Summary: Cilia and flagella are evolutionarily conserved appendage-like organelles that sense the extracellular environment, drive the movement of individual cells, or transport fluids. Defects of ciliary functions lead to numerous diseases termed the ciliopathies, which result in a variety of congenital disorders and cause a broad spectrum of symptoms. The outer-arm dynein (OAD) is a key motor protein that generates most mechanical forces to power the ciliary beating by ATP hydrolysis. OAD mutations were found in over half of the primary ciliary dyskinesia (PCD) patients. These mutations have orthologs in algae and ciliates, which also lead to cilia/flagellar dysfunctions, suggesting that the lower species and humans have important commonalities on the mechanisms of ciliary motility. However, lacking an atomic model of most ciliary components has been a main barrier to our understanding the cilium system. We will use the model systems T. thermophila and C. reinhardtii to elucidate the cilium assembly and dynein-driven ciliary motility in the following years, with an emphasis on OAD and its regulation. We aim to reveal the mechanisms in atomic details by a combination of cryo-EM/ET, correlative light and electron microscopy (CLEM), biochemistry, cell biology, single- molecule biophysics, and computational modeling etc. Our aims for the following years are to understand how OAD arrays are formed in cilia, how OADs coordinate with each other during beating, how the OAD activity is regulated by other ciliary components (such as central pair) and extracellular signals, and build an atomic model of axoneme. We will co-develop cryo-EM/ET methods to address long-standing problems. The revealed mechanisms will provide more accurate information for our future mutagenesis in mammalian systems and human disease models.