[{"day":"01","author":[{"last_name":"Filipović Marijić","first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka"},{"last_name":"Krasnici","full_name":"Krasnici, Nesrete","first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"first_name":"Damir","full_name":"Valić, Damir","last_name":"Valić"},{"last_name":"Kapetanović","first_name":"Damir","full_name":"Kapetanović, Damir"},{"full_name":"Vardić Smrzlić, Irena","first_name":"Irena","last_name":"Vardić Smrzlić"},{"first_name":"Maja","full_name":"Jordanova, Maja","last_name":"Jordanova"},{"last_name":"Rebok","full_name":"Rebok, Katerina","first_name":"Katerina"},{"first_name":"Sheriban","full_name":"Ramani, Sheriban","last_name":"Ramani"},{"first_name":"Vasil","full_name":"Kostov, Vasil","last_name":"Kostov"},{"last_name":"Nastova","full_name":"Nastova, Rodne","first_name":"Rodne"},{"full_name":"Dragun, Zrinka","first_name":"Zrinka","last_name":"Dragun"}],"type":"journal_article","citation":{"apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>.","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521.","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>."},"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","language":[{"iso":"eng"}],"doi":"10.1007/s11356-023-26844-2","acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","pmid":1,"month":"05","date_created":"2023-04-23T22:01:03Z","page":"63510-63521","department":[{"_id":"LifeSc"}],"quality_controlled":"1","publication":"Environmental Science and Pollution Research","status":"public","intvolume":"        30","publisher":"Springer Nature","isi":1,"article_type":"original","oa_version":"None","year":"2023","date_updated":"2023-10-04T11:23:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"abstract":[{"lang":"eng","text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems."}],"_id":"12863","date_published":"2023-05-01T00:00:00Z","article_processing_charge":"No","volume":30,"publication_status":"published"},{"date_created":"2023-05-19T11:12:25Z","month":"05","intvolume":"        13","status":"public","quality_controlled":"1","department":[{"_id":"Bio"}],"publication":"Scientific Reports","isi":1,"publisher":"Springer Nature","author":[{"last_name":"Zavadakova","first_name":"Anna","full_name":"Zavadakova, Anna"},{"last_name":"Vistejnova","full_name":"Vistejnova, Lucie","first_name":"Lucie"},{"id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova","first_name":"Tereza","full_name":"Belinova, Tereza"},{"last_name":"Tichanek","first_name":"Filip","full_name":"Tichanek, Filip"},{"first_name":"Dagmar","full_name":"Bilikova, Dagmar","last_name":"Bilikova"},{"last_name":"Mouton","full_name":"Mouton, Peter R.","first_name":"Peter R."}],"type":"journal_article","day":"17","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","citation":{"mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023)."},"doi":"10.1038/s41598-023-35162-z","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"_id":"13033","abstract":[{"lang":"eng","text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases."}],"date_published":"2023-05-17T00:00:00Z","article_number":"7959","file":[{"date_updated":"2023-05-22T07:57:37Z","access_level":"open_access","checksum":"8c1b769693ff4288df8376e59ad1176d","file_name":"2023_ScientificReports_Zavadakova.pdf","creator":"dernst","file_size":3055077,"success":1,"date_created":"2023-05-22T07:57:37Z","content_type":"application/pdf","file_id":"13047","relation":"main_file"}],"issue":"1","article_processing_charge":"No","volume":13,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-05-22T07:57:37Z","oa":1,"publication_status":"published","year":"2023","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["2045-2322"]},"date_updated":"2023-08-01T14:46:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000995271600104"]},"scopus_import":"1"},{"publication_status":"epub_ahead","oa":1,"main_file_link":[{"url":"https://doi.org/10.1039/d3fd00088e","open_access":"1"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","_id":"13044","abstract":[{"text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.","lang":"eng"}],"date_published":"2023-05-17T00:00:00Z","external_id":{"isi":["001070423500001"]},"date_updated":"2023-12-13T11:19:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"article_type":"original","year":"2023","oa_version":"Published Version","publisher":"Royal Society of Chemistry","isi":1,"publication":"Faraday Discussions","quality_controlled":"1","department":[{"_id":"StFr"},{"_id":"Bio"}],"status":"public","month":"05","date_created":"2023-05-22T06:53:34Z","keyword":["Physical and Theoretical Chemistry"],"language":[{"iso":"eng"}],"doi":"10.1039/d3fd00088e","citation":{"mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>, Royal Society of Chemistry, 2023, doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2023. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions.","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2023.","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>.","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., &#38; Freunberger, S. A. (2023). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. 2023. doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions (2023)."},"title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","day":"17","type":"journal_article","author":[{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","first_name":"Soumyadip","last_name":"Mondal"},{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","last_name":"Jethwa"},{"id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","last_name":"Pant","first_name":"Bhargavi","full_name":"Pant, Bhargavi"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"}]},{"month":"04","place":"New York, NY","series_title":"MIMB","date_created":"2023-05-22T08:41:48Z","page":"137-147","publication":"The Immune Synapse","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"quality_controlled":"1","intvolume":"      2654","status":"public","publisher":"Springer Nature","day":"28","author":[{"last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"citation":{"mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>.","chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>.","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147."},"ec_funded":1,"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","language":[{"iso":"eng"}],"doi":"10.1007/978-1-0716-3135-5_9","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"}],"pmid":1,"acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","_id":"13052","abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}],"date_published":"2023-04-28T00:00:00Z","article_processing_charge":"No","volume":2654,"publication_status":"published","oa_version":"None","year":"2023","editor":[{"first_name":"Cosima","full_name":"Baldari, Cosima","last_name":"Baldari"},{"last_name":"Dustin","first_name":"Michael","full_name":"Dustin, Michael"}],"scopus_import":"1","external_id":{"pmid":["37106180"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T08:44:53Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_identifier":{"eisbn":["9781071631355"],"issn":["1064-3745"],"isbn":["9781071631348"],"eissn":["1940-6029"]}},{"intvolume":"        57","status":"public","publication":"Developmental Cell","quality_controlled":"1","department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"isi":1,"publisher":"Cell Press ; Elsevier","date_created":"2022-01-30T23:01:33Z","month":"01","page":"47-62.e9","ddc":["570"],"doi":"10.1016/j.devcel.2021.11.024","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"12726","status":"public"},{"relation":"dissertation_contains","id":"14530","status":"public"},{"relation":"dissertation_contains","id":"12401","status":"public"}]},"pmid":1,"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"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.","author":[{"full_name":"Gaertner, Florian","first_name":"Florian","last_name":"Gaertner"},{"first_name":"Patricia","full_name":"Reis-Rodrigues, Patricia","last_name":"Reis-Rodrigues"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","first_name":"Miroslav","full_name":"Hons, Miroslav","last_name":"Hons"},{"last_name":"Aguilera","full_name":"Aguilera, Juan","first_name":"Juan"},{"full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","first_name":"Saren","last_name":"Tasciyan"},{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","full_name":"Kopf, Aglaja","last_name":"Kopf"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"type":"journal_article","day":"10","title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","citation":{"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>","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>","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.","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>.","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.","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>."},"ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":57,"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497"}],"oa":1,"publication_status":"published","date_published":"2022-01-10T00:00:00Z","_id":"10703","abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","issue":"1","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"scopus_import":"1","external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"date_updated":"2024-03-25T23:30:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","oa_version":"Published Version","article_type":"original"},{"file_date_updated":"2022-07-29T07:53:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":2,"publication_status":"published","oa":1,"file":[{"date_updated":"2022-07-29T07:53:20Z","access_level":"open_access","checksum":"5ce3f907848f5c7caf77f1adfe5826c6","file_name":"2022_ACSPhysChemAU_Dubini.pdf","file_size":2351220,"creator":"dernst","success":1,"date_created":"2022-07-29T07:53:20Z","content_type":"application/pdf","relation":"main_file","file_id":"11692"}],"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."}],"_id":"10758","date_published":"2022-02-11T00:00:00Z","article_processing_charge":"Yes (via OA deal)","issue":"3","external_id":{"pmid":["35637781"]},"scopus_import":"1","date_updated":"2023-01-31T07:33:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2694-2445"]},"article_type":"original","oa_version":"Published Version","year":"2022","has_accepted_license":"1","publication":"ACS Physical Chemistry Au","department":[{"_id":"NMR"}],"quality_controlled":"1","status":"public","intvolume":"         2","publisher":"American Chemical Society","month":"02","date_created":"2022-02-16T11:18:21Z","page":"237-246","language":[{"iso":"eng"}],"doi":"10.1021/acsphyschemau.1c00050","ddc":["540"],"pmid":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"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","day":"11","author":[{"first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A.","last_name":"Dubini"},{"full_name":"Korytiaková, Eva","first_name":"Eva","last_name":"Korytiaková"},{"last_name":"Schinkel","first_name":"Thea","full_name":"Schinkel, Thea"},{"last_name":"Heinrichs","first_name":"Pia","full_name":"Heinrichs, Pia"},{"last_name":"Carell","first_name":"Thomas","full_name":"Carell, Thomas"},{"orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo","full_name":"Rovo, Petra","first_name":"Petra"}],"type":"journal_article","citation":{"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.","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>.","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.","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>","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>"},"title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives"},{"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","ec_funded":1,"citation":{"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>","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>","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).","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>.","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.","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.","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>."},"author":[{"last_name":"Slovakova","full_name":"Slovakova, Jana","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","last_name":"Arslan","full_name":"Arslan, Feyza N","first_name":"Feyza N"},{"last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","full_name":"Krens, Gabriel","last_name":"Krens"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"type":"journal_article","day":"14","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.).","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9750"}]},"doi":"10.1073/pnas.2122030119","ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2022-02-20T23:01:31Z","month":"02","isi":1,"publisher":"Proceedings of the National Academy of Sciences","intvolume":"       119","status":"public","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2022","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["10916490"]},"date_updated":"2023-08-02T14:26:51Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000766926900009"]},"issue":"8","article_processing_charge":"No","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"}],"_id":"10766","date_published":"2022-02-14T00:00:00Z","article_number":"e2122030119","file":[{"date_updated":"2022-02-21T08:45:11Z","access_level":"open_access","checksum":"d49f83c3580613966f71768ddb9a55a5","file_name":"2022_PNAS_Slovakova.pdf","creator":"dernst","file_size":1609678,"success":1,"date_created":"2022-02-21T08:45:11Z","content_type":"application/pdf","relation":"main_file","file_id":"10780"}],"oa":1,"publication_status":"published","volume":119,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2022-02-21T08:45:11Z"},{"oa_version":"Published Version","has_accepted_license":"1","year":"2022","article_type":"original","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"publication_identifier":{"eissn":["2753-149X"]},"date_updated":"2023-11-30T10:55:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","article_processing_charge":"No","_id":"10791","date_published":"2022-07-07T00:00:00Z","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."}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"14061","success":1,"date_created":"2023-08-16T08:00:30Z","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","creator":"dernst","file_size":4846551,"date_updated":"2023-08-16T08:00:30Z","access_level":"open_access","checksum":"822e76e056c07099d1fb27d1ece5941b"}],"article_number":"kvac009","oa":1,"publication_status":"published","volume":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-08-16T08:00:30Z","title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","ec_funded":1,"citation":{"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>.","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>.","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.","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.","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>","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>","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)."},"author":[{"first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"last_name":"Riedl","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","last_name":"Heger","full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena"},{"full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"first_name":"Li Huei","full_name":"Tsai, Li Huei","last_name":"Tsai"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"07","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.","related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"14530","status":"public"}]},"project":[{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}],"doi":"10.1093/oons/kvac009","ddc":["570"],"language":[{"iso":"eng"}],"date_created":"2022-02-25T07:52:11Z","month":"07","publisher":"Oxford Academic","status":"public","intvolume":"         1","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"Oxford Open Neuroscience"},{"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"Plant Cell","status":"public","intvolume":"        34","publisher":"Oxford Academic","isi":1,"month":"06","date_created":"2022-03-08T13:47:51Z","page":"2150-2173","language":[{"iso":"eng"}],"doi":"10.1093/plcell/koac071","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).","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"pmid":1,"day":"01","author":[{"last_name":"Dahhan","first_name":"DA","full_name":"Dahhan, DA"},{"first_name":"GD","full_name":"Reynolds, GD","last_name":"Reynolds"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yperman","first_name":"K","full_name":"Yperman, K"},{"first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vang","first_name":"N","full_name":"Vang, N"},{"full_name":"Yan, X","first_name":"X","last_name":"Yan"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"full_name":"Heese, A","first_name":"A","last_name":"Heese"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"last_name":"Pan","full_name":"Pan, J","first_name":"J"},{"full_name":"Bednarek, SY","first_name":"SY","last_name":"Bednarek"}],"type":"journal_article","citation":{"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>.","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>.","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.","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.","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>","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>","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."},"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","volume":34,"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"oa":1,"date_published":"2022-06-01T00:00:00Z","_id":"10841","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."}],"issue":"6","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-02T14:46:48Z","scopus_import":"1","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"article_type":"original","oa_version":"Preprint","year":"2022"},{"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.","ddc":["570"],"doi":"10.1002/cpz1.407","language":[{"iso":"eng"}],"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","citation":{"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>.","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.","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.","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>.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","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>","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>"},"type":"journal_article","author":[{"last_name":"Kroll","full_name":"Kroll, Janina","first_name":"Janina"},{"first_name":"Mauricio J.A.","full_name":"Ruiz-Fernandez, Mauricio J.A.","last_name":"Ruiz-Fernandez"},{"full_name":"Braun, Malte B.","first_name":"Malte B.","last_name":"Braun"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"first_name":"Jörg","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"}],"day":"05","publisher":"Wiley","status":"public","intvolume":"         2","publication":"Current Protocols","quality_controlled":"1","department":[{"_id":"NanoFab"}],"date_created":"2022-04-17T22:01:46Z","month":"04","publication_identifier":{"eissn":["2691-1299"]},"scopus_import":"1","external_id":{"pmid":["35384410"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-05-02T08:18:00Z","oa_version":"Published Version","year":"2022","has_accepted_license":"1","article_type":"original","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":2,"file_date_updated":"2022-05-02T08:16:10Z","article_processing_charge":"No","issue":"4","_id":"11182","date_published":"2022-04-05T00:00:00Z","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."}],"file":[{"date_created":"2022-05-02T08:16:10Z","success":1,"relation":"main_file","file_id":"11347","content_type":"application/pdf","checksum":"72152d005c367777f6cf2f6a477f0d52","access_level":"open_access","date_updated":"2022-05-02T08:16:10Z","file_size":2142703,"creator":"dernst","file_name":"2022_CurrentProtocols_Kroll.pdf"}],"article_number":"e407"},{"year":"2022","oa_version":"Submitted Version","article_type":"original","publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-02-21T09:51:29Z","_id":"11444","date_published":"2022-04-01T00:00:00Z","abstract":[{"text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.","lang":"eng"}],"article_processing_charge":"No","issue":"1","volume":38,"main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"oa":1,"publication_status":"published","author":[{"orcid":"0000-0002-3385-3865","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","last_name":"Chlebak","first_name":"Clara A","full_name":"Chlebak, Clara A"},{"full_name":"Reid, Peter H.","first_name":"Peter H.","last_name":"Reid"}],"type":"journal_article","day":"01","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","citation":{"mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>.","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41."},"doi":"10.3366/lih.2022.0097","language":[{"iso":"eng"}],"date_created":"2022-06-12T22:01:45Z","month":"04","page":"23-41","status":"public","intvolume":"        38","publication":"Library and Information History","department":[{"_id":"E-Lib"}],"quality_controlled":"1","publisher":"Edinburgh University Press"},{"has_accepted_license":"1","oa_version":"Published Version","year":"2022","article_type":"original","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:23:52Z","scopus_import":"1","external_id":{"isi":["000828274200001"]},"_id":"11705","date_published":"2022-08-26T00:00:00Z","abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"article_number":"e202207002","file":[{"file_size":4072650,"creator":"dernst","file_name":"2022_AngewandteChemieInternat_Chang.pdf","access_level":"open_access","date_updated":"2023-02-02T08:01:00Z","checksum":"ad601f2b9e26e46ab4785162be58b5ed","relation":"main_file","file_id":"12476","content_type":"application/pdf","success":1,"date_created":"2023-02-02T08:01:00Z"}],"issue":"35","article_processing_charge":"Yes (via OA deal)","volume":61,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-02-02T08:01:00Z","oa":1,"publication_status":"published","type":"journal_article","author":[{"orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","first_name":"Cheng"},{"first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"last_name":"Spadaro","full_name":"Spadaro, Maria","first_name":"Maria"},{"last_name":"Koskela","first_name":"Kristopher M.","full_name":"Koskela, Kristopher M."},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias","full_name":"Kleinhanns, Tobias"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","last_name":"Costanzo","full_name":"Costanzo, Tommaso","first_name":"Tommaso"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Brutchey, Richard L.","first_name":"Richard L.","last_name":"Brutchey"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria"}],"day":"26","title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","ec_funded":1,"citation":{"short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>."},"ddc":["540"],"doi":"10.1002/anie.202207002","language":[{"iso":"eng"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-07-31T22:01:48Z","month":"08","intvolume":"        61","status":"public","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"Angewandte Chemie - International Edition","isi":1,"publisher":"Wiley"},{"article_type":"original","oa_version":"Published Version","year":"2022","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T13:47:56Z","scopus_import":"1","external_id":{"isi":["000860787000001"]},"publication_identifier":{"eissn":["2380-8195"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"issue":"9","article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2022_ACSEnergyLetters_Prehal.pdf","creator":"dernst","file_size":3827583,"checksum":"cf0bed3a2535c11d27244cd029dbc1d0","date_updated":"2023-01-20T08:43:51Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12319","date_created":"2023-01-20T08:43:51Z","success":1}],"date_published":"2022-08-29T00:00:00Z","_id":"12065","abstract":[{"lang":"eng","text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth."}],"publication_status":"published","oa":1,"file_date_updated":"2023-01-20T08:43:51Z","volume":7,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","apa":"Prehal, C., Mondal, S., Lovicar, L., &#38; Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? <i>ACS Energy Letters</i>. 2022;7(9):3112-3119. doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>","ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” <i>ACS Energy Letters</i>, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022.","chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">https://doi.org/10.1021/acsenergylett.2c01711</a>.","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” <i>ACS Energy Letters</i>, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:<a href=\"https://doi.org/10.1021/acsenergylett.2c01711\">10.1021/acsenergylett.2c01711</a>."},"title":"Exclusive solution discharge in Li-O₂ batteries?","day":"29","type":"journal_article","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Mondal","full_name":"Mondal, Soumyadip","first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"last_name":"Lovicar","first_name":"Ludek","full_name":"Lovicar, Ludek","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger"}],"acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","language":[{"iso":"eng"}],"ddc":["540"],"doi":"10.1021/acsenergylett.2c01711","page":"3112-3119","month":"08","date_created":"2022-09-08T09:51:09Z","publisher":"American Chemical Society","isi":1,"department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"ACS Energy Letters","intvolume":"         7","status":"public"},{"volume":6,"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"publication_status":"published","_id":"12109","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"date_published":"2022-12-29T00:00:00Z","article_number":"125605","issue":"12","article_processing_charge":"No","arxiv":1,"publication_identifier":{"eissn":["2475-9953"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T14:11:29Z","external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"scopus_import":"1","oa_version":"Preprint","year":"2022","article_type":"original","status":"public","intvolume":"         6","quality_controlled":"1","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"publication":"Physical Review Materials","isi":1,"publisher":"American Physical Society","date_created":"2023-01-08T23:00:53Z","month":"12","doi":"10.1103/PhysRevMaterials.6.125605","language":[{"iso":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120"}],"author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix","full_name":"Pertl, Felix","last_name":"Pertl"},{"id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce"},{"last_name":"Shafeek","first_name":"Lubuna B","full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050"},{"last_name":"Cramer","full_name":"Cramer, Tobias","first_name":"Tobias"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","first_name":"Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"29","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","ec_funded":1,"citation":{"short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>."}},{"article_type":"original","oa_version":"Published Version","year":"2022","has_accepted_license":"1","external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-16T11:29:12Z","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"article_number":"e202107134","file":[{"success":1,"date_created":"2023-08-16T11:24:53Z","content_type":"application/pdf","relation":"main_file","file_id":"14065","date_updated":"2023-08-16T11:24:53Z","access_level":"open_access","checksum":"0c9af38f82af30c6ce528f2caece4246","file_name":"2023_JCB_Weier.pdf","file_size":11090179,"creator":"dernst"}],"date_published":"2022-12-05T00:00:00Z","_id":"12122","abstract":[{"text":"Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.","lang":"eng"}],"article_processing_charge":"No","issue":"12","file_date_updated":"2023-08-16T11:24:53Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"volume":221,"publication_status":"published","oa":1,"day":"05","type":"journal_article","author":[{"first_name":"Ann-Kathrin","full_name":"Weier, Ann-Kathrin","last_name":"Weier"},{"last_name":"Homrich","first_name":"Mirka","full_name":"Homrich, Mirka"},{"full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie","last_name":"Ebbinghaus"},{"full_name":"Juda, Pavel","first_name":"Pavel","last_name":"Juda"},{"first_name":"Eliška","full_name":"Miková, Eliška","last_name":"Miková"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","full_name":"Zhang, Lili","first_name":"Lili"},{"first_name":"Thomas","full_name":"Quast, Thomas","last_name":"Quast"},{"first_name":"Elvira","full_name":"Mass, Elvira","last_name":"Mass"},{"last_name":"Schlitzer","first_name":"Andreas","full_name":"Schlitzer, Andreas"},{"first_name":"Waldemar","full_name":"Kolanus, Waldemar","last_name":"Kolanus"},{"last_name":"Burgdorf","first_name":"Sven","full_name":"Burgdorf, Sven"},{"last_name":"Gruß","first_name":"Oliver J.","full_name":"Gruß, Oliver J."},{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons"},{"last_name":"Wieser","first_name":"Stefan","full_name":"Wieser, Stefan"},{"first_name":"Eva","full_name":"Kiermaier, Eva","last_name":"Kiermaier"}],"citation":{"ama":"Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>","apa":"Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>","short":"A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022).","mla":"Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>.","chicago":"Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>.","ista":"Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134.","ieee":"A.-K. Weier <i>et al.</i>, “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022."},"title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","keyword":["Cell Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1083/jcb.202107134","pmid":1,"project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"}],"acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","month":"12","date_created":"2023-01-12T12:01:09Z","publication":"Journal of Cell Biology","department":[{"_id":"Bio"}],"quality_controlled":"1","status":"public","intvolume":"       221","publisher":"Rockefeller University Press","isi":1},{"article_type":"original","year":"2022","oa_version":"Published Version","has_accepted_license":"1","date_updated":"2023-08-04T09:25:59Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000811777900003"]},"scopus_import":"1","publication_identifier":{"issn":["2399-3642"]},"file":[{"success":1,"date_created":"2023-01-27T08:23:46Z","content_type":"application/pdf","relation":"main_file","file_id":"12417","date_updated":"2023-01-27T08:23:46Z","access_level":"open_access","checksum":"bd95be1e77090208b79bc45ea8785d0b","file_name":"2022_CommBiology_Muhia.pdf","file_size":3968356,"creator":"dernst"}],"article_number":"589","_id":"12224","date_published":"2022-06-15T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","file_date_updated":"2023-01-27T08:23:46Z","volume":5,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"day":"15","type":"journal_article","author":[{"full_name":"Muhia, Mary W","first_name":"Mary W","last_name":"Muhia","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d"},{"last_name":"YuanXiang","full_name":"YuanXiang, PingAn","first_name":"PingAn"},{"last_name":"Sedlacik","first_name":"Jan","full_name":"Sedlacik, Jan"},{"full_name":"Schwarz, Jürgen R.","first_name":"Jürgen R.","last_name":"Schwarz"},{"full_name":"Heisler, Frank F.","first_name":"Frank F.","last_name":"Heisler"},{"first_name":"Kira V.","full_name":"Gromova, Kira V.","last_name":"Gromova"},{"full_name":"Thies, Edda","first_name":"Edda","last_name":"Thies"},{"first_name":"Petra","full_name":"Breiden, Petra","last_name":"Breiden"},{"full_name":"Pechmann, Yvonne","first_name":"Yvonne","last_name":"Pechmann"},{"full_name":"Kreutz, Michael R.","first_name":"Michael R.","last_name":"Kreutz"},{"first_name":"Matthias","full_name":"Kneussel, Matthias","last_name":"Kneussel"}],"citation":{"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).","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>","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>","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>.","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.","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.","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>."},"title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"doi":"10.1038/s42003-022-03446-1","ddc":["570"],"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.","month":"06","date_created":"2023-01-16T09:48:19Z","quality_controlled":"1","department":[{"_id":"PreCl"}],"publication":"Communications Biology","intvolume":"         5","status":"public","publisher":"Springer Nature","isi":1},{"file_date_updated":"2023-01-27T10:28:45Z","volume":61,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"e202211945","file":[{"content_type":"application/pdf","file_id":"12422","relation":"main_file","success":1,"date_created":"2023-01-27T10:28:45Z","file_name":"2022_AngewandteChemieInternat_Xu.pdf","file_size":1076715,"creator":"dernst","date_updated":"2023-01-27T10:28:45Z","access_level":"open_access","checksum":"4e8152454d12025d13f6e6e9ca06b5d0"}],"_id":"12228","date_published":"2022-11-07T00:00:00Z","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."}],"issue":"45","article_processing_charge":"No","date_updated":"2023-08-04T09:32:42Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000866428500001"]},"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"article_type":"original","oa_version":"Published Version","year":"2022","has_accepted_license":"1","department":[{"_id":"NMR"}],"quality_controlled":"1","publication":"Angewandte Chemie International Edition","status":"public","intvolume":"        61","publisher":"Wiley","isi":1,"month":"11","date_created":"2023-01-16T09:49:05Z","language":[{"iso":"eng"}],"keyword":["General Chemistry","Catalysis"],"ddc":["540"],"doi":"10.1002/anie.202211945","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.","day":"07","type":"journal_article","author":[{"first_name":"Felix","full_name":"Xu, Felix","last_name":"Xu"},{"full_name":"Crisp, Antony","first_name":"Antony","last_name":"Crisp"},{"first_name":"Thea","full_name":"Schinkel, Thea","last_name":"Schinkel"},{"last_name":"Dubini","full_name":"Dubini, Romeo C. A.","first_name":"Romeo C. A."},{"first_name":"Sarah","full_name":"Hübner, Sarah","last_name":"Hübner"},{"last_name":"Becker","first_name":"Sidney","full_name":"Becker, Sidney"},{"last_name":"Schelter","first_name":"Florian","full_name":"Schelter, Florian"},{"last_name":"Rovo","full_name":"Rovo, Petra","first_name":"Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","orcid":"0000-0001-8729-7326"},{"full_name":"Carell, Thomas","first_name":"Thomas","last_name":"Carell"}],"citation":{"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>.","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>.","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.","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>","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>","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)."},"title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA"},{"has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["1674-2052"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2023-08-04T09:39:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"issue":"10","article_processing_charge":"Yes (via OA deal)","_id":"12239","date_published":"2022-10-03T00:00:00Z","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"}],"file":[{"success":1,"date_created":"2023-01-30T07:46:51Z","file_id":"12435","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T07:46:51Z","checksum":"04d5c12490052d03e4dc4412338a43dd","file_size":2307251,"creator":"dernst","file_name":"2022_MolecularPlant_Johnson.pdf"}],"oa":1,"publication_status":"published","volume":15,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-01-30T07:46:51Z","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","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>","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>","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."},"author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tommaso","full_name":"Costanzo, Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"last_name":"Dahhan","full_name":"Dahhan, Dana A.","first_name":"Dana A."},{"last_name":"Bednarek","first_name":"Sebastian Y.","full_name":"Bednarek, Sebastian Y."},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"type":"journal_article","day":"03","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,"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1016/j.molp.2022.09.003","ddc":["580"],"language":[{"iso":"eng"}],"keyword":["Plant Science","Molecular Biology"],"page":"1533-1542","date_created":"2023-01-16T09:51:49Z","month":"10","isi":1,"publisher":"Elsevier","status":"public","intvolume":"        15","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"quality_controlled":"1","publication":"Molecular Plant"},{"date_created":"2023-01-16T09:58:16Z","month":"09","isi":1,"publisher":"AIP Publishing","status":"public","intvolume":"        32","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","quality_controlled":"1","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","citation":{"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>.","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.","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.","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>.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","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>","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>"},"type":"journal_article","author":[{"last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Suri, Balachandra","first_name":"Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"},{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"}],"day":"26","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.”","doi":"10.1063/5.0102904","ddc":["530"],"keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"language":[{"iso":"eng"}],"article_processing_charge":"No","issue":"9","arxiv":1,"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"}],"_id":"12259","date_published":"2022-09-26T00:00:00Z","file":[{"content_type":"application/pdf","file_id":"12445","relation":"main_file","success":1,"date_created":"2023-01-30T09:41:12Z","file_name":"2022_Chaos_Choueiri.pdf","creator":"dernst","file_size":3209644,"date_updated":"2023-01-30T09:41:12Z","access_level":"open_access","checksum":"17881eff8b21969359a2dd64620120ba"}],"article_number":"093138","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":32,"file_date_updated":"2023-01-30T09:41:12Z","oa_version":"Published Version","has_accepted_license":"1","year":"2022","article_type":"original","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"external_id":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:51:17Z"},{"status":"public","intvolume":"        29","department":[{"_id":"EM-Fac"}],"quality_controlled":"1","publication":"Nature Structural & Molecular Biology","isi":1,"publisher":"Springer Nature","date_created":"2023-01-16T09:59:06Z","month":"09","page":"942-953","ddc":["570"],"doi":"10.1038/s41594-022-00832-5","language":[{"iso":"eng"}],"keyword":["Molecular Biology","Structural Biology"],"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.","pmid":1,"author":[{"last_name":"Prattes","first_name":"Michael","full_name":"Prattes, Michael"},{"first_name":"Irina","full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hetzmannseder","first_name":"Christina","full_name":"Hetzmannseder, Christina"},{"last_name":"Zisser","full_name":"Zisser, Gertrude","first_name":"Gertrude"},{"last_name":"Sailer","first_name":"Carolin","full_name":"Sailer, Carolin"},{"last_name":"Kargas","full_name":"Kargas, Vasileios","first_name":"Vasileios"},{"first_name":"Mathias","full_name":"Loibl, Mathias","last_name":"Loibl"},{"full_name":"Gerhalter, Magdalena","first_name":"Magdalena","last_name":"Gerhalter"},{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"full_name":"Warren, Alan J.","first_name":"Alan J.","last_name":"Warren"},{"first_name":"Florian","full_name":"Stengel, Florian","last_name":"Stengel"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"},{"last_name":"Bergler","first_name":"Helmut","full_name":"Bergler, Helmut"}],"type":"journal_article","day":"12","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","citation":{"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>","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>","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.","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>.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","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."},"volume":29,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2023-01-30T10:00:04Z","oa":1,"publication_status":"published","date_published":"2022-09-12T00:00:00Z","_id":"12262","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"}],"file":[{"success":1,"date_created":"2023-01-30T10:00:04Z","file_id":"12447","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T10:00:04Z","checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_size":9935057,"creator":"dernst","file_name":"2022_NatureStrucMolecBio_Prattes.pdf"}],"issue":"9","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:52:20Z","external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","year":"2022","article_type":"original"}]