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Guet, Science 356 (2017) 311–315.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","ieee":"T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf4762","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762"},"article_type":"original","page":"311 - 315","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"issue":"6335","type":"journal_article","oa_version":"None","_id":"665","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","status":"public","intvolume":" 356","month":"04","publication_identifier":{"issn":["00368075"]},"doi":"10.1126/science.aaf4762","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"publist_id":"7064","author":[{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"last_name":"Andersson","first_name":"Anna M","orcid":"0000-0003-2912-6769","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","full_name":"Andersson, Anna M"},{"last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5560"}]},"date_updated":"2024-02-21T13:49:00Z","date_created":"2018-12-11T11:47:48Z","volume":356,"year":"2017","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"publisher":"American Association for the Advancement of Science"},{"day":"06","month":"11","article_processing_charge":"No","has_accepted_license":"1","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:78.","mla":"Vicoso, Beatriz. 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Vicoso, (2017).","mla":"Vicoso, Beatriz. Code for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:79 .","ieee":"B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","apa":"Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:79 ","ista":"Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:79 .","ama":"Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:10.15479/AT:ISTA:79 "},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","month":"11","day":"06","related_material":{"record":[{"id":"542","relation":"research_paper","status":"public"}]},"author":[{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"file":[{"creator":"system","file_size":49823,"content_type":"application/zip","access_level":"open_access","file_name":"IST-2017-79-v1+1_Code.zip","checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:05:15Z","file_id":"5643","relation":"main_file"}],"oa_version":"Submitted Version","date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:48:28Z","_id":"5572","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Code for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","ddc":["576"],"file_date_updated":"2020-07-14T12:47:05Z","abstract":[{"lang":"eng","text":"Code described in the Supplementary Methods of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.)"}],"type":"research_data","datarep_id":"79"},{"date_published":"2017-06-19T00:00:00Z","citation":{"short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792.","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792."},"publication":"eLife","article_processing_charge":"Yes","has_accepted_license":"1","day":"19","scopus_import":"1","file":[{"file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","access_level":"open_access","content_type":"application/pdf","file_size":19581847,"creator":"system","relation":"main_file","file_id":"5315","date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z","checksum":"9af3398cb0d81f99d79016a616df22e9"}],"oa_version":"Published Version","pubrep_id":"847","intvolume":" 6","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"946","abstract":[{"text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.7554/eLife.26792","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Molecular basis of root growth inhibition by auxin","call_identifier":"FWF","grant_number":"M02128","_id":"2572ED28-B435-11E9-9278-68D0E5697425"},{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"isi":["000404728300001"]},"month":"06","volume":6,"date_updated":"2024-02-21T13:49:34Z","date_created":"2018-12-11T11:49:21Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5566"}]},"author":[{"full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","first_name":"Daniel"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publication_status":"published","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","year":"2017","ec_funded":1,"publist_id":"6471","file_date_updated":"2020-07-14T12:48:15Z","article_number":"e26792"},{"abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"issue":"119","type":"journal_article","file":[{"relation":"main_file","file_id":"5219","date_created":"2018-12-12T10:16:31Z","date_updated":"2018-12-12T10:16:31Z","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","access_level":"open_access","file_size":57678,"content_type":"application/pdf","creator":"system"},{"creator":"system","content_type":"application/pdf","file_size":1317820,"access_level":"open_access","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-12T10:16:32Z","file_id":"5220","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"808","ddc":["580"],"title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","status":"public","intvolume":" 2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1078","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-01-18T00:00:00Z","publication":"Journal of visualized experiments JoVE","citation":{"ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017)."},"file_date_updated":"2018-12-12T10:16:32Z","ec_funded":1,"publist_id":"6302","article_number":"e55044","date_created":"2018-12-11T11:50:01Z","date_updated":"2024-02-21T13:49:12Z","volume":2017,"author":[{"full_name":"Von Wangenheim, Daniel","first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5565"}]},"publication_status":"published","publisher":"Journal of Visualized Experiments","department":[{"_id":"JiFr"},{"_id":"Bio"}],"year":"2017","month":"01","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.3791/55044","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"oa":1,"external_id":{"isi":["000397847200041"]}},{"type":"research_data","datarep_id":"66","publist_id":"6302","ec_funded":1,"file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. "}],"_id":"5565","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"fund: FP7-ERC 0101109","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","ddc":["580"],"status":"public","title":"Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel","related_material":{"record":[{"id":"1078","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4","file_size":101497758,"content_type":"video/mp4","creator":"system","relation":"main_file","file_id":"5599","checksum":"b7552fc23540a85dc5a22fd4484eae71","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:33Z"}],"date_updated":"2024-02-21T13:49:13Z","date_created":"2018-12-12T12:31:34Z","article_processing_charge":"No","has_accepted_license":"1","day":"10","month":"04","citation":{"ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, 10.15479/AT:ISTA:66.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:66","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66.","mla":"von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:66.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017)."},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"date_published":"2017-04-10T00:00:00Z","doi":"10.15479/AT:ISTA:66"},{"has_accepted_license":"1","article_processing_charge":"No","day":"21","month":"07","keyword":["tool","tracking","confocal microscopy"],"date_published":"2017-07-21T00:00:00Z","doi":"10.15479/AT:ISTA:69","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"ama":"Hauschild R. Live tracking of moving samples in confocal microscopy for vertically grown roots. 2017. doi:10.15479/AT:ISTA:69","ista":"Hauschild R. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots, Institute of Science and Technology Austria, 10.15479/AT:ISTA:69.","apa":"Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:69","ieee":"R. Hauschild, “Live tracking of moving samples in confocal microscopy for vertically grown roots.” Institute of Science and Technology Austria, 2017.","mla":"Hauschild, Robert. Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:69.","short":"R. Hauschild, (2017).","chicago":"Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:69."},"oa":1,"file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"text":"Current minimal version of TipTracker","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"research_data","datarep_id":"69","related_material":{"record":[{"id":"946","status":"public","relation":"research_paper"}]},"author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"}],"file":[{"file_size":1587986,"content_type":"application/zip","creator":"system","access_level":"open_access","file_name":"IST-2017-69-v1+2_TipTrackerZeissLSM700.zip","checksum":"a976000e6715106724a271cc9422be4a","date_created":"2018-12-12T13:04:12Z","date_updated":"2020-07-14T12:47:04Z","relation":"main_file","file_id":"5636"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:34Z","date_updated":"2024-02-21T13:49:34Z","_id":"5566","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","status":"public"},{"publist_id":"7399","year":"2017","editor":[{"full_name":"Loebl, Martin","last_name":"Loebl","first_name":"Martin"},{"full_name":"Nešetřil, Jaroslav","last_name":"Nešetřil","first_name":"Jaroslav"},{"full_name":"Thomas, Robin","last_name":"Thomas","first_name":"Robin"}],"department":[{"_id":"UlWa"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1512"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"date_updated":"2024-02-28T12:59:37Z","date_created":"2018-12-11T11:46:24Z","publication_identifier":{"isbn":["978-331944479-6"]},"month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.4613v3"}],"oa":1,"quality_controlled":"1","doi":"10.1007/978-3-319-44479-6_17","language":[{"iso":"eng"}],"type":"book_chapter","abstract":[{"lang":"eng","text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b, d) such that the following holds. If F is a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤ i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced Z2-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these [d/2] first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map C*(K)→C*(Rd)."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"424","title":"Bounding helly numbers via betti numbers","status":"public","oa_version":"Published Version","scopus_import":1,"series_title":"A Journey Through Discrete Mathematics","day":"06","citation":{"chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers.” In A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, edited by Martin Loebl, Jaroslav Nešetřil, and Robin Thomas, 407–47. A Journey Through Discrete Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-44479-6_17.","mla":"Goaoc, Xavier, et al. “Bounding Helly Numbers via Betti Numbers.” A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, edited by Martin Loebl et al., Springer, 2017, pp. 407–47, doi:10.1007/978-3-319-44479-6_17.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, M. Loebl, J. Nešetřil, R. Thomas (Eds.), A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, Springer, 2017, pp. 407–447.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2017.Bounding helly numbers via betti numbers. In: A Journey through Discrete Mathematics: A Tribute to Jiri Matousek. , 407–447.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). Bounding helly numbers via betti numbers. In M. Loebl, J. Nešetřil, & R. Thomas (Eds.), A Journey through Discrete Mathematics: A Tribute to Jiri Matousek (pp. 407–447). Springer. https://doi.org/10.1007/978-3-319-44479-6_17","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding helly numbers via betti numbers,” in A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, M. Loebl, J. Nešetřil, and R. Thomas, Eds. Springer, 2017, pp. 407–447.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding helly numbers via betti numbers. In: Loebl M, Nešetřil J, Thomas R, eds. A Journey through Discrete Mathematics: A Tribute to Jiri Matousek. A Journey Through Discrete Mathematics. Springer; 2017:407-447. doi:10.1007/978-3-319-44479-6_17"},"publication":"A Journey through Discrete Mathematics: A Tribute to Jiri Matousek","page":"407 - 447","date_published":"2017-10-06T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"463","intvolume":" 27","ddc":["530"],"title":"Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow","status":"public","file":[{"checksum":"0731f9d416760c1062db258ca51f8bdc","date_updated":"2020-07-14T12:46:32Z","date_created":"2019-10-24T15:14:30Z","file_id":"6970","relation":"main_file","creator":"dernst","file_size":7714020,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_Chaos_Altmeyer.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"text":"We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow.","lang":"eng"}],"citation":{"short":"S. Altmeyer, Y. Do, S. Ryu, Chaos 27 (2017).","mla":"Altmeyer, Sebastian, et al. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos, vol. 27, no. 11, 113112, AIP Publishing, 2017, doi:10.1063/1.5002771.","chicago":"Altmeyer, Sebastian, Younghae Do, and Soorok Ryu. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos. AIP Publishing, 2017. https://doi.org/10.1063/1.5002771.","ama":"Altmeyer S, Do Y, Ryu S. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 2017;27(11). doi:10.1063/1.5002771","ieee":"S. Altmeyer, Y. Do, and S. Ryu, “Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow,” Chaos, vol. 27, no. 11. AIP Publishing, 2017.","apa":"Altmeyer, S., Do, Y., & Ryu, S. (2017). Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. AIP Publishing. https://doi.org/10.1063/1.5002771","ista":"Altmeyer S, Do Y, Ryu S. 2017. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 27(11), 113112."},"publication":"Chaos","article_type":"original","date_published":"2017-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2017","publisher":"AIP Publishing","department":[{"_id":"BjHo"}],"publication_status":"published","author":[{"full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","last_name":"Altmeyer","first_name":"Sebastian"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"last_name":"Ryu","first_name":"Soorok","full_name":"Ryu, Soorok"}],"volume":27,"date_created":"2018-12-11T11:46:37Z","date_updated":"2024-02-28T13:02:12Z","article_number":"113112","publist_id":"7358","file_date_updated":"2020-07-14T12:46:32Z","oa":1,"quality_controlled":"1","doi":"10.1063/1.5002771","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10541500"]},"month":"11"},{"language":[{"iso":"eng"}],"doi":"10.1063/1.4983703","isi":1,"quality_controlled":"1","external_id":{"isi":["000405089400047"]},"main_file_link":[{"url":"https://arxiv.org/abs/1704.03684","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["00219606"]},"month":"06","volume":147,"date_created":"2018-12-11T11:49:36Z","date_updated":"2024-02-28T13:02:26Z","author":[{"full_name":"Shepperson, Benjamin","first_name":"Benjamin","last_name":"Shepperson"},{"full_name":"Chatterley, Adam","last_name":"Chatterley","first_name":"Adam"},{"last_name":"Søndergaard","first_name":"Anders","full_name":"Søndergaard, Anders"},{"full_name":"Christiansen, Lars","last_name":"Christiansen","first_name":"Lars"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","publication_status":"published","year":"2017","publist_id":"6403","article_number":"013946","date_published":"2017-06-01T00:00:00Z","citation":{"ista":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 147(1), 013946.","apa":"Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko, M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4983703","ieee":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no. 1. AIP Publishing, 2017.","ama":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703","chicago":"Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen, Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4983703.","mla":"Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147, no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.","short":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, H. Stapelfeldt, The Journal of Chemical Physics 147 (2017)."},"publication":"The Journal of Chemical Physics","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 147","status":"public","title":"Strongly aligned molecules inside helium droplets in the near-adiabatic regime","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"996","issue":"1","abstract":[{"lang":"eng","text":"Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. "}],"type":"journal_article"},{"type":"journal_article","issue":"8","abstract":[{"text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n","lang":"eng"}],"intvolume":" 58","status":"public","title":"A lower bound for the BCS functional with boundary conditions at infinity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"912","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 2017;58(8). doi:10.1063/1.4996580","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 58(8), 081901.","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing, 2017.","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:10.1063/1.4996580.","short":"A. Deuchert, Journal of Mathematical Physics 58 (2017).","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4996580."},"publication":" Journal of Mathematical Physics","date_published":"2017-08-01T00:00:00Z","article_number":"081901","ec_funded":1,"publist_id":"6531","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","year":"2017","volume":58,"date_created":"2018-12-11T11:49:10Z","date_updated":"2024-02-28T13:07:56Z","author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["00222488"]},"month":"08","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.04616"}],"oa":1,"external_id":{"isi":["000409197200015"]},"language":[{"iso":"eng"}],"doi":"10.1063/1.4996580"},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000396318300121"]},"tmp":{"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)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0174066","publication_identifier":{"issn":["19326203"]},"month":"03","department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2017","volume":12,"date_updated":"2024-03-28T23:30:04Z","date_created":"2018-12-11T11:49:46Z","related_material":{"record":[{"id":"5556","relation":"popular_science","status":"public"},{"id":"6392","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin"},{"full_name":"Landon, Matthieu","last_name":"Landon","first_name":"Matthieu"},{"full_name":"Jajoo, Rishi","first_name":"Rishi","last_name":"Jajoo"}],"article_number":"e0174066","publist_id":"6361","file_date_updated":"2018-12-12T10:09:47Z","citation":{"chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066"},"publication":"PLoS One","date_published":"2017-03-16T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"16","intvolume":" 12","status":"public","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1029","file":[{"file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","access_level":"open_access","file_size":3429381,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4772","date_updated":"2018-12-12T10:09:47Z","date_created":"2018-12-12T10:09:47Z"}],"oa_version":"Published Version","pubrep_id":"800","type":"journal_article","issue":"3","abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}]},{"doi":"10.1016/j.immuni.2017.04.006","date_published":"2017-04-18T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006."},"publication":"Immunity","page":"519 - 520","quality_controlled":"1","publication_identifier":{"issn":["10747613"]},"month":"04","day":"18","scopus_import":1,"related_material":{"record":[{"id":"6947","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen","full_name":"Assen, Frank P"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"volume":46,"oa_version":"None","date_updated":"2024-03-28T23:30:09Z","date_created":"2018-12-11T11:47:47Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"664","year":"2017","intvolume":" 46","department":[{"_id":"MiSi"}],"publisher":"Cell Press","status":"public","title":"The dynamic cytokine niche","publication_status":"published","issue":"4","publist_id":"7065","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry."}],"issue":"6","_id":"682","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"title":"PirB regulates asymmetries in hippocampal circuitry","status":"public","intvolume":" 12","pubrep_id":"897","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","content_type":"application/pdf","file_size":5798454,"creator":"system","relation":"main_file","file_id":"4934","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:12:16Z"}],"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"PLoS One","citation":{"short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377."},"article_type":"original","date_published":"2017-06-01T00:00:00Z","article_number":"e0179377","file_date_updated":"2020-07-14T12:47:40Z","publist_id":"7034","year":"2017","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"RySh"}],"author":[{"full_name":"Ukai, Hikari","last_name":"Ukai","first_name":"Hikari"},{"first_name":"Aiko","last_name":"Kawahara","full_name":"Kawahara, Aiko"},{"last_name":"Hirayama","first_name":"Keiko","full_name":"Hirayama, Keiko"},{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","first_name":"Matthew J","full_name":"Case, Matthew J"},{"last_name":"Aino","first_name":"Shotaro","full_name":"Aino, Shotaro"},{"last_name":"Miyabe","first_name":"Masahiro","full_name":"Miyabe, Masahiro"},{"full_name":"Wakita, Ken","first_name":"Ken","last_name":"Wakita"},{"full_name":"Oogi, Ryohei","first_name":"Ryohei","last_name":"Oogi"},{"full_name":"Kasayuki, Michiyo","last_name":"Kasayuki","first_name":"Michiyo"},{"full_name":"Kawashima, Shihomi","last_name":"Kawashima","first_name":"Shihomi"},{"full_name":"Sugimoto, Shunichi","first_name":"Shunichi","last_name":"Sugimoto"},{"first_name":"Kanako","last_name":"Chikamatsu","full_name":"Chikamatsu, Kanako"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"full_name":"Koga, Tsuneyuki","first_name":"Tsuneyuki","last_name":"Koga"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Takai, Toshiyuki","last_name":"Takai","first_name":"Toshiyuki"},{"first_name":"Isao","last_name":"Ito","full_name":"Ito, Isao"}],"related_material":{"record":[{"id":"51","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:47:54Z","date_updated":"2024-03-28T23:30:12Z","volume":12,"month":"06","publication_identifier":{"issn":["19326203"]},"oa":1,"tmp":{"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)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0179377","language":[{"iso":"eng"}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20","citation":{"ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998."},"publication":"Angewandte Chemie - International Edition","page":"4608-4611","date_published":"2017-03-20T00:00:00Z","type":"journal_article","issue":"16","abstract":[{"text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1028","intvolume":" 56","status":"public","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","ddc":["540"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5845","success":1,"date_updated":"2019-01-18T09:39:55Z","date_created":"2019-01-18T09:39:55Z","access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","file_size":2614942,"content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"issn":["14337851"]},"month":"03","external_id":{"isi":["000398154000038"]},"tmp":{"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)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Molecular Drug Targets [do not use to be deleted]","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1002/anie.201611998","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"6362","file_date_updated":"2019-01-18T09:39:55Z","year":"2017","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","publisher":"Wiley-Blackwell","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"},{"status":"public","relation":"part_of_dissertation","id":"7680"}]},"author":[{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"},{"full_name":"Distel, Martin","first_name":"Martin","last_name":"Distel"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"volume":56,"date_updated":"2024-03-28T23:30:13Z","date_created":"2018-12-11T11:49:46Z"},{"has_accepted_license":"1","day":"17","scopus_import":1,"date_published":"2017-03-17T00:00:00Z","citation":{"ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1."},"publication":"Auxins and Cytokinins in Plant Biology","page":"1 - 29","abstract":[{"text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.","lang":"eng"}],"type":"journal_article","alternative_title":["Methods in Molecular Biology"],"pubrep_id":"1019","file":[{"access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","creator":"system","file_size":840646,"content_type":"application/pdf","file_id":"5068","relation":"main_file","date_created":"2018-12-12T10:14:18Z","date_updated":"2019-10-15T07:47:05Z"}],"oa_version":"Submitted Version","_id":"1024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 1569","title":"Methodological advances in auxin and cytokinin biology","ddc":["575"],"status":"public","publication_identifier":{"issn":["10643745"]},"month":"03","doi":"10.1007/978-1-4939-6831-2_1","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16"}],"quality_controlled":"1","publist_id":"6369","file_date_updated":"2019-10-15T07:47:05Z","related_material":{"record":[{"id":"539","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426","first_name":"Andrej","last_name":"Hurny","full_name":"Hurny, Andrej"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"volume":1569,"date_updated":"2024-03-28T23:30:17Z","date_created":"2018-12-11T11:49:45Z","year":"2017","publisher":"Springer","department":[{"_id":"EvBe"}],"publication_status":"published"},{"abstract":[{"text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"679","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","status":"public","intvolume":" 127","day":"01","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","publication":"The Journal of Clinical Investigation","citation":{"ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","ieee":"F. Ebner et al., “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” The Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:10.1172/JCI80631.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631."},"page":"2051 - 2065","publist_id":"7038","author":[{"full_name":"Ebner, Florian","last_name":"Ebner","first_name":"Florian"},{"full_name":"Sedlyarov, Vitaly","first_name":"Vitaly","last_name":"Sedlyarov"},{"last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren"},{"full_name":"Ivin, Masa","last_name":"Ivin","first_name":"Masa"},{"last_name":"Kratochvill","first_name":"Franz","full_name":"Kratochvill, Franz"},{"last_name":"Gratz","first_name":"Nina","full_name":"Gratz, Nina"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"last_name":"Villunger","first_name":"Andreas","full_name":"Villunger, Andreas"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:47:53Z","date_updated":"2024-03-28T23:30:23Z","volume":127,"year":"2017","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"American Society for Clinical Investigation","month":"06","publication_identifier":{"issn":["00219738"]},"doi":"10.1172/JCI80631","language":[{"iso":"eng"}],"external_id":{"pmid":["28504646"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The biochemical basis of PAR polarization"},{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}]},{"oa_version":"Published Version","file":[{"file_id":"6905","relation":"main_file","checksum":"bc25125fb664706cdf180e061429f91d","date_updated":"2020-07-14T12:47:39Z","date_created":"2019-09-24T06:56:22Z","access_level":"open_access","file_name":"2017_Development_Krens.pdf","creator":"dernst","file_size":8194516,"content_type":"application/pdf"}],"_id":"676","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","ddc":["570"],"intvolume":" 144","abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"issue":"10","type":"journal_article","date_published":"2017-05-15T00:00:00Z","publication":"Development","citation":{"ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806."},"article_type":"original","page":"1798 - 1806","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"author":[{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"first_name":"Jim","last_name":"Veldhuis","full_name":"Veldhuis, Jim"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa"},{"full_name":"Capek, Daniel","last_name":"Capek","first_name":"Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maître, Jean-Léon","first_name":"Jean-Léon","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474"},{"full_name":"Brodland, Wayne","last_name":"Brodland","first_name":"Wayne"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"50"}]},"date_created":"2018-12-11T11:47:52Z","date_updated":"2024-03-28T23:30:26Z","volume":144,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"Bio"},{"_id":"CaHe"}],"publisher":"Company of Biologists","file_date_updated":"2020-07-14T12:47:39Z","publist_id":"7047","doi":"10.1242/dev.144964","language":[{"iso":"eng"}],"external_id":{"pmid":["28512197"]},"tmp":{"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)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"05","publication_identifier":{"issn":["09501991"]}},{"year":"2017","department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5564"},{"relation":"dissertation_contains","status":"public","id":"26"}]},"author":[{"full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","first_name":"Magdalena","last_name":"Steinrück"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"volume":6,"date_created":"2018-12-11T11:48:01Z","date_updated":"2024-03-28T23:30:28Z","article_number":"e25100","publist_id":"6990","file_date_updated":"2020-07-14T12:47:48Z","tmp":{"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)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.7554/eLife.25100","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050084X"]},"month":"07","_id":"704","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["576"],"status":"public","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","pubrep_id":"890","oa_version":"Published Version","file":[{"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","access_level":"open_access","file_size":2092088,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4975","date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:54Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571"},{"date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:55Z","checksum":"ca21530389b720243552678125fdba35","file_id":"4976","relation":"main_file","creator":"system","file_size":3428681,"content_type":"application/pdf","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"citation":{"chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100"},"publication":"eLife","date_published":"2017-07-25T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"25"}]