Eukaryotic flagella (also referred to as cilia) are microtubule-based organelles that protrude from the cell body into the extracellular environment. In addition to powering cell motility and fluid low, flagella mediate the reception of numerous signaling processes that direct developmental programs. Because flagella serve such diverse roles, defects in flagellar morphology produce a pleiotropic array of human diseases.

The assembly and maintenance of flagella relies on intraflagellar transport (IFT), the molecular motor driven traffic of large protein complexes (called trains) carrying flagellar proteins between the cell body and the flagellar tip. To better understand the relationship between flagellar length and IFT, we developed a method to quantify IFT in the flagella of Chlamydomonas reinhardtii using total internal reflection fluorescence microscopy (TIRF, described in detail in chapter 2). In chapter 1, we measured changes in anterograde (base to tip) IFT during flagellar regeneration and found that IFT train size is inversely proportional to flagellar length, and may thus determine the steady state length of flagella. In chapter 3, we performed a pharmacological screen for impaired cell motility in Chlamydomonas and identified a small molecule that reduces flagellar length in several organisms, while affecting both IFT and actin dynamics. In chapter 4, we performed a genetic screen for impaired Chlamydomonas cell motility and isolated a temperature-sensitive mutant in the heavy chain of IFT dynein, the retrograde motor that returns IFT trains from the flagellar tip to the cell body. Unlike mutations in the anterograde kinesin motor, which impede both flagellar assembly and maintenance, the dynein mutant (named dhc1b-3) experiences defects in assembly but not maintenance despite significant reductions in both dynein protein and IFT activity. This surprising observation has forced us to rethink the relationship between IFT and the control of flagellar length.