I did leaf fixation with methanol and acetic acid and I observed a lot of precipitation inside mesophyll cells like crystals. Does anyone know why ? And how to avoid this?
I don't know exactly what you are seeing, but the cells contain many compounds that are insoluble in methanol, so it could be any one of those things. The first thing that comes to mind is that it may be starch granules. Starch granules can be stained with iodine solution (I2+KI), so that is one way you can check if you're so inclined.
Addition of methanol and acidification by acetic acid (besides its proper chemical effect) drastically change the physical properties of a solvent, whichever it is. When you change the dielectric constant of a solvent, you change its structure and its interaction with solute molecules; breaking the weak chemical bonds between solvent and solutes therefore changes the physico-chemical characteristics of the medium. Plant cells have large vacuoles that contain organic acids (oxalic, tartaric...), proteins and other substances; many of them may then precipitate. Incidentally, this is a classical method to separate a mixture in its particular components, e.g., proteins. A way to limit that effect – if it really needs to be avoided - is to change the nature and proportion of added chemicals. (By the way, you didn't expound what you were looking for.)
! part glacial acetic acid and 3 parts methanol or ethanol (1:3 ratio) has been used as fixative of cells/ tissues for staining purposes. Precipitation occurs as a result of alcohol reaction within cell components but does not interfere in staining such as chromosomes.
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