I know toluidine blue is used to prepare plastic-embedded thin sections for EM. Has anyone used as a bacterial nuclear stain on thicker (5uM), formalin-fixed, paraffin embedded sections?
There should be no problem with the stain. Its a basic dyeToluidine blue is (was?) used in a mixture with thionin and methylene blue for staining paraffin sections of CNS for Nissl granules. More commonly used today as a stain for mast cells.
Whether it will differentially stain what you want it to- you will need to check by trial and error.
Toluidine blue has been standard in histological procedures, often used to differentiate "mucins" (glycoproteins, mucopolysaccacharides - highly and weakly sulfated, etc.) and often with paraffin sections. High DNA/RNA binding makes it a fair nuclear stain. When staining, pH matters. Fixative used can also alter results. Toluidine blue is also metachromatic, so different colors of the final stain can be significant and informative. See any basic histotechnique book for explanations, limits and protocols.