Publisher Summary Flagellar apparatus can be released from cells in a complex that includes the flagella, the basal bodies, the rootlet microtubules, the structures linking the basal bodies to the nucleus (nucleus-basal body connectors), and a chromatin-containing nuclear remnant. This complex is called the nucleoflagellar apparatus, or NFAp. Studies of isolated Chlamydomonas NFAps, in both wild-type and mutant organisms have led to a better understanding of the structures that makeup this basic unit of the basal apparatus and have allowed for detailed analysis of its components at the cytological and biochemical levels. The juxtaposition of mitochondria, nucleus, and basal body apparatus makes it problematic to determine, in a whole cell, whether a protein is localizing to the basal body apparatus, whereas the distinction can readily be made using isolated NFAps. Isolated NFAps greatly simplified protein composition as compared with whole cells. The cytoskeleton, the flagellar apparatus, and the nucleus exist as a physically integrated complex. Two strains have been used for most of the basal body apparatus isolations: the “cell wall”-less strain cw 92 (CC503) and the wild-type strain 137c (CC125). cw 92 cells are easily lysed with nonionic detergents, facilitating separation of the NFAps from the other cellular components, while detergent extraction of walled cells allows for the isolation of cell “ghosts” with the NFAps trapped inside. There are details of the solutions and the procedures—preparation of NFAps on glass slides for light microscopy and electron microscopy, immunofluorescence microscopy, isolation of NFAps, and preparation of cell ghosts containing NFAps for light or electron microscopy. Additional treatments like Flagella can be removed prior to sample preparation; removal of Mg 2+ from the nucleus buffer results in the preparation of flagellar apparatuses without attached nuclei possibly as a result of loss of the nucleus-basal body connectors, etcetera.
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