[{"date_published":"2019-12-20T00:00:00Z","ddc":["570"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11393"}]},"month":"12","page":"256-268","author":[{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","full_name":"Tabata, Shigekazu","last_name":"Tabata"},{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","full_name":"Jevtic, Marijo","first_name":"Marijo","last_name":"Jevtic"},{"full_name":"Kurashige, Nobutaka","first_name":"Nobutaka","last_name":"Kurashige"},{"last_name":"Fuchida","full_name":"Fuchida, Hirokazu","first_name":"Hirokazu"},{"first_name":"Munetsugu","full_name":"Kido, Munetsugu","last_name":"Kido"},{"full_name":"Tani, Kazushi","first_name":"Kazushi","last_name":"Tani"},{"last_name":"Zenmyo","full_name":"Zenmyo, Naoki","first_name":"Naoki"},{"last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei","first_name":"Shohei"},{"full_name":"Harada, Harumi","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","last_name":"Harada"},{"last_name":"Itakura","first_name":"Makoto","full_name":"Itakura, Makoto"},{"full_name":"Hamachi, Itaru","first_name":"Itaru","last_name":"Hamachi"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"date_updated":"2026-10-03T22:30:17Z","issue":"12","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"ieee":"S. Tabata <i>et al.</i>, “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” <i>iScience</i>, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>iScience</i>. 2019;22(12):256-268. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>."},"date_created":"2020-01-29T15:56:56Z","language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:57Z","article_processing_charge":"No","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","publication_identifier":{"issn":["2589-0042"]},"scopus_import":"1","corr_author":"1","external_id":{"pmid":["31786521"],"isi":["000504652000020"]},"article_type":"original","doi":"10.1016/j.isci.2019.11.025","abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"project":[{"call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1"}],"publication":"iScience","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"7391","publication_status":"published","quality_controlled":"1","file":[{"date_created":"2020-02-04T10:48:36Z","file_name":"2019_iScience_Tabata.pdf","access_level":"open_access","file_size":7197776,"creator":"dernst","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","relation":"main_file","date_updated":"2020-07-14T12:47:57Z","content_type":"application/pdf","file_id":"7448"}],"oa":1,"volume":22,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"isi":1,"ec_funded":1,"type":"journal_article","year":"2019","oa_version":"Published Version","publisher":"Elsevier","day":"20","intvolume":"        22","fulldoi":"https://doi.org/10.1016/j.isci.2019.11.025","status":"public"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9804"},{"relation":"dissertation_contains","id":"11388","status":"public"}]},"month":"06","ddc":["576"],"date_published":"2019-06-06T00:00:00Z","citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>, vol. 8, e42014, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>.","ieee":"J. P. Castro <i>et al.</i>, “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019."},"author":[{"first_name":"João Pl","full_name":"Castro, João Pl","last_name":"Castro"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"orcid":"0000-0002-9849-498X","first_name":"Stefanie","full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy"},{"last_name":"Hiramatsu","full_name":"Hiramatsu, Layla","first_name":"Layla"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"last_name":"Beluch","full_name":"Beluch, William H.","first_name":"William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","full_name":"Skuplik, Isabella","first_name":"Isabella"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"}],"date_updated":"2026-10-03T22:30:21Z","article_processing_charge":"No","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","file_date_updated":"2020-07-14T12:47:38Z","department":[{"_id":"NiBa"}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2019-07-28T21:59:17Z","external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"doi":"10.7554/eLife.42014","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"6713","publication_status":"published","publication":"eLife","oa":1,"file":[{"content_type":"application/pdf","file_id":"6721","creator":"apreinsp","relation":"main_file","date_updated":"2020-07-14T12:47:38Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_name":"2019_eLife_Castro.pdf","access_level":"open_access","file_size":6748249,"date_created":"2019-07-29T07:41:18Z"}],"quality_controlled":"1","volume":8,"pmid":1,"isi":1,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"         8","status":"public","article_number":"e42014","fulldoi":"https://doi.org/10.7554/eLife.42014","oa_version":"Published Version","publisher":"eLife Sciences Publications","type":"journal_article","year":"2019","day":"06"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","day":"07","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","ec_funded":1,"year":"2019","type":"dissertation","status":"public","fulldoi":"https://doi.org/10.15479/AT:ISTA:6435","_id":"6435","publication_status":"published","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"doi":"10.15479/AT:ISTA:6435","oa":1,"alternative_title":["ISTA Thesis"],"file":[{"date_created":"2019-05-13T09:16:20Z","file_name":"tesisDoctoradoBC.pdf","file_size":3895187,"access_level":"open_access","creator":"casillas","relation":"main_file","date_updated":"2021-02-11T11:17:15Z","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","content_type":"application/pdf","file_id":"6438","embargo":"2020-05-08"},{"file_size":7365118,"access_level":"closed","file_name":"tesisDoctoradoBC.zip","date_created":"2019-05-13T09:16:20Z","file_id":"6439","content_type":"application/zip","checksum":"3d221aaff7559a7060230a1ff610594f","relation":"source_file","date_updated":"2020-07-14T12:47:30Z","creator":"casillas","embargo_to":"open_access"}],"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868"}],"date_created":"2019-05-13T08:58:35Z","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","title":"Collective defenses of garden ants against a fungal pathogen","file_date_updated":"2021-02-11T11:17:15Z","department":[{"_id":"SyCr"}],"corr_author":"1","ddc":["570","006","578","592"],"date_published":"2019-05-07T00:00:00Z","page":"183","related_material":{"record":[{"status":"public","id":"1999","relation":"part_of_dissertation"}]},"month":"05","degree_awarded":"PhD","date_updated":"2026-04-08T14:02:12Z","author":[{"last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"}],"citation":{"apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019."},"OA_place":"publisher"},{"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"date_updated":"2026-10-03T22:30:30Z","issue":"5","citation":{"mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. <i>Neuron</i>. 2019;103(5):750-752. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>","apa":"Contreras, X., &#38; Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” <i>Neuron</i>, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752."},"date_published":"2019-09-04T00:00:00Z","ddc":["570"],"month":"09","related_material":{"record":[{"status":"public","id":"7902","relation":"part_of_dissertation"}]},"page":"750-752","external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"article_type":"letter_note","date_created":"2019-08-25T22:00:50Z","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"title":"Memo1 tiles the radial glial cell grid","article_processing_charge":"No","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"scopus_import":"1","quality_controlled":"1","oa":1,"volume":103,"doi":"10.1016/j.neuron.2019.08.021","_id":"6830","publication_status":"published","publication":"Neuron","type":"journal_article","year":"2019","publisher":"Elsevier","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"day":"04","intvolume":"       103","fulldoi":"https://doi.org/10.1016/j.neuron.2019.08.021","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"isi":1},{"scopus_import":"1","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","article_processing_charge":"No","file_date_updated":"2020-10-21T07:22:34Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"language":[{"iso":"eng"}],"date_created":"2019-06-02T21:59:12Z","article_type":"original","external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","page":"1463-1479.e18","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8350"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/"}]},"month":"05","ddc":["570"],"date_published":"2019-05-30T00:00:00Z","citation":{"apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18."},"issue":"6","date_updated":"2026-10-03T22:30:31Z","author":[{"last_name":"Shamipour","first_name":"Shayan","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kardos","full_name":"Kardos, Roland","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xue","full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"isi":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","status":"public","fulldoi":"https://doi.org/10.1016/j.cell.2019.04.030","intvolume":"       177","day":"30","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.04.030"}],"oa_version":"Published Version","publisher":"Elsevier","ec_funded":1,"type":"journal_article","year":"2019","publication_status":"published","_id":"6508","publication":"Cell","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we 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 oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"doi":"10.1016/j.cell.2019.04.030","volume":177,"oa":1,"quality_controlled":"1","file":[{"creator":"dernst","date_updated":"2020-10-21T07:22:34Z","checksum":"aea43726d80e35ce3885073a5f05c3e3","relation":"main_file","success":1,"content_type":"application/pdf","file_id":"8686","date_created":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","file_size":3356292,"access_level":"open_access"}]},{"intvolume":"       179","status":"public","fulldoi":"https://doi.org/10.1016/j.cell.2019.10.006","oa_version":"Submitted Version","publisher":"Cell Press","type":"journal_article","ec_funded":1,"year":"2019","day":"31","pmid":1,"isi":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","file":[{"content_type":"application/pdf","file_id":"8684","success":1,"creator":"dernst","relation":"main_file","date_updated":"2020-10-21T07:09:45Z","checksum":"33dac4bb77ee630e2666e936b4d57980","file_name":"2019_Cell_Schwayer_accepted.pdf","access_level":"open_access","file_size":8805878,"date_created":"2020-10-21T07:09:45Z"}],"volume":179,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"doi":"10.1016/j.cell.2019.10.006","publication_status":"published","_id":"7001","publication":"Cell","article_type":"original","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"article_processing_charge":"No","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"file_date_updated":"2020-10-21T07:09:45Z","scopus_import":"1","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"date_created":"2019-11-12T12:51:06Z","issue":"4","citation":{"apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18."},"author":[{"last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"first_name":"Shayan","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour"},{"last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer"},{"last_name":"Balda","full_name":"Balda, M","first_name":"M"},{"first_name":"M","full_name":"Tada, M","last_name":"Tada"},{"last_name":"Matter","full_name":"Matter, K","first_name":"K"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-03T22:30:31Z","page":"937-952.e18","related_material":{"record":[{"status":"public","id":"7186","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8350"}],"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release","description":"News auf IST Website"}]},"month":"10","ddc":["570"],"date_published":"2019-10-31T00:00:00Z"},{"file":[{"checksum":"00d100d6468e31e583051e0a006b640c","date_updated":"2020-10-17T22:30:03Z","relation":"source_file","embargo_to":"open_access","creator":"akopf","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6950","date_created":"2019-10-15T05:28:42Z","access_level":"closed","file_size":74735267,"file_name":"Kopf_PhD_Thesis.docx"},{"date_updated":"2020-10-17T22:30:03Z","relation":"main_file","checksum":"5d1baa899993ae6ca81aebebe1797000","creator":"akopf","content_type":"application/pdf","file_id":"6951","embargo":"2020-10-16","date_created":"2019-10-15T05:28:47Z","access_level":"open_access","file_size":52787224,"file_name":"Kopf_PhD_Thesis1.pdf"}],"alternative_title":["ISTA Thesis"],"oa":1,"abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"doi":"10.15479/AT:ISTA:6891","project":[{"_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems"}],"publication_status":"published","_id":"6891","year":"2019","type":"dissertation","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","day":"24","fulldoi":"https://doi.org/10.15479/AT:ISTA:6891","status":"public","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Kopf","orcid":"0000-0002-2187-6656","first_name":"Aglaja","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-06-18T17:44:11Z","OA_place":"publisher","citation":{"apa":"Kopf, A. (2019). <i>The implication of cytoskeletal dynamics on leukocyte migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>","mla":"Kopf, Aglaja. <i>The Implication of Cytoskeletal Dynamics on Leukocyte Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019."},"date_published":"2019-07-24T00:00:00Z","ddc":["570"],"degree_awarded":"PhD","month":"07","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}],"record":[{"relation":"part_of_dissertation","id":"6877","status":"public"},{"relation":"part_of_dissertation","id":"6328","status":"public"},{"id":"15","status":"public","relation":"part_of_dissertation"}]},"page":"171","corr_author":"1","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"date_created":"2019-09-19T08:19:44Z","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-10-17T22:30:03Z","title":"The implication of cytoskeletal dynamics on leukocyte migration","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]}},{"doi":"10.1038/s41586-019-1087-5","abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","grant_number":"281556"},{"grant_number":"724373","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"265FAEBA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"}],"publication":"Nature","_id":"6328","publication_status":"published","quality_controlled":"1","oa":1,"volume":568,"acknowledged_ssus":[{"_id":"SSU"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"isi":1,"type":"journal_article","year":"2019","ec_funded":1,"publisher":"Springer Nature","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/"}],"day":"25","intvolume":"       568","fulldoi":"https://doi.org/10.1038/s41586-019-1087-5","status":"public","date_published":"2019-04-25T00:00:00Z","month":"04","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/"}],"record":[{"status":"public","id":"14697","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"6891","status":"public"}]},"page":"546-550","author":[{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz"},{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid","first_name":"Ingrid","last_name":"de Vries"},{"first_name":"Meghan K.","full_name":"Driscoll, Meghan K.","last_name":"Driscoll"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"last_name":"Welf","first_name":"Erik S.","full_name":"Welf, Erik S."},{"last_name":"Danuser","full_name":"Danuser, Gaudenz","first_name":"Gaudenz"},{"last_name":"Fiolka","full_name":"Fiolka, Reto","first_name":"Reto"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"date_updated":"2026-10-03T22:30:33Z","citation":{"apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. 2019;568:546-550. doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 546–50, doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","ieee":"J. Renkawitz <i>et al.</i>, “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” <i>Nature</i>, vol. 568. Springer Nature, pp. 546–550, 2019.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550."},"date_created":"2019-04-17T06:52:28Z","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"article_processing_charge":"No","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","scopus_import":"1","external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"article_type":"letter_note"},{"isi":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.cell.2019.08.047","status":"public","intvolume":"       179","day":"19","type":"journal_article","year":"2019","oa_version":"None","publisher":"Elsevier","publication":"Cell","_id":"6877","publication_status":"published","doi":"10.1016/j.cell.2019.08.047","volume":179,"quality_controlled":"1","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"scopus_import":"1","department":[{"_id":"MiSi"}],"title":"The neural crest pitches in to remove apoptotic debris","article_processing_charge":"No","date_created":"2019-09-15T22:00:46Z","language":[{"iso":"eng"}],"article_type":"original","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"related_material":{"record":[{"status":"public","id":"6891","relation":"dissertation_contains"}]},"month":"09","page":"51-53","date_published":"2019-09-19T00:00:00Z","citation":{"chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>.","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” <i>Cell</i>, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","apa":"Kopf, A., &#38; Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. 2019;179(1):51-53. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>"},"issue":"1","date_updated":"2026-10-03T22:30:33Z","author":[{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}]},{"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.cell.2019.04.015","abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"_id":"6351","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication_status":"published","publication":"Cell","oa":1,"file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:28Z","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","creator":"dernst","content_type":"application/pdf","file_id":"6411","date_created":"2019-05-13T06:12:45Z","access_level":"open_access","file_size":10272032,"file_name":"2019_Cell_Marhava.pdf"}],"quality_controlled":"1","volume":177,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"isi":1,"publisher":"Elsevier","oa_version":"Published Version","type":"journal_article","year":"2019","ec_funded":1,"day":"02","intvolume":"       177","status":"public","fulldoi":"https://doi.org/10.1016/j.cell.2019.04.015","ddc":["570"],"date_published":"2019-05-02T00:00:00Z","page":"957-969.e13","related_material":{"link":[{"url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"month":"05","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra","last_name":"Marhavá"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"},{"last_name":"Yoshida","orcid":"0000-0001-6111-9353","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","first_name":"Peter","orcid":"0000-0001-5227-5741"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_updated":"2026-10-03T22:30:35Z","issue":"4","citation":{"ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019."},"language":[{"iso":"eng"}],"date_created":"2019-04-28T21:59:14Z","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:47:28Z","scopus_import":"1","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"corr_author":"1","external_id":{"pmid":["31051107"],"isi":["000466843000015"]}},{"citation":{"apa":"Hörmayer, L., &#38; Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. 2019;52:124-130. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>, vol. 52, Elsevier, 2019, pp. 124–30, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>.","chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>.","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” <i>Current Opinion in Plant Biology</i>, vol. 52. Elsevier, pp. 124–130, 2019.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130."},"author":[{"orcid":"0000-0001-8295-2926","first_name":"Lukas","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"date_updated":"2026-10-03T22:30:35Z","month":"12","related_material":{"record":[{"status":"public","id":"9992","relation":"dissertation_contains"}]},"page":"124-130","date_published":"2019-12-01T00:00:00Z","ddc":["580"],"article_type":"original","corr_author":"1","external_id":{"isi":["000502890600017"],"pmid":["31585333"]},"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:45Z","title":"Targeted cell ablation-based insights into wound healing and restorative patterning","article_processing_charge":"No","publication_identifier":{"issn":["1369-5266"]},"scopus_import":"1","date_created":"2019-10-14T07:00:24Z","language":[{"iso":"eng"}],"file":[{"date_created":"2019-10-14T14:48:21Z","access_level":"open_access","file_size":1659288,"file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","relation":"main_file","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","date_updated":"2020-07-14T12:47:45Z","creator":"dernst","file_id":"6946","content_type":"application/pdf"}],"quality_controlled":"1","oa":1,"volume":52,"doi":"10.1016/j.pbi.2019.08.006","abstract":[{"text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration.","lang":"eng"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"6943","publication_status":"published","publication":"Current Opinion in Plant Biology","intvolume":"        52","fulldoi":"https://doi.org/10.1016/j.pbi.2019.08.006","status":"public","ec_funded":1,"type":"journal_article","year":"2019","publisher":"Elsevier","oa_version":"Published Version","day":"01","pmid":1,"isi":1,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_type":"original","external_id":{"isi":["000462738000034"]},"scopus_import":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_processing_charge":"No","title":"The entorhinal cognitive map is attracted to goals","file_date_updated":"2020-07-14T12:47:23Z","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"date_created":"2019-04-04T08:39:30Z","citation":{"apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., &#38; Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. <i>Science</i>. 2019;363(6434):1443-1447. doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” <i>Science</i>, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>.","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447."},"issue":"6434","date_updated":"2026-10-03T22:30:36Z","author":[{"last_name":"Boccara","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte N.","first_name":"Charlotte N.","id":"3FC06552-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin"},{"full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","orcid":"0000-0001-9439-3148","last_name":"Stella"},{"last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"page":"1443-1447","month":"03","related_material":{"record":[{"status":"public","id":"6062","relation":"popular_science"},{"relation":"dissertation_contains","id":"11932","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","relation":"press_release","description":"News on IST Homepage"}]},"ddc":["570"],"date_published":"2019-03-29T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.1126/science.aav4837","intvolume":"       363","day":"29","publisher":"American Association for the Advancement of Science","oa_version":"Submitted Version","type":"journal_article","year":"2019","ec_funded":1,"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","volume":363,"oa":1,"quality_controlled":"1","file":[{"relation":"main_file","date_updated":"2020-07-14T12:47:23Z","checksum":"5e6b16742cde10a560cfaf2130764da1","creator":"dernst","content_type":"application/pdf","file_id":"7826","date_created":"2020-05-14T09:11:10Z","file_size":9045923,"access_level":"open_access","file_name":"2019_Science_Boccara.pdf"}],"publication_status":"published","_id":"6194","publication":"Science","project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space.","lang":"eng"}],"doi":"10.1126/science.aav4837"},{"volume":122,"quality_controlled":"1","oa":1,"_id":"6189","publication_status":"published","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.122.114502","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"fulldoi":"https://doi.org/10.1103/PhysRevLett.122.114502","article_number":"114502","status":"public","intvolume":"       122","day":"22","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"type":"journal_article","year":"2019","oa_version":"Preprint","publisher":"American Physical Society","isi":1,"pmid":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” <i>Physical Review Letters</i>, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","apa":"Agrawal, N., Choueiri, G. H., &#38; Hof, B. (2019). Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. 2019;122(11). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>"},"issue":"11","arxiv":1,"date_updated":"2026-10-03T22:30:35Z","author":[{"last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","first_name":"George H"},{"last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"month":"03","related_material":{"record":[{"relation":"dissertation_contains","id":"9728","status":"public"}]},"date_published":"2019-03-22T00:00:00Z","external_id":{"arxiv":["1809.06358"],"pmid":["30951357"],"isi":["000461922000006"]},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"scopus_import":"1","department":[{"_id":"BjHo"}],"title":"Transition to turbulence in particle laden flows","article_processing_charge":"No","date_created":"2019-03-31T21:59:12Z","language":[{"iso":"eng"}]},{"volume":141,"oa":1,"quality_controlled":"1","_id":"6486","publication_status":"published","publication":"Journal of Fluids Engineering","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"}],"doi":"10.1115/1.4043494","abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"status":"public","fulldoi":"https://doi.org/10.1115/1.4043494","article_number":"111105","intvolume":"       141","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.07625"}],"oa_version":"Preprint","publisher":"ASME","type":"journal_article","year":"2019","ec_funded":1,"isi":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Kühnen, J., Scarselli, D., &#38; Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. ASME. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. 2019;141(11). doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11, 111105, ASME, 2019, doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>.","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11. ASME, 2019.","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>. ASME, 2019. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>.","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019)."},"arxiv":1,"issue":"11","date_updated":"2026-10-03T22:30:38Z","author":[{"first_name":"Jakob","full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","last_name":"Kühnen"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","first_name":"Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"month":"11","related_material":{"record":[{"status":"public","id":"7258","relation":"dissertation_contains"}]},"date_published":"2019-11-01T00:00:00Z","article_type":"original","external_id":{"arxiv":["1809.07625"],"isi":["000487748600005"]},"scopus_import":"1","publication_identifier":{"eissn":["1528-901X"],"issn":["0098-2202"]},"article_processing_charge":"No","title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"date_created":"2019-05-26T21:59:13Z"},{"citation":{"short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” <i>Journal of Fluid Mechanics</i>, vol. 867. Cambridge University Press, pp. 934–948, 2019.","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. 2019;867:934-948. doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>.","apa":"Scarselli, D., Kühnen, J., &#38; Hof, B. (2019). Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>"},"arxiv":1,"date_updated":"2026-10-03T22:30:38Z","author":[{"last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Kühnen"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn"}],"page":"934-948","month":"05","related_material":{"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}],"record":[{"relation":"dissertation_contains","id":"7258","status":"public"}]},"date_published":"2019-05-25T00:00:00Z","external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"scopus_import":"1","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"title":"Relaminarising pipe flow by wall movement","article_processing_charge":"No","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"date_created":"2019-04-07T21:59:14Z","volume":867,"oa":1,"quality_controlled":"1","_id":"6228","publication_status":"published","publication":"Journal of Fluid Mechanics","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","name":"Eliminating turbulence in oil pipelines","grant_number":"737549","call_identifier":"H2020"}],"doi":"10.1017/jfm.2019.191","abstract":[{"lang":"eng","text":"Following  the  recent  observation  that  turbulent  pipe  flow  can  be  relaminarised  bya  relatively  simple  modification  of  the  mean  velocity  profile,  we  here  carry  out  aquantitative  experimental  investigation  of  this  phenomenon.  Our  study  confirms  thata  flat  velocity  profile  leads  to  a  collapse  of  turbulence  and  in  order  to  achieve  theblunted  profile  shape,  we  employ  a  moving  pipe  segment  that  is  briefly  and  rapidlyshifted  in  the  streamwise  direction.  The  relaminarisation  threshold  and  the  minimumshift  length  and  speeds  are  determined  as  a  function  of  Reynolds  number.  Althoughturbulence  is  still  active  after  the  acceleration  phase,  the  modulated  profile  possessesa  severely  decreased  lift-up  potential  as  measured  by  transient  growth.  As  shown,this  results  in  an  exponential  decay  of  fluctuations  and  the  flow  relaminarises.  Whilethis  method  can  be  easily  applied  at  low  to  moderate  flow  speeds,  the  minimumstreamwise  length  over  which  the  acceleration  needs  to  act  increases  linearly  with  theReynolds  number."}],"status":"public","fulldoi":"https://doi.org/10.1017/jfm.2019.191","intvolume":"       867","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05357"}],"day":"25","publisher":"Cambridge University Press","oa_version":"Preprint","year":"2019","ec_funded":1,"type":"journal_article","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","oa":1,"volume":570,"doi":"10.1038/s41586-019-1320-2","abstract":[{"text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons.","lang":"eng"}],"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"publication":"Nature","_id":"6609","publication_status":"published","ec_funded":1,"type":"journal_article","year":"2019","oa_version":"Preprint","publisher":"Nature Publishing Group","main_file_link":[{"url":"https://arxiv.org/abs/1809.05865","open_access":"1"}],"day":"27","intvolume":"       570","fulldoi":"https://doi.org/10.1038/s41586-019-1320-2","status":"public","acknowledged_ssus":[{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko"},{"last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"last_name":"Wulf","first_name":"Matthias","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378"},{"last_name":"Lewis","first_name":"Dylan","full_name":"Lewis, Dylan"},{"last_name":"Arnold","full_name":"Arnold, Georg M","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M"}],"date_updated":"2026-10-03T22:30:41Z","arxiv":1,"citation":{"apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., &#38; Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>","ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. <i>Nature</i>. 2019;570:480-483. doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>.","ieee":"S. Barzanjeh <i>et al.</i>, “Stationary entangled radiation from micromechanical motion,” <i>Nature</i>, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>.","ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483."},"date_published":"2019-06-27T00:00:00Z","month":"06","related_material":{"record":[{"id":"18871","status":"public","relation":"dissertation_contains"}]},"page":"480-483","external_id":{"isi":["000472860000042"],"arxiv":["1809.05865"]},"date_created":"2019-07-07T21:59:20Z","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"article_processing_charge":"No","title":"Stationary entangled radiation from micromechanical motion","scopus_import":"1"},{"year":"2019","type":"dissertation","publisher":"IST Austria","oa_version":"Published Version","day":"09","fulldoi":"https://doi.org/10.15479/AT:ISTA:6392","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-05-10T13:51:49Z","file_name":"Thesis_Draft_v3.4Final.docx","file_size":43740796,"access_level":"closed","embargo_to":"open_access","creator":"mlukacisin","relation":"hidden","checksum":"829bda074444857c7935171237bb7c0c","date_updated":"2020-07-14T12:47:29Z","file_id":"6409","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"embargo":"2020-04-17","file_id":"6410","content_type":"application/pdf","relation":"main_file","checksum":"56cb5e97f5f8fc41692401b53832d8e0","date_updated":"2021-02-11T11:17:16Z","creator":"mlukacisin","access_level":"open_access","file_size":35228388,"file_name":"Thesis_Draft_v3.4FinalA.pdf","date_created":"2019-05-10T14:13:42Z"}],"oa":1,"alternative_title":["IST Austria Thesis"],"doi":"10.15479/AT:ISTA:6392","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"publication_status":"published","_id":"6392","extern":"1","date_created":"2019-05-09T19:53:00Z","supervisor":[{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"}],"language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"file_date_updated":"2021-02-11T11:17:16Z","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin"}],"date_updated":"2025-07-10T11:49:51Z","citation":{"ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>."},"date_published":"2019-05-09T00:00:00Z","ddc":["570"],"month":"05","related_material":{"record":[{"id":"1029","status":"public","relation":"part_of_dissertation"}]},"page":"103"},{"corr_author":"1","file_date_updated":"2021-02-11T23:30:15Z","department":[{"_id":"JiFr"}],"title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"date_created":"2019-04-09T14:37:06Z","supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"language":[{"iso":"eng"}],"OA_place":"publisher","citation":{"ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","apa":"Narasimhan, M. (2019). <i>Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>","mla":"Narasimhan, Madhumitha. <i>Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>."},"author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"}],"date_updated":"2026-04-08T14:00:24Z","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"412","relation":"part_of_dissertation"}]},"month":"02","page":"138","date_published":"2019-02-04T00:00:00Z","ddc":["575"],"fulldoi":"https://doi.org/10.15479/at:ista:th1075","status":"public","type":"dissertation","year":"2019","oa_version":"Published Version","publisher":"Institute of Science and Technology 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Thesis"],"abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"doi":"10.15479/at:ista:th1075","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"6269","publication_status":"published"},{"citation":{"ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>","mla":"Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>"},"OA_place":"publisher","date_updated":"2026-04-08T13:56:27Z","author":[{"orcid":"0000-0001-7777-546X","first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"}],"page":"152","month":"05","related_material":{"record":[{"relation":"part_of_dissertation","id":"67","status":"public"},{"relation":"popular_science","status":"public","id":"5585"}]},"degree_awarded":"PhD","ddc":["576","579"],"date_published":"2019-05-03T00:00:00Z","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","article_processing_charge":"No","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"}],"date_created":"2019-05-03T11:55:51Z","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"alternative_title":["ISTA Thesis"],"oa":1,"file":[{"creator":"cigler","date_updated":"2021-02-11T11:17:13Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da","relation":"main_file","embargo":"2020-05-02","file_id":"6373","content_type":"application/pdf","date_created":"2019-05-03T11:54:52Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","access_level":"open_access","file_size":12597663},{"date_created":"2019-05-03T11:54:54Z","file_size":34644426,"access_level":"closed","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","date_updated":"2020-07-14T12:47:28Z","relation":"source_file","creator":"cigler","embargo_to":"open_access","file_id":"6374","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"publication_status":"published","_id":"6371","project":[{"grant_number":"24573","name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.   \r\n","lang":"eng"}],"doi":"10.15479/AT:ISTA:6371","status":"public","fulldoi":"https://doi.org/10.15479/AT:ISTA:6371","day":"03","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","year":"2019","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1"},{"month":"04","related_material":{"record":[{"id":"21","status":"public","relation":"part_of_dissertation"}]},"page":"140","degree_awarded":"PhD","date_published":"2019-04-30T00:00:00Z","ddc":["570"],"citation":{"ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>","mla":"Espinoza Martinez, Claudia. <i>Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>.","apa":"Espinoza Martinez, C. (2019). <i>Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019."},"OA_place":"publisher","date_updated":"2026-04-08T13:57:19Z","author":[{"last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia "}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"file_date_updated":"2021-02-11T11:17:15Z","department":[{"_id":"PeJo"}],"article_processing_charge":"No","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","date_created":"2019-04-30T11:56:10Z","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas"}],"corr_author":"1","publication_status":"published","_id":"6363","doi":"10.15479/AT:ISTA:6363","abstract":[{"lang":"eng","text":"Distinguishing  between  similar  experiences  is  achieved  by  the  brain  in  a  process called  pattern  separation.  In  the  hippocampus,  pattern  separation  reduces  the interference of memories and increases the storage capacity by decorrelating similar inputs  patterns  of  neuronal  activity  into  non-overlapping output  firing  patterns. Winners-take-all  (WTA)  mechanism  is  a  theoretical  model  for  pattern  separation  in which  a  \"winner\"  cell  suppresses  the  activity  of  the  neighboring  neurons  through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of  feedback  inhibition  in  which  a  GC  inhibits  other  GCs  but  not  itself  through  the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron  connectivity  was  more  spatially  confined  but  less  abundant  than  PV+interneurons–GC  connectivity,  leading  to  an  asymmetrical  distribution  of  excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the  primary  mechanism.  This  process  relied  on  lateral  inhibition,  fast-signaling properties  of  PV+interneurons  and  the  asymmetrical  distribution  of  excitatory  and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in  vivoleads  to  acute  deficits  in  discrimination  between  similar  environments, suggesting  that  PV+interneuron  networks  are  necessary  for  behavioral  relevant computations.  Our   results   demonstrate   that   PV+interneurons  possess  unique connectivity  and  fast  signaling  properties  that confer  to  the  dentate  gyrus  network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"file":[{"content_type":"application/pdf","embargo":"2020-05-09","file_id":"6389","creator":"cespinoza","date_updated":"2021-02-11T11:17:15Z","checksum":"77c6c05cfe8b58c8abcf1b854375d084","relation":"main_file","file_name":"Espinozathesis_all2.pdf","file_size":13966891,"access_level":"open_access","date_created":"2019-05-07T16:00:39Z"},{"embargo_to":"open_access","creator":"cespinoza","checksum":"f6aa819f127691a2b0fc21c76eb09746","date_updated":"2020-07-14T12:47:28Z","relation":"source_file","file_id":"6390","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-05-07T16:00:48Z","file_name":"Espinoza_Thesis.docx","file_size":11159900,"access_level":"closed"}],"oa":1,"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:6363","status":"public","day":"30","year":"2019","type":"dissertation","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria"}]