Objective: to achieve an absolute understanding of the positional relationships of elements inside a protist cell.

There are several ways one can make progress with understanding the flagellar apparatus. Immunocytochemical and fluorescent techniques, whole mounts, the study of thick preparations and the study of thin sections (typically 50-80 nm) may all contribute. The most usual method is to reconstruct from thin sections. This ensures that small details - such as individual microtubules - are not missed. It does, however, create the challenge of building a 3-dimensional shape from a series of planar sections.

To eliminate the incomplete and inconsistent nature of the data, serial sections are preferred over random sections.

The material is fixed, typically in glutaraldehyde and osmium, dehydrated and embedded in resin. Thin sections are taken with a microtome. Typically the sections will be 50-80 nm thick. A minimum of 20 sections will be needed if we are to capture all of the skeletal elements that are associated with the basal bodies.

Ribbons of sections are collected on a grid. For serial sections, slot grids are used. Some companies, such as Pelco, market grids that are numbered. It is then possible to make long series of sections, break them into ribbons, and retain a record of how a series extend from one ribbon to the next.

Two types of grids used to support thin sections. The one to the left is a hex grid, the fine bars provide support for the sections. The grids to the right are large single-hole grids (or slot-grids). The grid needs to be coated with a thin layer of plastic and the sections then rest on the plastic. Image from the Pelco web site.

Ribbons of sections aligned on a slot grid. Image by D. J. Patterson.

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