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Lignin is a chemical compound derived from wood and is found in the secondary cell walls of plants. It is a polymer of aromatic subunits derived from phenylalanine. Lignin is found in the spaces in the cell wall between cellulose, hemicelluloses and pectin components. It is covalently linked to hemicelluloses. It is cross linked to different polysaccharides and thus provides mechanical strength to the cell wall and also to the whole plant. Lignin polymers are hydrophobic and hence impermeable to water whereas the polysachharides are permeable to water.
The use of dyes to make structures within sections of plant material visible, has been used for an extensive period of time. Dye substances may be used to differentiate between primary and secondary wall structures, show the presence or absence of lignin within the walls, show the presence or absence of other specialized chemical substances within cell walls, and may stain nuclei, or chromosomes within living cells. These substances rely on the cationic or anionic nature of the substances within the cell walls, or within the cytoplasm of the cells themselves. By carefully selecting dyes and relatively simple chemical reactions, one may undertake histochemical analysis of the wall, and the cytoplasm. These simple tests are thus invaluable if we are to determine the nature of living plant cells.