{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T08:38:13Z","timestamp":1779352693274,"version":"3.51.4"},"reference-count":44,"publisher":"The Company of Biologists","issue":"12","license":[{"start":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T00:00:00Z","timestamp":1557964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.biologists.com\/user-licence-1-1\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["RO1GM108964"],"award-info":[{"award-number":["RO1GM108964"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Biological tubes are essential for animal survival, and their functions are dependent on tube shape. Analyzing the contributions of cell shape and organization to the morphogenesis of small tubes has been hampered by the limitations of existing programs in quantifying cell geometry on highly curved tubular surfaces and calculating tube-specific parameters. We therefore developed QuBiT (Quantitative Tool for Biological Tubes) and used it to analyze morphogenesis of the embryonic Drosophila trachea (airway). In the main tube, we find previously unknown anterior-to-posterior (A-P) gradients of cell apical orientation and aspect ratio, and periodicity in the organization of apical cell surfaces. Inferred cell intercalation during development dampens an A-P gradient of the number of cells per cross-section of the tube, but does not change the patterns of cell connectivity. Computationally \u2018unrolling\u2019 the apical surface of wild-type trachea and the hindgut reveals previously unrecognized spatial patterns of the apical marker Uninflatable and a non-redundant role for the Na+\/K+ ATPase in apical marker organization. These unexpected findings demonstrate the importance of a computational tool for analyzing small diameter biological tubes.<\/jats:p>","DOI":"10.1242\/dev.172759","type":"journal-article","created":{"date-parts":[[2019,4,9]],"date-time":"2019-04-09T09:26:16Z","timestamp":1554801976000},"source":"Crossref","is-referenced-by-count":6,"title":["QuBiT: a quantitative tool for analyzing epithelial tubes reveals unexpected patterns of organization in the\n                    <i>Drosophila<\/i>\n                    trachea"],"prefix":"10.1242","volume":"146","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6104-2691","authenticated-orcid":false,"given":"Ran","family":"Yang","sequence":"first","affiliation":[{"name":"Northwestern University 1 Department of Molecular Biosciences , , Evanston, IL 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3348-2515","authenticated-orcid":false,"given":"Eric","family":"Li","sequence":"additional","affiliation":[{"name":"Northwestern University 1 Department of Molecular Biosciences , , Evanston, IL 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7632-3779","authenticated-orcid":false,"given":"Yong-Jae","family":"Kwon","sequence":"additional","affiliation":[{"name":"Northwestern University 1 Department of Molecular Biosciences , , Evanston, IL 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Madhav","family":"Mani","sequence":"additional","affiliation":[{"name":"Northwestern University 1 Department of Molecular Biosciences , , Evanston, IL 60208 , USA"},{"name":"Northwestern University 2 Department of Engineering Sciences and Applied Mathematics , , Evanston, IL 60208 , USA"},{"name":"NSF-Simons Center for Quantitative Biology, Northwestern University 3 , Evanston, IL 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4413-6324","authenticated-orcid":false,"given":"Greg J.","family":"Beitel","sequence":"additional","affiliation":[{"name":"Northwestern University 1 Department of Molecular Biosciences , , Evanston, IL 60208 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"237","published-online":{"date-parts":[[2019,5,16]]},"reference":[{"key":"2024061300561931400_DEV172759C1","doi-asserted-by":"publisher","first-page":"2055","DOI":"10.1242\/dev.014498","article-title":"Tracheal branching morphogenesis in Drosophila: new insights into cell behaviour and organ architecture","volume":"135","author":"Affolter","year":"2008","journal-title":"Development"},{"key":"2024061300561931400_DEV172759C2","doi-asserted-by":"publisher","first-page":"05864","DOI":"10.7554\/eLife.05864","article-title":"MorphoGraphX: a platform for quantifying morphogenesis in 4D","volume":"4","author":"Barbier de Reuille","year":"2015","journal-title":"Elife"},{"key":"2024061300561931400_DEV172759C3","doi-asserted-by":"crossref","first-page":"3271","DOI":"10.1242\/dev.127.15.3271","article-title":"Genetic control of epithelial tube size in the Drosophila tracheal system","volume":"127","author":"Beitel","year":"2000","journal-title":"Development"},{"key":"2024061300561931400_DEV172759C4","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1016\/j.devcel.2006.09.007","article-title":"Multicellular rosette formation links planar cell polarity to tissue morphogenesis","volume":"11","author":"Blankenship","year":"2006","journal-title":"Dev. 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