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Because of the highly conserved nature of the basic axonemal structure, many different model systems have proven useful for the study of ciliopathies, especially the unicellular, biflagellate green alga <jats:italic>Chlamydomonas reinhardtii<\/jats:italic>. Although the basic axonemal structure of cilia and flagella is highly conserved, these organelles often perform specialized functions unique to the cell or tissue in which they are found. These differences in function are likely reflected in differences in structural organization. In this work, we directly compare the structure of isolated axonemes from human cilia and Chlamydomonas flagella to identify similarities and differences that potentially play key roles in determining their functionality. Using transmission electron microscopy and 2D image averaging techniques, our analysis has confirmed the overall structural similarity between these two species, but also revealed clear differences in the structure of the outer dynein arms, the central pair projections, and the radial spokes. We also show how the application of 2D image averaging can clarify the underlying structural defects associated with primary ciliary dyskinesia (PCD). Overall, our results document the remarkable similarity between these two structures separated evolutionarily by over a billion years, while highlighting several significant differences, and demonstrate the potential of 2D image averaging to improve the diagnosis and understanding of PCD. \u00a9 2012 Wiley Periodicals, Inc<\/jats:p>","DOI":"10.1002\/cm.21035","type":"journal-article","created":{"date-parts":[[2012,5,9]],"date-time":"2012-05-09T16:24:22Z","timestamp":1336580662000},"page":"577-590","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Computer\u2010assisted image analysis of human cilia and Chlamydomonas flagella reveals both similarities and differences in axoneme structure"],"prefix":"10.1002","volume":"69","author":[{"given":"Eileen T.","family":"O'Toole","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Thomas 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