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Numerous eukaryotic cells carry whip-like appendages (cilia or eukaryotic flagella) whose inner core consists of a highly-conserved cytoskeletal structure called the axoneme.

The axoneme serves as the "skeleton" of these organelles, both giving support to the structure and, in most cases, causing it to bend. Though distinctions of function and/or length may be made between cilia and flagella, the internal structure of the axoneme is common to both.

The characteristic feature of the axoneme is its “9 + 2” arrangement of microtubules and associated proteins, as shown in the image at right. Nine pairs of "doublet" microtubules, a component of the cellular cytoskeleton, form a ring around a "central pair" of single microtubules. Ciliary dynein arms, the motor complexes which allow the axoneme to bend, are anchored to these microtubules. The interactions between the ciliary dynein proteins and outer doublet microtubules generate force by sliding the doublets parallel to each other, which bends the cilium and enables it to beat.

Motile cilia and flagella are ubiquitous:

• Flagellar beat propels spermatozoa and some unicellular eukaryots such as chlamydomonas.
• Ciliar arrays transport mucus in the trachea.
• Nodal cilia play a role in the determination of the left-right-axis of vertebrates via morphogen transport during embryonic development.

Not surprisingly, defects in the dynein motors of vertebrates can result in infertility, respiratory disease, and failures in determination of the left-right body axis during embryonic development.

The radial spoke, a protein complex important in regulating the motion of the axoneme, is also housed in the axoneme; it projects from each set of outer doublets toward the central microtubules.

The doublets and central sheaths are linked by proteins known as nexins.

The axoneme structure in non-motile primary cilium shows some variation from the canonical “9 + 2” anatomy. No dynein arms are found on the outer doublet microtubules, and there is no pair of central microtubule singlets. This organization of axoneme is referred as “9 + 0”. In addition, “9 + 1” axonemes, with only a single central microtubule, have been found to exist. Non-motile primary cilia are expressed by many sensory cells including olfactory sensory neurons, auditory hair cells and retinal cone cells.

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