_id":"14471","date_created":"2023-10-30T13:38:48Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_name":"2023_FrontiersMicrobiology_DElia.pdf","success":1,"checksum":"6c0acdd8fa111a699826957b8dff19d5","date_updated":"2023-10-30T13:38:48Z","file_size":505078}],"article_number":"1257002","month":"09","date_updated":"2023-12-13T13:07:21Z","doi":"10.3389/fmicb.2023.1257002","publisher":"Frontiers","publication":"Frontiers in Microbiology","article_processing_charge":"Yes","publication_identifier":{"eissn":["1664-302X"]},"file_date_updated":"2023-10-30T13:38:48Z","scopus_import":"1","isi":1,"citation":{"chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>.","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>, vol. 14, 1257002, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">10.3389/fmicb.2023.1257002</a>.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","ieee":"D. D’Elia <i>et al.</i>, “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.","ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1257002\">https://doi.org/10.3389/fmicb.2023.1257002</a>"},"intvolume":"        14","has_accepted_license":"1","status":"public","acknowledgement":"This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.","pmid":1,"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","_id":"14449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.","lang":"eng"}]},{"date_created":"2024-01-10T09:41:21Z","publication_status":"published","day":"11","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"author":[{"last_name":"Westerich","first_name":"Kim Joana","full_name":"Westerich, Kim Joana"},{"first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna","last_name":"Tarbashevich"},{"first_name":"Jan","full_name":"Schick, Jan","last_name":"Schick"},{"last_name":"Gupta","full_name":"Gupta, Antra","first_name":"Antra"},{"last_name":"Zhu","first_name":"Mingzhao","full_name":"Zhu, Mingzhao"},{"last_name":"Hull","first_name":"Kenneth","full_name":"Hull, Kenneth"},{"last_name":"Romo","first_name":"Daniel","full_name":"Romo, Daniel"},{"first_name":"Dagmar","full_name":"Zeuschner, Dagmar","last_name":"Zeuschner"},{"first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","full_name":"Goudarzi, Mohammad","last_name":"Goudarzi"},{"full_name":"Gross-Thebing, Theresa","first_name":"Theresa","last_name":"Gross-Thebing"},{"first_name":"Erez","full_name":"Raz, Erez","last_name":"Raz"}],"page":"1578-1592.e5","department":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"year":"2023","oa_version":"Preprint","article_type":"original","external_id":{"pmid":["37463577"]},"volume":58,"date_published":"2023-09-11T00:00:00Z","type":"journal_article","month":"09","oa":1,"quality_controlled":"1","article_processing_charge":"No","publication":"Developmental Cell","date_updated":"2024-01-16T08:56:36Z","publisher":"Elsevier","doi":"10.1016/j.devcel.2023.06.009","publication_identifier":{"issn":["1534-5807"]},"issue":"17","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244"}],"intvolume":"        58","citation":{"apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>.","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>."},"status":"public","pmid":1,"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14781","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1"},{"acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","_id":"12106","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"citation":{"ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823."},"intvolume":"        41","has_accepted_license":"1","status":"public","file_date_updated":"2023-08-16T11:30:45Z","scopus_import":"1","isi":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"oa":1,"file":[{"content_type":"application/pdf","date_created":"2023-08-16T11:30:45Z","file_id":"14066","creator":"dernst","relation":"main_file","success":1,"file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","checksum":"668447a1c8d360b68f8aaf9e08ed644f","date_updated":"2023-08-16T11:30:45Z","file_size":12040976}],"quality_controlled":"1","month":"06","doi":"10.1038/s41587-022-01560-3","publisher":"Springer Nature","date_updated":"2023-08-16T11:32:33Z","publication":"Nature Biotechnology","article_processing_charge":"No","article_type":"original","external_id":{"isi":["000909067600003"]},"oa_version":"Published Version","date_published":"2023-06-01T00:00:00Z","type":"journal_article","volume":41,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"year":"2023","ddc":["570"],"day":"01","publication_status":"published","date_created":"2023-01-08T23:00:53Z","page":"813–823","author":[{"orcid":"0000-0003-1732-1559","last_name":"Yeung","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake"},{"full_name":"Florescu, Maria","first_name":"Maria","last_name":"Florescu"},{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton"},{"full_name":"Wellenstein, Max D.","first_name":"Max D.","last_name":"Wellenstein"},{"last_name":"Van Oudenaarden","full_name":"Van Oudenaarden, Alexander","first_name":"Alexander"}]},{"article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2023-08-04T09:25:59Z","doi":"10.1038/s42003-022-03446-1","publication":"Communications Biology","month":"06","file":[{"date_updated":"2023-01-27T08:23:46Z","file_size":3968356,"access_level":"open_access","file_name":"2022_CommBiology_Muhia.pdf","success":1,"checksum":"bd95be1e77090208b79bc45ea8785d0b","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"12417","date_created":"2023-01-27T08:23:46Z"}],"oa":1,"quality_controlled":"1","article_number":"589","type":"journal_article","date_published":"2022-06-15T00:00:00Z","volume":5,"external_id":{"isi":["000811777900003"]},"article_type":"original","oa_version":"Published Version","ddc":["570"],"year":"2022","language":[{"iso":"eng"}],"department":[{"_id":"PreCl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"author":[{"last_name":"Muhia","first_name":"Mary W","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","full_name":"Muhia, Mary W"},{"first_name":"PingAn","full_name":"YuanXiang, PingAn","last_name":"YuanXiang"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"last_name":"Schwarz","full_name":"Schwarz, Jürgen R.","first_name":"Jürgen R."},{"full_name":"Heisler, Frank F.","first_name":"Frank F.","last_name":"Heisler"},{"last_name":"Gromova","first_name":"Kira V.","full_name":"Gromova, Kira V."},{"first_name":"Edda","full_name":"Thies, Edda","last_name":"Thies"},{"last_name":"Breiden","first_name":"Petra","full_name":"Breiden, Petra"},{"first_name":"Yvonne","full_name":"Pechmann, Yvonne","last_name":"Pechmann"},{"last_name":"Kreutz","first_name":"Michael R.","full_name":"Kreutz, Michael R."},{"first_name":"Matthias","full_name":"Kneussel, Matthias","last_name":"Kneussel"}],"date_created":"2023-01-16T09:48:19Z","day":"15","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine <jats:italic>Mkln1</jats:italic> knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that <jats:italic>Mkln1</jats:italic> deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from <jats:italic>Mkln1</jats:italic> ablation."}],"title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","_id":"12224","acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","status":"public","intvolume":"         5","citation":{"apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","ieee":"M. W. Muhia <i>et al.</i>, “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>, vol. 5, 589, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>.","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>."},"has_accepted_license":"1","scopus_import":"1","isi":1,"file_date_updated":"2023-01-27T08:23:46Z","publication_identifier":{"issn":["2399-3642"]}},{"year":"2022","language":[{"iso":"eng"}],"ddc":["540"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"NMR"}],"author":[{"first_name":"Felix","full_name":"Xu, Felix","last_name":"Xu"},{"first_name":"Antony","full_name":"Crisp, Antony","last_name":"Crisp"},{"last_name":"Schinkel","full_name":"Schinkel, Thea","first_name":"Thea"},{"last_name":"Dubini","first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A."},{"last_name":"Hübner","full_name":"Hübner, Sarah","first_name":"Sarah"},{"first_name":"Sidney","full_name":"Becker, Sidney","last_name":"Becker"},{"first_name":"Florian","full_name":"Schelter, Florian","last_name":"Schelter"},{"last_name":"Rovo","orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","full_name":"Rovo, Petra"},{"last_name":"Carell","first_name":"Thomas","full_name":"Carell, Thomas"}],"keyword":["General Chemistry","Catalysis"],"publication_status":"published","day":"07","date_created":"2023-01-16T09:49:05Z","publication":"Angewandte Chemie International Edition","doi":"10.1002/anie.202211945","publisher":"Wiley","date_updated":"2023-08-04T09:32:42Z","article_processing_charge":"No","article_number":"e202211945","oa":1,"file":[{"checksum":"4e8152454d12025d13f6e6e9ca06b5d0","success":1,"access_level":"open_access","file_name":"2022_AngewandteChemieInternat_Xu.pdf","file_size":1076715,"date_updated":"2023-01-27T10:28:45Z","date_created":"2023-01-27T10:28:45Z","file_id":"12422","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"quality_controlled":"1","month":"11","volume":61,"date_published":"2022-11-07T00:00:00Z","type":"journal_article","oa_version":"Published Version","article_type":"original","external_id":{"isi":["000866428500001"]},"isi":1,"scopus_import":"1","file_date_updated":"2023-01-27T10:28:45Z","issue":"45","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"_id":"12228","title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA","abstract":[{"lang":"eng","text":"The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Stefan Wiedemann for the synthesis of reference compounds and Pia Heinrichs for assistance in the NMR measurements of the oligonucleotides. We also thank Dr. Luis Escobar and Jonas Feldmann for valued discussions. This work was supported by the German Research Foundation (DFG) for financial support via CRC1309 (Project ID 325871075, A04), CRC1361 (Project ID 893547839, P02) and CRC1032 (Project ID 201269156, A5). This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under grant agreement No 741912 (EpiR). We are grateful for additional funding from the Volkswagen Foundation (EvoRib). Open Access funding enabled and organized by Projekt DEAL.","status":"public","has_accepted_license":"1","intvolume":"        61","citation":{"chicago":"Xu, Felix, Antony Crisp, Thea Schinkel, Romeo C. A. Dubini, Sarah Hübner, Sidney Becker, Florian Schelter, Petra Rovo, and Thomas Carell. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” <i>Angewandte Chemie International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202211945\">https://doi.org/10.1002/anie.202211945</a>.","ama":"Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. <i>Angewandte Chemie International Edition</i>. 2022;61(45). doi:<a href=\"https://doi.org/10.1002/anie.202211945\">10.1002/anie.202211945</a>","mla":"Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” <i>Angewandte Chemie International Edition</i>, vol. 61, no. 45, e202211945, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202211945\">10.1002/anie.202211945</a>.","short":"F. Xu, A. Crisp, T. Schinkel, R.C.A. Dubini, S. Hübner, S. Becker, F. Schelter, P. Rovo, T. Carell, Angewandte Chemie International Edition 61 (2022).","ieee":"F. Xu <i>et al.</i>, “Isoxazole nucleosides as building blocks for a plausible proto‐RNA,” <i>Angewandte Chemie International Edition</i>, vol. 61, no. 45. Wiley, 2022.","ista":"Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovo P, Carell T. 2022. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 61(45), e202211945.","apa":"Xu, F., Crisp, A., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S., … Carell, T. (2022). Isoxazole nucleosides as building blocks for a plausible proto‐RNA. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202211945\">https://doi.org/10.1002/anie.202211945</a>"}},{"article_type":"original","oa_version":"Published Version","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"volume":15,"date_published":"2022-10-03T00:00:00Z","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"type":"journal_article","oa":1,"quality_controlled":"1","file":[{"checksum":"04d5c12490052d03e4dc4412338a43dd","access_level":"open_access","file_name":"2022_MolecularPlant_Johnson.pdf","success":1,"file_size":2307251,"date_updated":"2023-01-30T07:46:51Z","file_id":"12435","date_created":"2023-01-30T07:46:51Z","content_type":"application/pdf","creator":"dernst","relation":"main_file"}],"month":"10","publication":"Molecular Plant","publisher":"Elsevier","date_updated":"2023-08-04T09:39:24Z","doi":"10.1016/j.molp.2022.09.003","article_processing_charge":"Yes (via OA deal)","publication_status":"published","day":"03","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-01-16T09:51:49Z","page":"1533-1542","author":[{"full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","full_name":"Costanzo, Tommaso"},{"last_name":"Dahhan","first_name":"Dana A.","full_name":"Dahhan, Dana A."},{"full_name":"Bednarek, Sebastian Y.","first_name":"Sebastian Y.","last_name":"Bednarek"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"keyword":["Plant Science","Molecular Biology"],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"ddc":["580"],"year":"2022","has_accepted_license":"1","citation":{"chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542."},"intvolume":"        15","status":"public","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","pmid":1,"_id":"12239","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1674-2052"]},"issue":"10","file_date_updated":"2023-01-30T07:46:51Z","isi":1,"scopus_import":"1"},{"volume":32,"date_published":"2022-09-26T00:00:00Z","type":"journal_article","external_id":{"isi":["000861009600005"],"arxiv":["2206.01531"]},"oa_version":"Published Version","article_type":"original","article_processing_charge":"No","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_updated":"2023-08-04T09:51:17Z","doi":"10.1063/5.0102904","publisher":"AIP Publishing","month":"09","article_number":"093138","oa":1,"quality_controlled":"1","file":[{"file_id":"12445","date_created":"2023-01-30T09:41:12Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","checksum":"17881eff8b21969359a2dd64620120ba","file_name":"2022_Chaos_Choueiri.pdf","access_level":"open_access","success":1,"file_size":3209644,"date_updated":"2023-01-30T09:41:12Z"}],"keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"author":[{"last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"full_name":"Suri, Balachandra","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"}],"arxiv":1,"date_created":"2023-01-16T09:58:16Z","publication_status":"published","day":"26","ddc":["530"],"language":[{"iso":"eng"}],"year":"2022","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"status":"public","has_accepted_license":"1","intvolume":"        32","citation":{"short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9. AIP Publishing, 2022.","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., &#38; Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>","chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>.","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2022;32(9). doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>","mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>."},"abstract":[{"text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. ","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12259","title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","issue":"9","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"isi":1,"scopus_import":"1","file_date_updated":"2023-01-30T09:41:12Z"},{"abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12262","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","pmid":1,"acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","status":"public","has_accepted_license":"1","intvolume":"        29","citation":{"short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural &#38; Molecular Biology 29 (2022) 942–953.","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>."},"isi":1,"scopus_import":"1","file_date_updated":"2023-01-30T10:00:04Z","issue":"9","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"article_processing_charge":"No","publication":"Nature Structural & Molecular Biology","publisher":"Springer Nature","date_updated":"2023-08-04T09:52:20Z","doi":"10.1038/s41594-022-00832-5","month":"09","file":[{"date_updated":"2023-01-30T10:00:04Z","file_size":9935057,"success":1,"file_name":"2022_NatureStrucMolecBio_Prattes.pdf","access_level":"open_access","checksum":"2d5c3ec01718fefd7553052b0b8a0793","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2023-01-30T10:00:04Z","file_id":"12447"}],"quality_controlled":"1","oa":1,"volume":29,"type":"journal_article","date_published":"2022-09-12T00:00:00Z","article_type":"original","oa_version":"Published Version","external_id":{"isi":["000852942100004"],"pmid":["36097293"]},"year":"2022","ddc":["570"],"language":[{"iso":"eng"}],"department":[{"_id":"EM-Fac"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Prattes","first_name":"Michael","full_name":"Prattes, Michael"},{"last_name":"Grishkovskaya","first_name":"Irina","full_name":"Grishkovskaya, Irina"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Christina","full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder"},{"last_name":"Zisser","first_name":"Gertrude","full_name":"Zisser, Gertrude"},{"first_name":"Carolin","full_name":"Sailer, Carolin","last_name":"Sailer"},{"last_name":"Kargas","first_name":"Vasileios","full_name":"Kargas, Vasileios"},{"full_name":"Loibl, Mathias","first_name":"Mathias","last_name":"Loibl"},{"first_name":"Magdalena","full_name":"Gerhalter, Magdalena","last_name":"Gerhalter"},{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"last_name":"Warren","first_name":"Alan J.","full_name":"Warren, Alan J."},{"first_name":"Florian","full_name":"Stengel, Florian","last_name":"Stengel"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"keyword":["Molecular Biology","Structural Biology"],"page":"942-953","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2023-01-16T09:59:06Z","publication_status":"published","day":"12"},{"scopus_import":"1","isi":1,"file_date_updated":"2023-11-02T17:12:37Z","issue":"7927","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","_id":"12291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","pmid":1,"status":"public","ec_funded":1,"intvolume":"       609","citation":{"short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>"},"has_accepted_license":"1","year":"2022","language":[{"iso":"eng"}],"ddc":["580"],"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"page":"575-581","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"orcid":"0000-0003-4783-1752","last_name":"Gelová","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana"},{"orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"last_name":"Živanović","full_name":"Živanović, Branka D.","first_name":"Branka D."},{"last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia"},{"full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini"},{"last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"last_name":"Kuhn","full_name":"Kuhn, Andre","first_name":"Andre"},{"full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","orcid":"0000-0002-8600-0671"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","last_name":"Randuch"},{"last_name":"Rýdza","full_name":"Rýdza, Nikola","first_name":"Nikola"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","full_name":"Teplova, Anastasiia"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"}],"day":"15","publication_status":"published","date_created":"2023-01-16T10:04:48Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publisher":"Springer Nature","date_updated":"2023-11-07T08:16:09Z","doi":"10.1038/s41586-022-05187-x","publication":"Nature","article_processing_charge":"No","oa":1,"quality_controlled":"1","file":[{"date_created":"2023-11-02T17:12:37Z","file_id":"14483","content_type":"application/pdf","creator":"amally","relation":"main_file","checksum":"a6055c606aefb900bf62ae3e7d15f921","success":1,"access_level":"open_access","file_name":"Friml Nature 2022_merged.pdf","file_size":79774945,"date_updated":"2023-11-02T17:12:37Z"}],"month":"09","type":"journal_article","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"date_published":"2022-09-15T00:00:00Z","volume":609,"article_type":"original","external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"oa_version":"Submitted Version"},{"publication_identifier":{"isbn":["978-3-200-08499-5"]},"file_date_updated":"2023-05-05T09:06:00Z","citation":{"apa":"Schlögl, A., Hornoiu, A., Elefante, S., &#38; Stadlbauer, S. (2022). Where is the sweet spot? A procurement story of general purpose compute nodes. In <i>ASHPC22 - Austrian-Slovenian HPC Meeting 2022</i> (p. 7). Grundlsee, Austria: EuroCC Austria c/o Universität Wien. <a href=\"https://doi.org/10.25365/phaidra.337\">https://doi.org/10.25365/phaidra.337</a>","ista":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7.","short":"A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7.","ieee":"A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet spot? A procurement story of general purpose compute nodes,” in <i>ASHPC22 - Austrian-Slovenian HPC Meeting 2022</i>, Grundlsee, Austria, 2022, p. 7.","mla":"Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” <i>ASHPC22 - Austrian-Slovenian HPC Meeting 2022</i>, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:<a href=\"https://doi.org/10.25365/phaidra.337\">10.25365/phaidra.337</a>.","ama":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A procurement story of general purpose compute nodes. In: <i>ASHPC22 - Austrian-Slovenian HPC Meeting 2022</i>. EuroCC Austria c/o Universität Wien; 2022:7. doi:<a href=\"https://doi.org/10.25365/phaidra.337\">10.25365/phaidra.337</a>","chicago":"Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In <i>ASHPC22 - Austrian-Slovenian HPC Meeting 2022</i>, 7. EuroCC Austria c/o Universität Wien, 2022. <a href=\"https://doi.org/10.25365/phaidra.337\">https://doi.org/10.25365/phaidra.337</a>."},"has_accepted_license":"1","status":"public","acknowledgement":"The abstracts in this booklet are licenced under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n","title":"Where is the sweet spot? A procurement story of general purpose compute nodes","_id":"12894","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","publication_status":"published","date_created":"2023-05-05T09:13:42Z","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2022-05-31","end_date":"2022-06-02","location":"Grundlsee, Austria"},"page":"7","author":[{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois"},{"last_name":"Hornoiu","first_name":"Andrei","id":"77129392-B450-11EA-8745-D4653DDC885E","full_name":"Hornoiu, Andrei"},{"last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano"},{"first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"department":[{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","language":[{"iso":"eng"}],"ddc":["000"],"oa_version":"Published Version","date_published":"2022-06-02T00:00:00Z","type":"conference_abstract","file":[{"checksum":"e3f8c240b85422ce2190e7b203cc2563","success":1,"file_name":"BOOKLET_ASHPC22.pdf","access_level":"open_access","file_size":7180531,"date_updated":"2023-05-05T09:06:00Z","date_created":"2023-05-05T09:06:00Z","file_id":"12895","content_type":"application/pdf","creator":"schloegl","relation":"main_file"}],"oa":1,"month":"06","date_updated":"2023-05-16T07:42:56Z","publisher":"EuroCC Austria c/o Universität Wien","doi":"10.25365/phaidra.337","publication":"ASHPC22 - Austrian-Slovenian HPC Meeting 2022","article_processing_charge":"No"},{"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"ddc":["570"],"language":[{"iso":"eng"}],"year":"2022","related_material":{"record":[{"id":"12726","status":"public","relation":"dissertation_contains"},{"id":"14530","relation":"dissertation_contains","status":"public"},{"id":"12401","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","day":"10","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"date_created":"2022-01-30T23:01:33Z","page":"47-62.e9","author":[{"full_name":"Gaertner, Florian","first_name":"Florian","last_name":"Gaertner"},{"first_name":"Patricia","full_name":"Reis-Rodrigues, Patricia","last_name":"Reis-Rodrigues"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries"},{"last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav"},{"first_name":"Juan","full_name":"Aguilera, Juan","last_name":"Aguilera"},{"last_name":"Riedl","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael"},{"last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan"},{"first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"full_name":"Zheden, Vanessa","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","last_name":"Zheden"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"oa":1,"quality_controlled":"1","month":"01","publication":"Developmental Cell","doi":"10.1016/j.devcel.2021.11.024","publisher":"Cell Press ; Elsevier","date_updated":"2024-03-25T23:30:12Z","article_processing_charge":"No","external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"article_type":"original","oa_version":"Published Version","volume":57,"project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"}],"date_published":"2022-01-10T00:00:00Z","type":"journal_article","isi":1,"scopus_import":"1","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"issue":"1","acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","pmid":1,"_id":"10703","title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","abstract":[{"text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"intvolume":"        57","citation":{"ieee":"F. Gaertner <i>et al.</i>, “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” <i>Developmental Cell</i>, vol. 57, no. 1. Cell Press ; Elsevier, p. 47–62.e9, 2022.","short":"F. Gaertner, P. Reis-Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","apa":"Gaertner, F., Reis-Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. Cell Press ; Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>","ista":"Gaertner F, Reis-Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","chicago":"Gaertner, Florian, Patricia Reis-Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>. Cell Press ; Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>.","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>, vol. 57, no. 1, Cell Press ; Elsevier, 2022, p. 47–62.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>.","ama":"Gaertner F, Reis-Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. 2022;57(1):47-62.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>"},"ec_funded":1,"status":"public"},{"publication_status":"published","day":"11","date_created":"2022-02-16T11:18:21Z","page":"237-246","author":[{"first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A.","last_name":"Dubini"},{"last_name":"Korytiaková","full_name":"Korytiaková, Eva","first_name":"Eva"},{"full_name":"Schinkel, Thea","first_name":"Thea","last_name":"Schinkel"},{"last_name":"Heinrichs","first_name":"Pia","full_name":"Heinrichs, Pia"},{"last_name":"Carell","full_name":"Carell, Thomas","first_name":"Thomas"},{"full_name":"Rovo, Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","orcid":"0000-0001-8729-7326","last_name":"Rovo"}],"department":[{"_id":"NMR"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"year":"2022","ddc":["540"],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"external_id":{"pmid":["35637781"]},"article_type":"original","oa_version":"Published Version","volume":2,"date_published":"2022-02-11T00:00:00Z","type":"journal_article","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"quality_controlled":"1","file":[{"access_level":"open_access","file_name":"2022_ACSPhysChemAU_Dubini.pdf","success":1,"checksum":"5ce3f907848f5c7caf77f1adfe5826c6","date_updated":"2022-07-29T07:53:20Z","file_size":2351220,"content_type":"application/pdf","file_id":"11692","date_created":"2022-07-29T07:53:20Z","creator":"dernst","relation":"main_file"}],"month":"02","publication":"ACS Physical Chemistry Au","date_updated":"2023-01-31T07:33:07Z","doi":"10.1021/acsphyschemau.1c00050","publisher":"American Chemical Society","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["2694-2445"]},"issue":"3","file_date_updated":"2022-07-29T07:53:20Z","scopus_import":"1","has_accepted_license":"1","citation":{"chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. 2022;2(3):237-246. doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:<a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">10.1021/acsphyschemau.1c00050</a>.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” <i>ACS Physical Chemistry Au</i>, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., &#38; Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. <i>ACS Physical Chemistry Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphyschemau.1c00050\">https://doi.org/10.1021/acsphyschemau.1c00050</a>"},"intvolume":"         2","status":"public","acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","pmid":1,"_id":"10758","title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","abstract":[{"lang":"eng","text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"isi":["000766926900009"]},"oa_version":"Published Version","article_type":"original","volume":119,"date_published":"2022-02-14T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","article_number":"e2122030119","oa":1,"file":[{"date_created":"2022-02-21T08:45:11Z","file_id":"10780","content_type":"application/pdf","relation":"main_file","creator":"dernst","checksum":"d49f83c3580613966f71768ddb9a55a5","success":1,"access_level":"open_access","file_name":"2022_PNAS_Slovakova.pdf","file_size":1609678,"date_updated":"2022-02-21T08:45:11Z"}],"quality_controlled":"1","month":"02","publication":"Proceedings of the National Academy of Sciences of the United States of America","doi":"10.1073/pnas.2122030119","date_updated":"2023-08-02T14:26:51Z","publisher":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","publication_status":"published","day":"14","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_created":"2022-02-20T23:01:31Z","author":[{"first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","last_name":"Slovakova"},{"last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K"},{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"year":"2022","ddc":["570"],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9750"}]},"has_accepted_license":"1","citation":{"ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022."},"intvolume":"       119","ec_funded":1,"status":"public","acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","_id":"10766","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["10916490"]},"issue":"8","file_date_updated":"2022-02-21T08:45:11Z","isi":1,"scopus_import":"1"},{"quality_controlled":"1","oa":1,"file":[{"checksum":"822e76e056c07099d1fb27d1ece5941b","success":1,"file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","access_level":"open_access","file_size":4846551,"date_updated":"2023-08-16T08:00:30Z","date_created":"2023-08-16T08:00:30Z","file_id":"14061","content_type":"application/pdf","creator":"dernst","relation":"main_file"}],"article_number":"kvac009","month":"07","date_updated":"2023-11-30T10:55:12Z","publisher":"Oxford Academic","doi":"10.1093/oons/kvac009","publication":"Oxford Open Neuroscience","article_processing_charge":"No","oa_version":"Published Version","article_type":"original","date_published":"2022-07-07T00:00:00Z","project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"type":"journal_article","volume":1,"department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"id":"14530","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"year":"2022","ddc":["570"],"day":"07","publication_status":"published","date_created":"2022-02-25T07:52:11Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"author":[{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","last_name":"Hansen"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laukoter","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"first_name":"Li Huei","full_name":"Tsai, Li Huei","last_name":"Tsai"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; 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.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","_id":"10791","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"citation":{"apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022).","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford Academic, 2022.","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>."},"intvolume":"         1","has_accepted_license":"1","status":"public","ec_funded":1,"file_date_updated":"2023-08-16T08:00:30Z","publication_identifier":{"eissn":["2753-149X"]},"issue":"1"},{"publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"file_date_updated":"2022-07-25T07:11:32Z","scopus_import":"1","isi":1,"citation":{"ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-022-01257-4\">https://doi.org/10.1038/s41590-022-01257-4</a>","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255.","ieee":"F. P. Assen <i>et al.</i>, “Multitier mechanics control stromal adaptations in swelling lymph nodes,” <i>Nature Immunology</i>, vol. 23. Springer Nature, pp. 1246–1255, 2022.","ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. <i>Nature Immunology</i>. 2022;23:1246-1255. doi:<a href=\"https://doi.org/10.1038/s41590-022-01257-4\">10.1038/s41590-022-01257-4</a>","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” <i>Nature Immunology</i>, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:<a href=\"https://doi.org/10.1038/s41590-022-01257-4\">10.1038/s41590-022-01257-4</a>.","chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” <i>Nature Immunology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41590-022-01257-4\">https://doi.org/10.1038/s41590-022-01257-4</a>."},"intvolume":"        23","has_accepted_license":"1","status":"public","ec_funded":1,"acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","_id":"9794","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion."}],"day":"11","publication_status":"published","date_created":"2021-08-06T09:09:11Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"page":"1246-1255","author":[{"full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"last_name":"Costanzo","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","full_name":"Costanzo, Tommaso"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"last_name":"Brown","full_name":"Brown, Markus","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ludewig, Burkhard","first_name":"Burkhard","last_name":"Ludewig"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Weninger","first_name":"Wolfgang","full_name":"Weninger, Wolfgang"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Sanjiv A.","full_name":"Luther, Sanjiv A.","last_name":"Luther"},{"last_name":"Stein","full_name":"Stein, Jens V.","first_name":"Jens V."},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt"}],"department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"language":[{"iso":"eng"}],"year":"2022","oa_version":"Published Version","article_type":"original","external_id":{"isi":["000822975900002"]},"project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"}],"date_published":"2022-07-11T00:00:00Z","type":"journal_article","volume":23,"quality_controlled":"1","oa":1,"file":[{"relation":"main_file","creator":"dernst","date_created":"2022-07-25T07:11:32Z","file_id":"11642","content_type":"application/pdf","file_size":11475325,"date_updated":"2022-07-25T07:11:32Z","checksum":"628e7b49809f22c75b428842efe70c68","success":1,"file_name":"2022_NatureImmunology_Assen.pdf","access_level":"open_access"}],"month":"07","date_updated":"2023-08-02T06:53:07Z","publisher":"Springer Nature","doi":"10.1038/s41590-022-01257-4","publication":"Nature Immunology","article_processing_charge":"No"},{"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"intvolume":"        34","citation":{"chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173."},"status":"public","pmid":1,"acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10841","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"issue":"6","isi":1,"scopus_import":"1","article_type":"original","oa_version":"Preprint","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"volume":34,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"type":"journal_article","date_published":"2022-06-01T00:00:00Z","month":"06","oa":1,"quality_controlled":"1","article_processing_charge":"No","publication":"Plant Cell","doi":"10.1093/plcell/koac071","date_updated":"2023-08-02T14:46:48Z","publisher":"Oxford Academic","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2022-03-08T13:47:51Z","publication_status":"published","day":"01","author":[{"last_name":"Dahhan","first_name":"DA","full_name":"Dahhan, DA"},{"last_name":"Reynolds","full_name":"Reynolds, GD","first_name":"GD"},{"last_name":"Cárdenas","first_name":"JJ","full_name":"Cárdenas, JJ"},{"last_name":"Eeckhout","full_name":"Eeckhout, D","first_name":"D"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"first_name":"K","full_name":"Yperman, K","last_name":"Yperman"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"full_name":"Vang, N","first_name":"N","last_name":"Vang"},{"full_name":"Yan, X","first_name":"X","last_name":"Yan"},{"first_name":"I","full_name":"Hwang, I","last_name":"Hwang"},{"last_name":"Heese","full_name":"Heese, A","first_name":"A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Van Damme","first_name":"D","full_name":"Van Damme, D"},{"full_name":"Pan, J","first_name":"J","last_name":"Pan"},{"last_name":"Bednarek","full_name":"Bednarek, SY","first_name":"SY"}],"page":"2150-2173","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"year":"2022"},{"issue":"4","publication_identifier":{"eissn":["2691-1299"]},"scopus_import":"1","file_date_updated":"2022-05-02T08:16:10Z","status":"public","has_accepted_license":"1","intvolume":"         2","citation":{"mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>, vol. 2, no. 4, e407, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>.","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. 2022;2(4). doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>","chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>.","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., &#38; Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. Wiley. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” <i>Current Protocols</i>, vol. 2, no. 4. Wiley, 2022."},"abstract":[{"lang":"eng","text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11182","title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","pmid":1,"acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","author":[{"last_name":"Kroll","full_name":"Kroll, Janina","first_name":"Janina"},{"full_name":"Ruiz-Fernandez, Mauricio J.A.","first_name":"Mauricio J.A.","last_name":"Ruiz-Fernandez"},{"first_name":"Malte B.","full_name":"Braun, Malte B.","last_name":"Braun"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"}],"date_created":"2022-04-17T22:01:46Z","publication_status":"published","day":"05","language":[{"iso":"eng"}],"ddc":["570"],"year":"2022","department":[{"_id":"NanoFab"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":2,"date_published":"2022-04-05T00:00:00Z","type":"journal_article","oa_version":"Published Version","external_id":{"pmid":["35384410"]},"article_type":"original","article_processing_charge":"No","publication":"Current Protocols","doi":"10.1002/cpz1.407","publisher":"Wiley","date_updated":"2022-05-02T08:18:00Z","month":"04","article_number":"e407","file":[{"success":1,"file_name":"2022_CurrentProtocols_Kroll.pdf","access_level":"open_access","checksum":"72152d005c367777f6cf2f6a477f0d52","date_updated":"2022-05-02T08:16:10Z","file_size":2142703,"content_type":"application/pdf","date_created":"2022-05-02T08:16:10Z","file_id":"11347","creator":"dernst","relation":"main_file"}],"quality_controlled":"1","oa":1}]