[{"author":[{"orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin"},{"full_name":"Kwiatkowski, Mateusz","first_name":"Mateusz","last_name":"Kwiatkowski"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair","first_name":"Scott A"},{"first_name":"Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Charo I.","last_name":"del Genio","full_name":"del Genio, Charo I."},{"full_name":"Kubeš, Martin F.","first_name":"Martin F.","last_name":"Kubeš"},{"full_name":"Napier, Richard","last_name":"Napier","first_name":"Richard"},{"first_name":"Krzysztof","last_name":"Jaworski","full_name":"Jaworski, Krzysztof"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf"}],"citation":{"ieee":"L. Qi <i>et al.</i>, “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” <i>Nature</i>, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022.","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. 2022;611(7934):133-138. doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>","ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>.","short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>"},"year":"2022","_id":"12144","oa":1,"pmid":1,"publication":"Nature","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants."}],"publication_status":"published","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"issue":"7934","volume":611,"publisher":"Springer Nature","article_type":"original","isi":1,"intvolume":"       611","status":"public","month":"11","date_created":"2023-01-12T12:06:05Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"03","oa_version":"Submitted Version","date_updated":"2023-10-03T11:04:53Z","type":"journal_article","department":[{"_id":"JiFr"}],"doi":"10.1038/s41586-022-05369-7","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ec_funded":1,"acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","page":"133-138","external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"date_published":"2022-11-03T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]}},{"article_type":"original","publisher":"Elsevier","file_date_updated":"2021-02-04T07:49:25Z","volume":303,"article_number":"110750","status":"public","month":"02","date_created":"2020-12-09T14:48:28Z","isi":1,"intvolume":"       303","year":"2021","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Gelová","first_name":"Zuzana","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalko","first_name":"Jaroslav","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zlata","last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata"},{"first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"last_name":"Hajny","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","first_name":"Teva","last_name":"Vernoux"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"quality_controlled":"1","citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>"},"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"publication_status":"published","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"_id":"8931","oa":1,"ddc":["580"],"related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"pmid":1,"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","publication":"Plant Science","file":[{"creator":"dernst","content_type":"application/pdf","file_size":12563728,"relation":"main_file","date_created":"2021-02-04T07:49:25Z","file_name":"2021_PlantScience_Gelova.pdf","checksum":"a7f2562bdca62d67dfa88e271b62a629","access_level":"open_access","success":1,"file_id":"9083","date_updated":"2021-02-04T07:49:25Z"}],"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"date_published":"2021-02-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0168-9452"]},"day":"01","oa_version":"Published Version","date_updated":"2024-10-29T10:22:43Z","type":"journal_article","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.plantsci.2020.110750","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"external_id":{"pmid":["33443153"],"isi":["000607270100018"]},"date_published":"2021-01-05T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"day":"05","oa_version":"Published Version","date_updated":"2023-08-04T11:20:46Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","department":[{"_id":"MaLo"},{"_id":"MiSi"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2010054118","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publisher":"National Academy of Sciences","article_type":"original","volume":118,"issue":"1","article_number":"e2010054118","status":"public","month":"01","date_created":"2021-01-03T23:01:23Z","isi":1,"intvolume":"       118","year":"2021","quality_controlled":"1","author":[{"orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F"},{"last_name":"Auer","first_name":"Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","last_name":"Canigova","first_name":"Nikola"},{"id":"3760F32C-F248-11E8-B48F-1D18A9856A87","full_name":"Loibl, Katrin","orcid":"0000-0002-2429-7668","last_name":"Loibl","first_name":"Katrin"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin"}],"citation":{"chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021).","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118.","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2010054118"}],"abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"publication_status":"published","project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"_id":"8988","oa":1,"pmid":1,"publication":"PNAS","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1"},{"day":"09","date_updated":"2024-10-29T10:22:44Z","type":"preprint","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","doi":"10.21203/rs.3.rs-266395/v3","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1,"date_published":"2021-09-09T00:00:00Z","publication_identifier":{"issn":["2693-5015"]},"year":"2021","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","first_name":"Jian","full_name":"Chen, Jian"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Sergey","last_name":"Shabala","full_name":"Shabala, Sergey"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"citation":{"apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395."},"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"publication_status":"accepted","abstract":[{"text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.","lang":"eng"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"},{"id":"10223","status":"public","relation":"later_version"}]},"_id":"10095","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","publication":"Research Square","article_number":"266395","status":"public","date_created":"2021-10-06T08:56:22Z","month":"09"},{"month":"11","date_created":"2021-11-07T23:01:25Z","status":"public","intvolume":"       599","isi":1,"publisher":"Springer Nature","article_type":"original","volume":599,"issue":"7884","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"publication_status":"published","pmid":1,"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","publication":"Nature","_id":"10223","related_material":{"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","relation":"press_release","description":"News on IST Webpage"}],"record":[{"id":"10095","relation":"earlier_version","status":"public"}]},"oa":1,"year":"2021","citation":{"apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277."},"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"scopus_import":"1","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"keyword":["Multidisciplinary"],"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"date_published":"2021-11-11T00:00:00Z","page":"273-277","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1,"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"doi":"10.1038/s41586-021-04037-6","language":[{"iso":"eng"}],"oa_version":"Preprint","type":"journal_article","date_updated":"2024-10-29T10:22:45Z","day":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No"},{"issue":"4","volume":213,"file_date_updated":"2021-11-15T13:11:27Z","article_type":"original","publisher":"Elsevier ","intvolume":"       213","isi":1,"month":"11","date_created":"2021-11-15T12:21:42Z","status":"public","article_number":"107808","citation":{"ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier , 2021.","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>"},"quality_controlled":"1","author":[{"first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","publication":"Journal of Structural Biology","_id":"10290","ddc":["572"],"related_material":{"record":[{"relation":"software","status":"public","id":"14502"}]},"oa":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","grant_number":"M02495"}],"abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"publication_status":"published","file":[{"relation":"main_file","date_created":"2021-11-15T13:11:27Z","content_type":"application/pdf","creator":"cchlebak","file_size":16818304,"success":1,"file_id":"10291","date_updated":"2021-11-15T13:11:27Z","file_name":"2021_JournalStructBiol_Dimchev.pdf","checksum":"6b209e4d44775d4e02b50f78982c15fa","access_level":"open_access"}],"keyword":["Structural Biology"],"external_id":{"isi":["000720259500002"]},"date_published":"2021-11-03T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["1047-8477"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2023-11-21T08:36:02Z","type":"journal_article","day":"03","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"has_accepted_license":"1","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2021.107808","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S."},{"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"page":"139","file":[{"date_created":"2021-11-22T14:48:21Z","relation":"main_file","embargo":"2022-11-23","content_type":"application/pdf","creator":"rabualia","file_size":28005730,"file_id":"10331","date_updated":"2022-12-20T23:30:06Z","access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf","checksum":"dea38b98aa4da1cea03dcd0f10862818"},{"date_updated":"2022-12-20T23:30:06Z","file_id":"10332","file_name":"AbualiaPhDthesisfinalv3.docx","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","access_level":"closed","embargo_to":"open_access","relation":"source_file","date_created":"2021-11-22T14:48:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rabualia","file_size":62841883}],"date_published":"2021-11-22T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"has_accepted_license":"1","doi":"10.15479/at:ista:10303","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"day":"22","oa_version":"Published Version","date_updated":"2023-09-19T14:42:45Z","type":"dissertation","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","month":"11","date_created":"2021-11-18T11:20:59Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-12-20T23:30:06Z","abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"publication_status":"published","_id":"10303","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9010"},{"id":"9913","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"47"}]},"oa":1,"ddc":["580","581"],"title":"Role of hormones in nitrate regulated growth","year":"2021","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia","first_name":"Rashed"}],"citation":{"mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021."}},{"month":"11","date_created":"2021-11-18T15:05:06Z","status":"public","degree_awarded":"PhD","file_date_updated":"2022-12-20T23:30:05Z","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"publication_status":"published","title":"Pathogenic Escherichia coli hijack the host immune response","_id":"10307","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"ddc":["570"],"year":"2021","citation":{"mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_name":"ThesisTomasekKathrin.pdf","checksum":"b39c9e0ef18d0484d537a67551effd02","access_level":"open_access","date_updated":"2022-12-20T23:30:05Z","file_id":"10308","file_size":13266088,"content_type":"application/pdf","creator":"ktomasek","embargo":"2022-11-18","relation":"main_file","date_created":"2021-11-18T15:07:31Z"},{"relation":"source_file","embargo_to":"open_access","date_created":"2021-11-18T15:07:46Z","file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ktomasek","file_id":"10309","date_updated":"2022-12-20T23:30:05Z","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_name":"ThesisTomasekKathrin.docx","access_level":"closed"}],"date_published":"2021-11-18T00:00:00Z","page":"73","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"doi":"10.15479/at:ista:10307","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"dissertation","date_updated":"2023-09-07T13:34:38Z","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"day":"18","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No"},{"intvolume":"        23","isi":1,"date_created":"2022-01-23T23:01:28Z","month":"12","status":"public","volume":23,"file_date_updated":"2022-01-24T07:43:09Z","publisher":"Elsevier","article_type":"original","publication":"Molecular Therapy - Methods and Clinical Development","title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","oa":1,"ddc":["570"],"_id":"10655","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n"}],"citation":{"ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23. Elsevier, pp. 210–224, 2021.","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. 2021;23:210-224. doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” <i>Molecular Therapy - Methods and Clinical Development</i>, vol. 23, Elsevier, 2021, pp. 210–24, doi:<a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">10.1016/j.omtm.2021.09.006</a>.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., &#38; Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. <i>Molecular Therapy - Methods and Clinical Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.omtm.2021.09.006\">https://doi.org/10.1016/j.omtm.2021.09.006</a>"},"author":[{"first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wögenstein","first_name":"Gabriele M.","full_name":"Wögenstein, Gabriele M."},{"last_name":"Colombo","first_name":"Gloria","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Casado Polanco","first_name":"Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","orcid":"0000-0001-8293-4568","full_name":"Casado Polanco, Raquel"},{"last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication_identifier":{"eissn":["2329-0501"]},"scopus_import":"1","date_published":"2021-12-10T00:00:00Z","external_id":{"isi":["000748748500019"]},"file":[{"relation":"main_file","date_created":"2022-01-24T07:43:09Z","file_size":4794147,"creator":"cchlebak","content_type":"application/pdf","success":1,"date_updated":"2022-01-24T07:43:09Z","file_id":"10657","checksum":"77dc540e8011c5475031bdf6ccef20a6","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","access_level":"open_access"}],"page":"210-224","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.omtm.2021.09.006","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"has_accepted_license":"1","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 no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-16T13:12:03Z","type":"journal_article","oa_version":"Published Version","day":"10"},{"oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-08T13:53:53Z","day":"28","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"department":[{"_id":"FlSc"}],"has_accepted_license":"1","doi":"10.1038/s41467-021-23506-0","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"external_id":{"isi":["000659145000011"]},"file":[{"checksum":"53ccc53d09a9111143839dbe7784e663","file_name":"2021_NatureCommunications_Obr.pdf","access_level":"open_access","success":1,"file_id":"9538","date_updated":"2021-06-09T15:21:14Z","file_size":6166295,"creator":"kschuh","content_type":"application/pdf","relation":"main_file","date_created":"2021-06-09T15:21:14Z"}],"date_published":"2021-05-28T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","citation":{"mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>","ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226."},"quality_controlled":"1","author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"full_name":"Nikulin, Nadia","last_name":"Nikulin","first_name":"Nadia"},{"full_name":"Feathers, Jon-Philip R.","last_name":"Feathers","first_name":"Jon-Philip R."},{"last_name":"Klanschnig","first_name":"Marco","full_name":"Klanschnig, Marco"},{"full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","first_name":"Andreas"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"publication_status":"published","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","publication":"Nature Communications","_id":"9431","oa":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","relation":"press_release","description":"News on IST Homepage"}]},"ddc":["570"],"file_date_updated":"2021-06-09T15:21:14Z","article_type":"original","publisher":"Nature Research","volume":12,"issue":"1","month":"05","date_created":"2021-05-28T14:25:50Z","article_number":"3226","status":"public","intvolume":"        12","isi":1},{"volume":35,"issue":"12","file_date_updated":"2021-06-28T14:06:24Z","article_type":"original","publisher":"Cell Press","intvolume":"        35","isi":1,"month":"06","date_created":"2021-06-27T22:01:48Z","article_number":"109274","status":"public","citation":{"mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>, vol. 35, no. 12, 109274, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. 2021;35(12). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>","ieee":"X. Contreras <i>et al.</i>, “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” <i>Cell Reports</i>, vol. 35, no. 12. Cell Press, 2021.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>."},"author":[{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Davaatseren, Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425","first_name":"Amarbayasgalan","last_name":"Davaatseren"},{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H"},{"first_name":"Johanna","last_name":"Sonntag","full_name":"Sonntag, Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Andersen, Lill","last_name":"Andersen","first_name":"Lill"},{"first_name":"Tina","last_name":"Bernthaler","full_name":"Bernthaler, Tina"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"first_name":"Anna-Magdalena","last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena"},{"full_name":"Johnson, Randy L.","last_name":"Johnson","first_name":"Randy L."},{"first_name":"Lindsay A.","last_name":"Schwarz","full_name":"Schwarz, Lindsay A."},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2021","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","publication":"Cell Reports","_id":"9603","ddc":["570"],"oa":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","description":"News on IST Homepage"}]},"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"publication_status":"published","file":[{"success":1,"date_updated":"2021-06-28T14:06:24Z","file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_name":"2021_CellReports_Contreras.pdf","access_level":"open_access","relation":"main_file","date_created":"2021-06-28T14:06:24Z","creator":"asandaue","content_type":"application/pdf","file_size":7653149}],"external_id":{"isi":["000664463600016"]},"date_published":"2021-06-22T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["22111247"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-10T13:55:00Z","day":"22","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"has_accepted_license":"1","doi":"10.1016/j.celrep.2021.109274","language":[{"iso":"eng"}],"acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H."},{"publication_identifier":{"eissn":["1091-6490"]},"file":[{"access_level":"open_access","file_name":"2021_PNAS_Johnson.pdf","checksum":"8d01e72e22c4fb1584e72d8601947069","file_id":"10546","date_updated":"2021-12-15T08:59:40Z","success":1,"creator":"cchlebak","content_type":"application/pdf","file_size":2757340,"date_created":"2021-12-15T08:59:40Z","relation":"main_file"}],"external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"date_published":"2021-12-14T00:00:00Z","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"doi":"10.1073/pnas.2113046118","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"day":"14","oa_version":"Published Version","date_updated":"2024-02-19T11:06:09Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","status":"public","article_number":"e2113046118","month":"12","date_created":"2021-08-11T14:11:43Z","isi":1,"intvolume":"       118","publisher":"National Academy of Sciences","article_type":"original","file_date_updated":"2021-12-15T08:59:40Z","volume":118,"issue":"51","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"publication_status":"published","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"_id":"9887","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}],"record":[{"id":"14510","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"research_data","id":"14988"}]},"oa":1,"ddc":["580"],"pmid":1,"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","publication":"Proceedings of the National Academy of Sciences","year":"2021","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","last_name":"Gnyliukh"},{"first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zheden","first_name":"Vanessa","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso"},{"full_name":"Mahou, Pierre","last_name":"Mahou","first_name":"Pierre"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","first_name":"Mónika","last_name":"Hrtyan"},{"last_name":"Wang","first_name":"Jie","full_name":"Wang, Jie"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","last_name":"Aguilera Servin"},{"full_name":"van Damme, Daniël","last_name":"van Damme","first_name":"Daniël"},{"full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire","first_name":"Emmanuel"},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"citation":{"mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>"}},{"day":"01","date_updated":"2023-08-11T10:34:44Z","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","doi":"10.3390/ijms22158350","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"date_published":"2021-08-01T00:00:00Z","file":[{"checksum":"a4bc06e9a2c803ceff5a91f10b174054","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","access_level":"open_access","success":1,"date_updated":"2021-08-16T09:35:56Z","file_id":"9923","content_type":"application/pdf","creator":"asandaue","file_size":6132410,"relation":"main_file","date_created":"2021-08-16T09:35:56Z"}],"external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"scopus_import":"1","year":"2021","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Labajová","first_name":"Naďa","full_name":"Labajová, Naďa"},{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova"},{"first_name":"Miroslav","last_name":"Jurásek","full_name":"Jurásek, Miroslav"},{"first_name":"Robert","last_name":"Vácha","full_name":"Vácha, Robert"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"first_name":"Imrich","last_name":"Barák","full_name":"Barák, Imrich"}],"quality_controlled":"1","citation":{"mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021.","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021)."},"publication_status":"published","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"}],"ddc":["570"],"oa":1,"_id":"9907","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","publication":"International Journal of Molecular Sciences","pmid":1,"article_type":"original","publisher":"MDPI","file_date_updated":"2021-08-16T09:35:56Z","volume":22,"issue":"15","article_number":"8350","status":"public","date_created":"2021-08-15T22:01:27Z","month":"08","isi":1,"intvolume":"        22"},{"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"day":"13","oa_version":"Published Version","type":"dissertation","date_updated":"2023-09-07T13:38:33Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"doi":"10.15479/at:ista:9992","language":[{"iso":"eng"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"page":"168","file":[{"access_level":"closed","file_name":"Thesis_vupload.docx","checksum":"c763064adaa720e16066c1a4f9682bbb","file_id":"9993","date_updated":"2021-09-15T22:30:26Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lhoermaye","file_size":25179004,"date_created":"2021-09-09T07:29:48Z","embargo_to":"open_access","relation":"source_file"},{"date_created":"2021-09-09T14:25:08Z","relation":"main_file","embargo":"2021-09-09","file_size":6246900,"content_type":"application/pdf","creator":"lhoermaye","file_id":"9996","date_updated":"2021-09-15T22:30:26Z","access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f"}],"date_published":"2021-09-13T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"author":[{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>."},"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"publication_status":"published","project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"_id":"9992","oa":1,"related_material":{"record":[{"id":"6351","status":"public","relation":"part_of_dissertation"},{"id":"6943","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8002"}]},"ddc":["575"],"title":"Wound healing in the Arabidopsis root meristem","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-15T22:30:26Z","status":"public","month":"09","date_created":"2021-09-09T07:37:20Z","degree_awarded":"PhD"},{"date_published":"2020-07-31T00:00:00Z","file":[{"success":1,"file_id":"8289","date_updated":"2020-08-24T13:31:53Z","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","file_name":"2020_eLife_Steiner.pdf","access_level":"open_access","relation":"main_file","date_created":"2020-08-24T13:31:53Z","content_type":"application/pdf","creator":"cziletti","file_size":7320493}],"external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"publication_identifier":{"eissn":["2050084X"]},"scopus_import":"1","day":"31","type":"journal_article","date_updated":"2023-09-07T13:14:08Z","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","doi":"10.7554/eLife.59407","language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"article_type":"original","publisher":"eLife Sciences Publications","file_date_updated":"2020-08-24T13:31:53Z","volume":9,"status":"public","article_number":"e59407","date_created":"2020-08-24T06:24:04Z","month":"07","isi":1,"intvolume":"         9","year":"2020","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Steiner"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"quality_controlled":"1","citation":{"chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Steiner, J., &#38; Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>, vol. 9, e59407, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>."},"publication_status":"published","abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8353","status":"public","relation":"dissertation_contains"}]},"oa":1,"ddc":["570"],"_id":"8284","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","publication":"eLife","pmid":1},{"date_published":"2020-08-27T00:00:00Z","file":[{"date_created":"2020-09-10T08:05:19Z","relation":"main_file","file_size":3455704,"creator":"dernst","content_type":"application/pdf","date_updated":"2020-09-10T08:05:19Z","file_id":"8357","success":1,"access_level":"open_access","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","file_name":"2020_NatureComm_Kubiasova.pdf"}],"external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"publication_identifier":{"eissn":["20411723"]},"scopus_import":"1","day":"27","date_updated":"2023-08-22T09:09:06Z","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17949-0","has_accepted_license":"1","department":[{"_id":"EvBe"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"publisher":"Springer Nature","article_type":"original","file_date_updated":"2020-09-10T08:05:19Z","volume":11,"article_number":"4285","status":"public","date_created":"2020-09-06T22:01:12Z","month":"08","isi":1,"intvolume":"        11","year":"2020","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Kubiasova","first_name":"Karolina","orcid":"0000-0001-5630-9419","full_name":"Kubiasova, Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C"},{"full_name":"Šamajová, Olga","first_name":"Olga","last_name":"Šamajová"},{"last_name":"Nisler","first_name":"Jaroslav","full_name":"Nisler, Jaroslav"},{"last_name":"Mik","first_name":"Václav","full_name":"Mik, Václav"},{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","last_name":"Semeradova"},{"full_name":"Plíhalová, Lucie","first_name":"Lucie","last_name":"Plíhalová"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Peter","last_name":"Marhavý","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"full_name":"Galuszka, Petr","last_name":"Galuszka","first_name":"Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"full_name":"Spíchal, Lukáš","first_name":"Lukáš","last_name":"Spíchal"}],"quality_controlled":"1","citation":{"ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>","ieee":"K. Kubiasova <i>et al.</i>, “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” <i>Nature Communications</i>, vol. 11, 4285, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>"},"publication_status":"published","abstract":[{"text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.","lang":"eng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"ddc":["580"],"oa":1,"_id":"8336","publication":"Nature Communications","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","pmid":1},{"page":"215","file":[{"content_type":"application/x-zip-compressed","creator":"dernst","file_size":65246782,"date_created":"2020-09-08T09:00:29Z","relation":"source_file","access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","file_id":"8342"},{"file_id":"8343","date_updated":"2021-09-16T12:49:12Z","checksum":"59a62275088b00b7241e6ff4136434c7","file_name":"2020_Urban_Bezeljak_Thesis.pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-08T09:00:27Z","creator":"dernst","content_type":"application/pdf","file_size":31259058}],"date_published":"2020-09-08T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"day":"08","oa_version":"Published Version","date_updated":"2023-09-07T13:17:06Z","type":"dissertation","department":[{"_id":"MaLo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8341","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-16T12:49:12Z","degree_awarded":"PhD","status":"public","month":"09","date_created":"2020-09-08T08:53:53Z","author":[{"first_name":"Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban"}],"citation":{"chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. <i>In Vitro Reconstitution of a Rab Activation Switch</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>.","apa":"Bezeljak, U. (2020). <i>In vitro reconstitution of a Rab activation switch</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>"},"year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"_id":"8341","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7580"}]},"ddc":["570"],"title":"In vitro reconstitution of a Rab activation switch","abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"publication_status":"published"},{"author":[{"first_name":"Julia","last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia"}],"citation":{"ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>","apa":"Steiner, J. (2020). <i>Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>","mla":"Steiner, Julia. <i>Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>."},"year":"2020","_id":"8353","related_material":{"record":[{"id":"8284","relation":"part_of_dissertation","status":"public"}]},"oa":1,"ddc":["572"],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"publication_status":"published","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-16T12:40:56Z","degree_awarded":"PhD","status":"public","month":"09","date_created":"2020-09-09T14:27:01Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"day":"09","oa_version":"None","date_updated":"2023-09-07T13:14:09Z","type":"dissertation","department":[{"_id":"LeSa"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:8353","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","page":"191","file":[{"access_level":"open_access","file_name":"Thesis_Julia_Steiner_pdfA.pdf","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","file_id":"8354","content_type":"application/pdf","creator":"jsteiner","file_size":117547589,"date_created":"2020-09-09T14:22:35Z","relation":"main_file"},{"date_created":"2020-09-09T14:23:25Z","relation":"source_file","creator":"jsteiner","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":223328668,"file_id":"8355","date_updated":"2020-09-15T08:48:37Z","access_level":"closed","file_name":"Thesis_Julia_Steiner.docx","checksum":"ba112f957b7145462d0ab79044873ee9"}],"date_published":"2020-09-09T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.301481"}],"citation":{"apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. .","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>."},"article_processing_charge":"No","author":[{"full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva"},{"full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Wachner"},{"last_name":"Gridchyn","first_name":"Igor","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Linder, Markus","first_name":"Markus","last_name":"Linder"},{"first_name":"Shamsi","last_name":"Emtenani","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Attila","last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sibilia","first_name":"Maria","full_name":"Sibilia, Maria"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","date_updated":"2024-03-25T23:30:12Z","oa_version":"Preprint","day":"18","year":"2020","acknowledged_ssus":[{"_id":"LifeSc"}],"ec_funded":1,"title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","publication":"bioRxiv","doi":"10.1101/2020.09.18.301481","oa":1,"related_material":{"record":[{"id":"10614","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8983"}]},"language":[{"iso":"eng"}],"_id":"8557","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"publication_status":"submitted","abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.","lang":"eng"}],"date_published":"2020-09-18T00:00:00Z","date_created":"2020-09-23T09:36:47Z","month":"09","status":"public"},{"quality_controlled":"1","author":[{"last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>"},"year":"2020","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"id":"14592","relation":"used_in_publication","status":"public"},{"id":"12491","relation":"dissertation_contains","status":"public"}]},"oa":1,"ddc":["570"],"_id":"8586","publication":"Journal of Structural Biology","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","publication_status":"published","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"issue":"3","volume":212,"article_type":"original","publisher":"Elsevier","file_date_updated":"2020-12-10T14:01:10Z","isi":1,"intvolume":"       212","article_number":"107633","status":"public","date_created":"2020-09-29T13:24:06Z","month":"12","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","date_updated":"2024-03-25T23:30:04Z","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2020.107633","department":[{"_id":"FlSc"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","date_published":"2020-12-01T00:00:00Z","file":[{"date_updated":"2020-12-10T14:01:10Z","file_id":"8937","success":1,"access_level":"open_access","file_name":"2020_JourStrucBiology_Faessler.pdf","checksum":"c48cbf594e84fc2f91966ffaafc0918c","date_created":"2020-12-10T14:01:10Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":7076870}],"external_id":{"isi":["000600997800008"]},"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"publication_identifier":{"issn":["1047-8477"]},"scopus_import":"1"}]