You need a dye that either binds covalently or becomes
completely insoluble. In the latter group, alcian blue
is worth trying. If the animals will survive a brief
exposure to alkali after staining this dye will be
changed to copper phthalocyanine, which is an extremely
stable and insoluble pigment. 

There are many reactive dyes and fluorochromes that
would combine covalently with the macromolecules in
your list, but they would be reactive also when
ingested, perhaps killing the copepods or otherwise
making your experiments invalid. Alcian blue might
also be toxic to these animals; you will need to do
tests. 

For what it's worth, I can attest that rats or mice
tolerate intravenously injected doses of alcian blue,
various reactive dyes and many other dyes and
suspensions of pigments - enough to bring about 
obvious colour changes in the skin of albino animals,
and dark coloration of the liver and spleen, when
the injected stuff was a pigment - without incurring
any easily observed ill-effects. If copepods are
as tough as rats & mice you may well be able to
label them with a reactive dye. 

Have you done a Web of Science search? There may be
many recent publications about staining living
crustaceans. Nearly everything has already been done, 
and nowadays it's easier than ever before to look
for the relevant publications.

----------------------------------------
John A. Kiernan
Department of Anatomy & Cell Biology
The University of Western Ontario
London,  Canada   N6A 5C1
   kiernan@uwo.ca
   http://publish.uwo.ca/~jkiernan
_____________________________________________  
On Tue, 25 Sep 2001, fsbab3 wrote to Histonet:
> a colleague and I are planning to stain the cuticle oflive
> copepods (small marine crustaceans). We are still looking for the appropriate
> stain and I wonder if you have any good ideas. There are different components
> in the cuticle layers of the copepods that we could stain. These are:
> - chitin (C8H13O5N)n: Polyacetylglukosamin
> - layer of polymerized protein (arthrodin) and lipoids
> - resilin: rubber-like protein, couldn't find more specific description
> - surface coat: mucopolysaccharides and carbohydrates
> - protein-chitin complexes (a protein called arthropodin)
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