Although the interference of secondary metabolites with staining procedures had been recognized for some time in cytophotometry (Greilhuber 1986), it was not until Noirot et al. (2000) and Price et al. (2000) published their findings that this effect was taken seriously in plant FCM. Until recently, this interference was thought to be fluorescence inhibition, but research carried out in the meantime appears to suggest that there are additional effects such as the aggregation of minor particles with nuclei that also play a role in this interference and can even lead to an apparent increase in nuclear fluorescence (Loureiro et al. 2006a). The role of autofluorescing metabolites is still hypothetical and needs investigation. Therefore, we distinguish here between inhibitors and coatings of debris, the latter being particles of endogenous substances sticking to the nuclei, resulting in a deterioration of the quality of the FCM histogram peaks without necessarily decreasing the overall nuclear fluorescence.
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