[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823.","ista":"Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee. FEBS Journal.","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823.","ama":"Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions as a mentee. FEBS Journal. 2021. doi:10.1111/febs.15823","apa":"Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E., Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823","ieee":"S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal. Wiley, 2021.","short":"S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk, N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021)."},"title":"Building and sustaining mentor interactions as a mentee","external_id":{"isi":["000636678800001"],"pmid":["33818917"]},"article_processing_charge":"No","author":[{"first_name":"Sarvenaz","full_name":"Sarabipour, Sarvenaz","last_name":"Sarabipour"},{"first_name":"Sarah J.","last_name":"Hainer","full_name":"Hainer, Sarah J."},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan"},{"first_name":"Charlotte M.","last_name":"De Winde","full_name":"De Winde, Charlotte M."},{"last_name":"Furlong","full_name":"Furlong, Emily","first_name":"Emily"},{"first_name":"Natalia","full_name":"Bielczyk, Natalia","last_name":"Bielczyk"},{"last_name":"Jadavji","full_name":"Jadavji, Nafisa M.","first_name":"Nafisa M."},{"full_name":"Shah, Aparna P.","last_name":"Shah","first_name":"Aparna P."},{"full_name":"Davla, Sejal","last_name":"Davla","first_name":"Sejal"}],"publication":"FEBS Journal","day":"05","year":"2021","isi":1,"date_created":"2021-04-18T22:01:43Z","date_published":"2021-04-05T00:00:00Z","doi":"10.1111/febs.15823","acknowledgement":"The authors thank Nicholas Asby of the University of Chicago for valuable comments on an earlier version of this work. A.P.S. was partially supported by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National Institutes of Health grant R35GM133732.","oa":1,"publisher":"Wiley","quality_controlled":"1","date_updated":"2023-08-08T13:12:55Z","department":[{"_id":"CaHe"}],"_id":"9336","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1742-464X"],"eissn":["1742-4658"]},"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success in careers. Early‐career researchers (ECRs), in particular, can benefit from mentorship to navigate challenges in academic and nonacademic life and careers. Yet, strategies for selecting mentors and maintaining interactions with them are often underdiscussed within research environments. In this Words of Advice, we provide recommendations for ECRs to seek and manage mentorship interactions. Our article draws from our experiences as ECRs and published work, to provide suggestions for mentees to proactively promote beneficial mentorship interactions. The recommended practices highlight the importance of identifying mentorship needs, planning and selecting multiple and diverse mentors, setting goals, and maintaining constructive, and mutually beneficial working relationships with mentors.","lang":"eng"}],"month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/febs.15823"}],"scopus_import":"1","alternative_title":["Words of Advice"]},{"title":"Holding it together: when cadherin meets cadherin","external_id":{"pmid":["33794149"],"isi":["000704646900006"]},"article_processing_charge":"No","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan"},{"full_name":"Eckert, Julia","last_name":"Eckert","first_name":"Julia"},{"full_name":"Schmidt, Thomas","last_name":"Schmidt","first_name":"Thomas"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal, vol. 120, Biophysical Society, 2021, pp. 4182–92, doi:10.1016/j.bpj.2021.03.025.","apa":"Arslan, F. N., Eckert, J., Schmidt, T., & Heisenberg, C.-P. J. (2021). Holding it together: when cadherin meets cadherin. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2021.03.025","ama":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when cadherin meets cadherin. Biophysical Journal. 2021;120:4182-4192. doi:10.1016/j.bpj.2021.03.025","ieee":"F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it together: when cadherin meets cadherin,” Biophysical Journal, vol. 120. Biophysical Society, pp. 4182–4192, 2021.","short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","chicago":"Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal. Biophysical Society, 2021. https://doi.org/10.1016/j.bpj.2021.03.025.","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192."},"oa":1,"publisher":"Biophysical Society","quality_controlled":"1","acknowledgement":"T.S. acknowledges funding by the research program “The Active Matter Physics of Collective Metastasis,” which is financed by the Dutch Research Council (NWO).","date_created":"2021-04-25T22:01:30Z","date_published":"2021-10-05T00:00:00Z","doi":"10.1016/j.bpj.2021.03.025","page":"4182-4192","publication":"Biophysical Journal","day":"05","year":"2021","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"9350","department":[{"_id":"CaHe"}],"date_updated":"2023-08-08T13:14:10Z","intvolume":" 120","month":"10","main_file_link":[{"url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Intercellular adhesion is the key to multicellularity, and its malfunction plays an important role in various developmental and disease-related processes. Although it has been intensively studied by both biologists and physicists, a commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell adhesion has been described at the molecular scale as a function of adhesion receptors controlling binding affinity, at the cellular scale as resistance to detachment forces or modulation of surface tension, and at the tissue scale as a regulator of cellular rearrangements and morphogenesis. In this review, we aim to summarize and discuss recent advances in the molecular, cellular, and theoretical description of cell-cell adhesion, ranging from biomimetic models to the complexity of cells and tissues in an organismal context. In particular, we will focus on cadherin-mediated cell-cell adhesion and the role of adhesion signaling and mechanosensation therein, two processes central for understanding the biological and physical basis of cell-cell adhesion.","lang":"eng"}],"related_material":{"record":[{"id":"12368","status":"public","relation":"dissertation_contains"}]},"volume":120,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]}},{"article_number":"e1009124","citation":{"ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Michael John","full_name":"Bartlett, Michael John","last_name":"Bartlett"},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566"},{"full_name":"Bankston, Adriana","last_name":"Bankston","first_name":"Adriana"},{"full_name":"Sarabipour, Sarvenaz","last_name":"Sarabipour","first_name":"Sarvenaz"}],"external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"article_processing_charge":"Yes","title":"Ten simple rules to improve academic work- life balance","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","publisher":"Public Library of Science","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"15","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1009124","date_published":"2021-07-15T00:00:00Z","date_created":"2021-08-01T22:01:21Z","_id":"9759","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-10T14:16:46Z","ddc":["613"],"department":[{"_id":"CaHe"}],"file_date_updated":"2021-08-05T12:06:49Z","oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 17","publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9771","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","creator":"cchlebak","file_size":693633,"date_updated":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf","date_created":"2021-08-05T12:06:49Z"}],"language":[{"iso":"eng"}],"issue":"7","volume":17,"license":"https://creativecommons.org/licenses/by/4.0/"},{"keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9999","department":[{"_id":"CaHe"}],"file_date_updated":"2022-05-13T08:03:37Z","ddc":["570"],"date_updated":"2023-08-14T06:53:33Z","intvolume":" 10","month":"08","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"ec_funded":1,"volume":10,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11371","checksum":"a3f82b0499cc822ac1eab48a01f3f57e","file_size":9010446,"date_updated":"2022-05-13T08:03:37Z","creator":"dernst","file_name":"2021_eLife_Pulgar.pdf","date_created":"2022-05-13T08:03:37Z"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e66483","title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","external_id":{"isi":["000700428500001"],"pmid":["34448451"]},"article_processing_charge":"Yes","author":[{"last_name":"Pulgar","full_name":"Pulgar, Eduardo","first_name":"Eduardo"},{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia"},{"full_name":"Guerrero, Néstor","last_name":"Guerrero","first_name":"Néstor"},{"first_name":"Loreto","full_name":"López, Loreto","last_name":"López"},{"first_name":"Susana","full_name":"Márquez, Susana","last_name":"Márquez"},{"last_name":"Härtel","full_name":"Härtel, Steffen","first_name":"Steffen"},{"first_name":"Rodrigo","full_name":"Soto, Rodrigo","last_name":"Soto"},{"first_name":"Carl Philipp","full_name":"Heisenberg, Carl Philipp","last_name":"Heisenberg"},{"first_name":"Miguel L.","last_name":"Concha","full_name":"Concha, Miguel L."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.66483.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).","ieee":"E. Pulgar et al., “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.66483","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 2021;10. doi:10.7554/eLife.66483","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife, vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483."},"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","date_created":"2021-09-12T22:01:23Z","date_published":"2021-08-27T00:00:00Z","doi":"10.7554/eLife.66483","publication":"eLife","day":"27","year":"2021","isi":1,"has_accepted_license":"1"},{"day":"19","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1038/s41467-021-26234-7","date_published":"2021-10-19T00:00:00Z","date_created":"2021-10-31T23:01:29Z","acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.","ieee":"S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7."},"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","author":[{"full_name":"Pradhan, Saurabh J.","last_name":"Pradhan","first_name":"Saurabh J."},{"last_name":"Reddy","full_name":"Reddy, Puli Chandramouli","first_name":"Puli Chandramouli"},{"last_name":"Smutny","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"full_name":"Sharma, Ankita","last_name":"Sharma","first_name":"Ankita"},{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"last_name":"Oak","full_name":"Oak, Meghana S.","first_name":"Meghana S."},{"first_name":"Rini","full_name":"Shah, Rini","last_name":"Shah"},{"first_name":"Mrinmoy","full_name":"Pal, Mrinmoy","last_name":"Pal"},{"first_name":"Ojas","last_name":"Deshpande","full_name":"Deshpande, Ojas"},{"full_name":"Dsilva, Greg","last_name":"Dsilva","first_name":"Greg"},{"first_name":"Yin","last_name":"Tang","full_name":"Tang, Yin"},{"first_name":"Rakesh","full_name":"Mishra, Rakesh","last_name":"Mishra"},{"last_name":"Deshpande","full_name":"Deshpande, Girish","first_name":"Girish"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"first_name":"Mahendra","full_name":"Sonawane, Mahendra","last_name":"Sonawane"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Sanjeev","full_name":"Galande, Sanjeev","last_name":"Galande"}],"external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"article_processing_charge":"Yes","article_number":"6094","file":[{"file_name":"2021_NatureComm_Pradhan.pdf","date_created":"2021-11-09T13:59:26Z","file_size":7144437,"date_updated":"2021-11-09T13:59:26Z","creator":"cziletti","success":1,"file_id":"10262","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","volume":12,"issue":"1","related_material":{"link":[{"description":"Preprint","url":"https://doi.org/10.1101/2020.11.23.394171 ","relation":"earlier_version"}]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant."}],"month":"10","intvolume":" 12","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-14T10:32:48Z","file_date_updated":"2021-11-09T13:59:26Z","department":[{"_id":"CaHe"}],"_id":"10202","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"citation":{"ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Ana Maria","last_name":"Lennon","full_name":"Lennon, Ana Maria"},{"last_name":"Mayor","full_name":"Mayor, Roberto","first_name":"Roberto"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"}],"external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"article_processing_charge":"No","title":"Special rebranding issue: “Quantitative cell and developmental biology”","article_number":"203758","isi":1,"year":"2021","day":"17","publication":"Cells and Development","date_published":"2021-11-17T00:00:00Z","doi":"10.1016/j.cdev.2021.203758","date_created":"2021-11-28T23:01:30Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-08-14T13:02:40Z","department":[{"_id":"CaHe"}],"_id":"10366","type":"journal_article","article_type":"letter_note","status":"public","publication_identifier":{"issn":["2667-2901"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"12","volume":168,"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"month":"11","intvolume":" 168"},{"scopus_import":"1","intvolume":" 55","month":"08","abstract":[{"text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future.","lang":"eng"}],"oa_version":"None","pmid":1,"ec_funded":1,"volume":55,"publication_status":"published","publication_identifier":{"eissn":["1545-2948"],"issn":["0066-4197"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"status":"public","_id":"10406","department":[{"_id":"CaHe"}],"date_updated":"2023-08-14T13:05:13Z","publisher":"Annual Reviews","quality_controlled":"1","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","page":"209-233","date_created":"2021-12-05T23:01:41Z","date_published":"2021-08-30T00:00:00Z","doi":"10.1146/annurev-genet-071819-103748","year":"2021","isi":1,"publication":"Annual Review of Genetics","day":"30","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"article_processing_charge":"No","author":[{"first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","last_name":"Mishra","orcid":"0000-0002-6425-5788","full_name":"Mishra, Nikhil"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","citation":{"chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"citation":{"ista":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. 2021. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 10, e75639.","chicago":"Godard, Benoit G, Remi Dumollard, Carl-Philipp J Heisenberg, and Alex Mcdougall. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.75639.","ieee":"B. G. Godard, R. Dumollard, C.-P. J. Heisenberg, and A. Mcdougall, “Combined effect of cell geometry and polarity domains determines the orientation of unequal division,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","apa":"Godard, B. G., Dumollard, R., Heisenberg, C.-P. J., & Mcdougall, A. (2021). Combined effect of cell geometry and polarity domains determines the orientation of unequal division. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.75639","ama":"Godard BG, Dumollard R, Heisenberg C-PJ, Mcdougall A. Combined effect of cell geometry and polarity domains determines the orientation of unequal division. eLife. 2021;10. doi:10.7554/eLife.75639","mla":"Godard, Benoit G., et al. “Combined Effect of Cell Geometry and Polarity Domains Determines the Orientation of Unequal Division.” ELife, vol. 10, e75639, eLife Sciences Publications, 2021, doi:10.7554/eLife.75639."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000733610100001"]},"author":[{"first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","last_name":"Godard","full_name":"Godard, Benoit G"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Mcdougall","full_name":"Mcdougall, Alex","first_name":"Alex"}],"title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division","article_number":"e75639","project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"21","date_created":"2022-01-09T23:01:26Z","doi":"10.7554/eLife.75639","date_published":"2021-12-21T00:00:00Z","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a collaborative grant from the French Government funding agency Agence National de la Recherche to McDougall (ANR 'MorCell': ANR-17-CE 13-0028) and the Austrian Science Fund to Heisenberg (FWF: I 3601-B27).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_updated":"2023-08-17T06:32:44Z","ddc":["570"],"department":[{"_id":"CaHe"}],"file_date_updated":"2022-01-10T09:40:37Z","_id":"10606","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_eLife_Godard.pdf","date_created":"2022-01-10T09:40:37Z","file_size":7769934,"date_updated":"2022-01-10T09:40:37Z","creator":"alisjak","success":1,"checksum":"759c7a873d554c48a6639e6350746ca6","file_id":"10611","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":10,"abstract":[{"lang":"eng","text":"Cell division orientation is thought to result from a competition between cell geometry and polarity domains controlling the position of the mitotic spindle during mitosis. Depending on the level of cell shape anisotropy or the strength of the polarity domain, one dominates the other and determines the orientation of the spindle. Whether and how such competition is also at work to determine unequal cell division (UCD), producing daughter cells of different size, remains unclear. Here, we show that cell geometry and polarity domains cooperate, rather than compete, in positioning the cleavage plane during UCDs in early ascidian embryos. We found that the UCDs and their orientation at the ascidian third cleavage rely on the spindle tilting in an anisotropic cell shape, and cortical polarity domains exerting different effects on spindle astral microtubules. By systematically varying mitotic cell shape, we could modulate the effect of attractive and repulsive polarity domains and consequently generate predicted daughter cell size asymmetries and position. We therefore propose that the spindle position during UCD is set by the combined activities of cell geometry and polarity domains, where cell geometry modulates the effect of cortical polarity domain(s)."}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"12"},{"department":[{"_id":"JiFr"},{"_id":"CaHe"}],"date_updated":"2023-10-16T09:43:56Z","article_type":"review","type":"journal_article","status":"public","_id":"9298","volume":17,"issue":"1","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2020.1797280"}],"month":"02","intvolume":" 17","abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"pmid":1,"oa_version":"Published Version","author":[{"first_name":"Daniel J.","last_name":"Klionsky","full_name":"Klionsky, Daniel J."},{"first_name":"Amal Kamal","last_name":"Abdel-Aziz","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","last_name":"Abdelfatah","first_name":"Sara"},{"first_name":"Mahmoud","full_name":"Abdellatif, Mahmoud","last_name":"Abdellatif"},{"first_name":"Asghar","full_name":"Abdoli, Asghar","last_name":"Abdoli"},{"full_name":"Abel, Steffen","last_name":"Abel","first_name":"Steffen"},{"full_name":"Abeliovich, Hagai","last_name":"Abeliovich","first_name":"Hagai"},{"first_name":"Marie H.","full_name":"Abildgaard, Marie H.","last_name":"Abildgaard"},{"first_name":"Yakubu Princely","last_name":"Abudu","full_name":"Abudu, Yakubu Princely"},{"full_name":"Acevedo-Arozena, Abraham","last_name":"Acevedo-Arozena","first_name":"Abraham"},{"last_name":"Adamopoulos","full_name":"Adamopoulos, Iannis E.","first_name":"Iannis E."},{"first_name":"Khosrow","full_name":"Adeli, Khosrow","last_name":"Adeli"},{"last_name":"Adolph","full_name":"Adolph, Timon E.","first_name":"Timon E."},{"first_name":"Annagrazia","full_name":"Adornetto, Annagrazia","last_name":"Adornetto"},{"first_name":"Elma","full_name":"Aflaki, Elma","last_name":"Aflaki"},{"full_name":"Agam, Galila","last_name":"Agam","first_name":"Galila"},{"first_name":"Anupam","last_name":"Agarwal","full_name":"Agarwal, Anupam"},{"first_name":"Bharat B.","last_name":"Aggarwal","full_name":"Aggarwal, Bharat B."},{"last_name":"Agnello","full_name":"Agnello, Maria","first_name":"Maria"},{"first_name":"Patrizia","full_name":"Agostinis, Patrizia","last_name":"Agostinis"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"first_name":"Alexander","last_name":"Agrotis","full_name":"Agrotis, Alexander"},{"last_name":"Aguilar","full_name":"Aguilar, Patricia V.","first_name":"Patricia V."},{"full_name":"Ahmad, S. Tariq","last_name":"Ahmad","first_name":"S. Tariq"},{"first_name":"Zubair M.","full_name":"Ahmed, Zubair M.","last_name":"Ahmed"},{"first_name":"Ulises","full_name":"Ahumada-Castro, Ulises","last_name":"Ahumada-Castro"},{"first_name":"Sonja","full_name":"Aits, Sonja","last_name":"Aits"},{"first_name":"Shu","full_name":"Aizawa, Shu","last_name":"Aizawa"},{"last_name":"Akkoc","full_name":"Akkoc, Yunus","first_name":"Yunus"},{"full_name":"Akoumianaki, Tonia","last_name":"Akoumianaki","first_name":"Tonia"},{"first_name":"Hafize Aysin","full_name":"Akpinar, Hafize Aysin","last_name":"Akpinar"},{"first_name":"Ahmed M.","full_name":"Al-Abd, Ahmed M.","last_name":"Al-Abd"},{"first_name":"Lina","last_name":"Al-Akra","full_name":"Al-Akra, Lina"},{"first_name":"Abeer","full_name":"Al-Gharaibeh, Abeer","last_name":"Al-Gharaibeh"},{"first_name":"Moulay A.","full_name":"Alaoui-Jamali, Moulay A.","last_name":"Alaoui-Jamali"},{"last_name":"Alberti","full_name":"Alberti, Simon","first_name":"Simon"},{"first_name":"Elísabet","full_name":"Alcocer-Gómez, Elísabet","last_name":"Alcocer-Gómez"},{"last_name":"Alessandri","full_name":"Alessandri, Cristiano","first_name":"Cristiano"},{"first_name":"Muhammad","full_name":"Ali, Muhammad","last_name":"Ali"},{"last_name":"Alim Al-Bari","full_name":"Alim Al-Bari, M. Abdul","first_name":"M. Abdul"},{"last_name":"Aliwaini","full_name":"Aliwaini, Saeb","first_name":"Saeb"},{"first_name":"Javad","full_name":"Alizadeh, Javad","last_name":"Alizadeh"},{"last_name":"Almacellas","full_name":"Almacellas, Eugènia","first_name":"Eugènia"},{"last_name":"Almasan","full_name":"Almasan, Alexandru","first_name":"Alexandru"},{"last_name":"Alonso","full_name":"Alonso, Alicia","first_name":"Alicia"},{"last_name":"Alonso","full_name":"Alonso, Guillermo D.","first_name":"Guillermo D."},{"first_name":"Nihal","full_name":"Altan-Bonnet, Nihal","last_name":"Altan-Bonnet"},{"last_name":"Altieri","full_name":"Altieri, Dario C.","first_name":"Dario C."},{"last_name":"Álvarez","full_name":"Álvarez, Élida M.C.","first_name":"Élida M.C."},{"full_name":"Alves, Sara","last_name":"Alves","first_name":"Sara"},{"last_name":"Alves Da Costa","full_name":"Alves Da Costa, Cristine","first_name":"Cristine"},{"first_name":"Mazen M.","last_name":"Alzaharna","full_name":"Alzaharna, Mazen M."},{"last_name":"Amadio","full_name":"Amadio, Marialaura","first_name":"Marialaura"},{"first_name":"Consuelo","last_name":"Amantini","full_name":"Amantini, Consuelo"},{"first_name":"Cristina","full_name":"Amaral, Cristina","last_name":"Amaral"},{"last_name":"Ambrosio","full_name":"Ambrosio, Susanna","first_name":"Susanna"},{"last_name":"Amer","full_name":"Amer, Amal O.","first_name":"Amal O."},{"first_name":"Veena","full_name":"Ammanathan, Veena","last_name":"Ammanathan"},{"full_name":"An, Zhenyi","last_name":"An","first_name":"Zhenyi"},{"first_name":"Stig U.","full_name":"Andersen, Stig U.","last_name":"Andersen"},{"full_name":"Andrabi, Shaida A.","last_name":"Andrabi","first_name":"Shaida A."},{"last_name":"Andrade-Silva","full_name":"Andrade-Silva, Magaiver","first_name":"Magaiver"},{"first_name":"Allen M.","full_name":"Andres, Allen M.","last_name":"Andres"},{"last_name":"Angelini","full_name":"Angelini, Sabrina","first_name":"Sabrina"},{"first_name":"David","last_name":"Ann","full_name":"Ann, David"},{"full_name":"Anozie, Uche C.","last_name":"Anozie","first_name":"Uche C."},{"first_name":"Mohammad Y.","last_name":"Ansari","full_name":"Ansari, Mohammad Y."},{"last_name":"Antas","full_name":"Antas, Pedro","first_name":"Pedro"},{"full_name":"Antebi, Adam","last_name":"Antebi","first_name":"Adam"},{"full_name":"Antón, Zuriñe","last_name":"Antón","first_name":"Zuriñe"},{"full_name":"Anwar, Tahira","last_name":"Anwar","first_name":"Tahira"},{"first_name":"Lionel","full_name":"Apetoh, Lionel","last_name":"Apetoh"},{"full_name":"Apostolova, Nadezda","last_name":"Apostolova","first_name":"Nadezda"},{"first_name":"Toshiyuki","last_name":"Araki","full_name":"Araki, Toshiyuki"},{"last_name":"Araki","full_name":"Araki, Yasuhiro","first_name":"Yasuhiro"},{"first_name":"Kohei","full_name":"Arasaki, Kohei","last_name":"Arasaki"},{"last_name":"Araújo","full_name":"Araújo, Wagner L.","first_name":"Wagner L."},{"full_name":"Araya, Jun","last_name":"Araya","first_name":"Jun"},{"full_name":"Arden, Catherine","last_name":"Arden","first_name":"Catherine"},{"first_name":"Maria Angeles","last_name":"Arévalo","full_name":"Arévalo, Maria Angeles"},{"full_name":"Arguelles, Sandro","last_name":"Arguelles","first_name":"Sandro"},{"last_name":"Arias","full_name":"Arias, Esperanza","first_name":"Esperanza"},{"full_name":"Arikkath, Jyothi","last_name":"Arikkath","first_name":"Jyothi"},{"full_name":"Arimoto, Hirokazu","last_name":"Arimoto","first_name":"Hirokazu"},{"first_name":"Aileen R.","last_name":"Ariosa","full_name":"Ariosa, Aileen R."},{"first_name":"Darius","last_name":"Armstrong-James","full_name":"Armstrong-James, Darius"},{"first_name":"Laetitia","full_name":"Arnauné-Pelloquin, Laetitia","last_name":"Arnauné-Pelloquin"},{"first_name":"Angeles","full_name":"Aroca, Angeles","last_name":"Aroca"},{"full_name":"Arroyo, Daniela 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Taylor & Francis, 2021. https://doi.org/10.1080/15548627.2020.1797280.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy, vol. 17, no. 1, Taylor & Francis, 2021, pp. 1–382, doi:10.1080/15548627.2020.1797280.","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. 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Zhao, L. Zhao, S. Zhao, T. Zhao, X.F. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, G. Zheng, K. Zheng, L. Zheng, S. Zheng, X.L. Zheng, Y. Zheng, Z.G. Zheng, B. Zhivotovsky, Q. Zhong, A. Zhou, B. Zhou, C. Zhou, G. Zhou, H. Zhou, H. Zhou, H. Zhou, J. Zhou, J. Zhou, J. Zhou, J. Zhou, K. Zhou, R. Zhou, X.J. Zhou, Y. Zhou, Y. Zhou, Y. Zhou, Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu, Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E. Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou, S. Zuryn, W. Zwerschke, B. Brand-Saberi, X.C. Dong, C.S. Kenchappa, Z. Li, Y. Lin, S. Oshima, Y. Rong, J.C. Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382.","ieee":"D. J. Klionsky et al., “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” Autophagy, vol. 17, no. 1. Taylor & Francis, pp. 1–382, 2021.","ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 2021;17(1):1-382. doi:10.1080/15548627.2020.1797280","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2020.1797280"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-382","date_published":"2021-02-08T00:00:00Z","doi":"10.1080/15548627.2020.1797280","date_created":"2021-03-28T22:01:44Z","isi":1,"year":"2021","day":"08","publication":"Autophagy","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support."},{"publication_identifier":{"eissn":["2296-634X"]},"publication_status":"published","file":[{"checksum":"8c8a03575d2f7583f88dc3b658b0976b","file_id":"9386","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-11T15:09:23Z","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","creator":"kschuh","date_updated":"2021-05-11T15:09:23Z","file_size":4076024}],"language":[{"iso":"eng"}],"volume":9,"abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 9","date_updated":"2023-10-18T08:19:49Z","ddc":["570"],"department":[{"_id":"CaHe"}],"file_date_updated":"2021-05-11T15:09:23Z","_id":"9379","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"has_accepted_license":"1","isi":1,"year":"2021","day":"13","publication":"Frontiers in Cell and Developmental Biology","doi":"10.3389/fcell.2021.649433","date_published":"2021-04-13T00:00:00Z","date_created":"2021-05-09T22:01:37Z","acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"citation":{"chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433.","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","ieee":"M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433","ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","first_name":"Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"last_name":"Choi","full_name":"Choi, Kate","first_name":"Kate"},{"full_name":"Cheung, Faith","last_name":"Cheung","first_name":"Faith"},{"first_name":"Yi Tian","full_name":"Liu, Yi Tian","last_name":"Liu"},{"first_name":"May","last_name":"Dang-Lawson","full_name":"Dang-Lawson, May"},{"first_name":"Nikola","full_name":"Deretic, Nikola","last_name":"Deretic"},{"last_name":"Keane","full_name":"Keane, Connor","first_name":"Connor"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"article_processing_charge":"No","external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","article_number":"649433"},{"citation":{"chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"}],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","page":"111","date_created":"2021-07-01T14:50:17Z","date_published":"2021-07-01T00:00:00Z","doi":"10.15479/at:ista:9623","_id":"9623","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","date_updated":"2023-09-07T13:33:27Z","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"ddc":["570"],"file_date_updated":"2022-07-02T22:30:06Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"PhDThesis_SCM.docx","date_created":"2021-07-01T14:48:54Z","file_size":131946790,"date_updated":"2022-07-02T22:30:06Z","creator":"scaballe","checksum":"e039225a47ef32666d59bf35ddd30ecf","file_id":"9624","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"embargo":"2022-07-01","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","date_created":"2021-07-01T14:46:25Z","file_size":17094958,"date_updated":"2022-07-02T22:30:06Z","creator":"scaballe"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9006","status":"public"}]}},{"issue":"2","volume":56,"related_material":{"record":[{"status":"public","id":"9623","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"scopus_import":"1","intvolume":" 56","month":"01","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"CaHe"}],"date_updated":"2024-03-27T23:30:18Z","type":"journal_article","article_type":"original","status":"public","_id":"9006","page":"P213-226","date_created":"2021-01-17T23:01:10Z","date_published":"2021-01-25T00:00:00Z","doi":"10.1016/j.devcel.2020.12.002","year":"2021","isi":1,"publication":"Developmental Cell","day":"25","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"article_processing_charge":"No","author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"title":"Cytoplasm's got moves","citation":{"ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002.","apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"language":[{"iso":"eng"}],"file":[{"file_name":"KHuljev_Thesis_corrections.docx","date_created":"2021-05-17T12:29:12Z","file_size":47799741,"date_updated":"2022-05-21T22:30:04Z","creator":"khuljev","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-05-20","file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba","creator":"khuljev","file_size":16542131,"date_updated":"2022-05-21T22:30:04Z","file_name":"new_KHuljev_Thesis_corrections.pdf","date_created":"2021-05-18T14:50:28Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"file_date_updated":"2022-05-21T22:30:04Z","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"ddc":["571"],"date_updated":"2023-09-07T13:32:32Z","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"status":"public","type":"dissertation","_id":"9397","date_created":"2021-05-17T12:31:30Z","doi":"10.15479/at:ista:9397","date_published":"2021-05-18T00:00:00Z","page":"101","day":"18","year":"2021","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","article_processing_charge":"No","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","full_name":"Huljev, Karla","last_name":"Huljev"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397."}},{"publication":"eLife","day":"06","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-05-25T15:01:40Z","date_published":"2020-04-06T00:00:00Z","doi":"10.7554/elife.55190","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190."},"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","external_id":{"isi":["000531544400001"],"pmid":["32250246"]},"article_processing_charge":"No","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra"},{"last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_number":"e55190","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:04Z","file_size":7744848,"creator":"dernst","date_created":"2020-05-25T15:15:43Z","file_name":"2020_eLife_Schauer.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7890","checksum":"f6aad884cf706846ae9357fcd728f8b5"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"ec_funded":1,"volume":9,"related_material":{"record":[{"id":"12891","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"intvolume":" 9","month":"04","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-21T06:25:49Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:48:04Z","_id":"7888","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"citation":{"chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000579169000053"]},"author":[{"first_name":"Tony Y.-C.","full_name":"Tsai, Tony Y.-C.","last_name":"Tsai"},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"last_name":"Xia","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng"},{"last_name":"Colak-Champollion","full_name":"Colak-Champollion, Tugba","first_name":"Tugba"},{"full_name":"Knaut, Holger","last_name":"Knaut","first_name":"Holger"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"year":"2020","isi":1,"publication":"Science","day":"02","page":"113-116","date_created":"2020-10-19T14:09:38Z","date_published":"2020-10-02T00:00:00Z","doi":"10.1126/science.aba6637","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","date_updated":"2023-08-22T10:36:35Z","department":[{"_id":"CaHe"}],"_id":"8680","type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6512","related_material":{"link":[{"url":"https://ist.ac.at/en/news/sticking-together/","relation":"press_release","description":"News on IST Homepage"}]},"volume":370,"abstract":[{"text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/803635v1","open_access":"1"}],"scopus_import":"1","intvolume":" 370","month":"10"},{"department":[{"_id":"CaHe"}],"date_updated":"2023-08-24T11:01:22Z","type":"journal_article","article_type":"original","status":"public","_id":"8957","issue":"6","volume":55,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/relaxing-cell-divisions/","description":"News on IST Homepage"}]},"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 55","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation."}],"oa_version":"None","pmid":1,"author":[{"id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","full_name":"Godard, Benoit G","last_name":"Godard"},{"last_name":"Dumollard","full_name":"Dumollard, Rémi","first_name":"Rémi"},{"first_name":"Edwin","last_name":"Munro","full_name":"Munro, Edwin"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"full_name":"Hebras, Céline","last_name":"Hebras","first_name":"Céline"},{"full_name":"Mcdougall, Alex","last_name":"Mcdougall","first_name":"Alex"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"article_processing_charge":"No","external_id":{"isi":["000600665700008"],"pmid":["33207225"]},"title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","citation":{"ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","ieee":"B. G. Godard et al., “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706. doi:10.1016/j.devcel.2020.10.016","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.10.016","mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"695-706","date_published":"2020-12-21T00:00:00Z","doi":"10.1016/j.devcel.2020.10.016","date_created":"2020-12-20T23:01:19Z","isi":1,"year":"2020","day":"21","publication":"Developmental Cell","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8)."},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00702153"]},"publication_status":"published","volume":136,"ec_funded":1,"oa_version":"None","pmid":1,"abstract":[{"text":"Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.","lang":"eng"}],"month":"06","intvolume":" 136","alternative_title":["Current Topics in Developmental Biology"],"scopus_import":"1","date_updated":"2023-09-06T14:54:36Z","department":[{"_id":"CaHe"}],"_id":"7227","status":"public","type":"book_chapter","day":"01","publication":"Gastrulation: From Embryonic Pattern to Form","isi":1,"year":"2020","date_published":"2020-06-01T00:00:00Z","doi":"10.1016/bs.ctdb.2019.10.009","date_created":"2020-01-05T23:00:46Z","page":"343-375","acknowledgement":"We thank Alexandra Schauer, Nicoletta Petridou and Feyza Nur Arslan for comments on the manuscript. Research in the Heisenberg laboratory is supported by an ERC Advanced Grant (MECSPEC 742573), ANR/FWF (I03601) and FWF/DFG (I03196) International Cooperation Grants. D. Pinheiro acknowledges a fellowship from EMBO ALTF (850-2017) and is currently supported by HFSP LTF (LT000429/2018-L2).","publisher":"Elsevier","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nunes Pinheiro, Diana C, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” In Gastrulation: From Embryonic Pattern to Form, 136:343–75. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.10.009.","ista":"Nunes Pinheiro DC, Heisenberg C-PJ. 2020.Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Current Topics in Developmental Biology, vol. 136, 343–375.","mla":"Nunes Pinheiro, Diana C., and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–75, doi:10.1016/bs.ctdb.2019.10.009.","short":"D.C. Nunes Pinheiro, C.-P.J. Heisenberg, in:, Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 343–375.","ieee":"D. C. Nunes Pinheiro and C.-P. J. Heisenberg, “Zebrafish gastrulation: Putting fate in motion,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–375.","apa":"Nunes Pinheiro, D. C., & Heisenberg, C.-P. J. (2020). Zebrafish gastrulation: Putting fate in motion. In Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 343–375). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.10.009","ama":"Nunes Pinheiro DC, Heisenberg C-PJ. Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Vol 136. Elsevier; 2020:343-375. doi:10.1016/bs.ctdb.2019.10.009"},"title":"Zebrafish gastrulation: Putting fate in motion","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"pmid":["31959295"],"isi":["000611830600013"]},"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"call_identifier":"FWF","_id":"2646861A-B435-11E9-9278-68D0E5697425","grant_number":"I03601","name":"Control of embryonic cleavage pattern"},{"call_identifier":"FWF","_id":"2608FC64-B435-11E9-9278-68D0E5697425","name":"Control of epithelial cell layer spreading in zebrafish","grant_number":"I03196"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"}]},{"article_processing_charge":"No","external_id":{"isi":["000611830600012"]},"author":[{"full_name":"Bruce, Ashley E.E.","last_name":"Bruce","first_name":"Ashley E.E."},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"Mechanisms of zebrafish epiboly: A current view","editor":[{"full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel","first_name":"Lilianna "}],"citation":{"ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.07.001.","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. Gastrulation: From Embryonic Pattern to Form. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:10.1016/bs.ctdb.2019.07.001","apa":"Bruce, A. E. E., & Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 319–341). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.07.001","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:10.1016/bs.ctdb.2019.07.001."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"319-341","date_created":"2020-01-30T09:24:06Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1016/bs.ctdb.2019.07.001","year":"2020","isi":1,"publication":"Gastrulation: From Embryonic Pattern to Form","day":"01","publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"CaHe"}],"date_updated":"2024-02-22T13:23:09Z","type":"book_chapter","status":"public","series_title":"Current Topics in Developmental Biology","_id":"7410","volume":136,"publication_status":"published","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 136","month":"01","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"oa_version":"None"},{"year":"2020","publication_status":"published","day":"20","language":[{"iso":"eng"}],"publication":"bioRxiv","page":"41","related_material":{"record":[{"relation":"later_version","status":"public","id":"10766"},{"id":"9623","status":"public","relation":"dissertation_contains"}]},"date_published":"2020-11-20T00:00:00Z","doi":"10.1101/2020.11.20.391284","date_created":"2021-07-29T11:29:50Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}],"month":"11","date_updated":"2024-03-27T23:30:18Z","citation":{"mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284.","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Slovakova, Jana","last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"_id":"9750","type":"preprint","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}]},{"article_processing_charge":"No","author":[{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour"}],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"107","date_created":"2020-09-09T11:12:10Z","doi":"10.15479/AT:ISTA:8350","date_published":"2020-09-09T00:00:00Z","year":"2020","has_accepted_license":"1","day":"09","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"file_date_updated":"2021-09-11T22:30:05Z","date_updated":"2023-09-27T14:16:45Z","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"8350","related_material":{"record":[{"status":"public","id":"661","relation":"part_of_dissertation"},{"status":"public","id":"6508","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7001","status":"public"},{"relation":"part_of_dissertation","id":"735","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","file_size":65194814,"date_created":"2020-09-09T11:06:27Z","file_name":"Shayan-Thesis-Final.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"6e47871c74f85008b9876112eb3fcfa1","file_id":"8351"},{"creator":"sshamip","file_size":23729605,"date_updated":"2021-09-11T22:30:05Z","file_name":"Shayan-Thesis-Final.pdf","date_created":"2020-09-09T11:06:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-09-10","file_id":"8352","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"None"}]