It's quite confusing to distinguish between the definitions. To me, autofluorescence fits all. But what is the correct terminology to use when talking about biological cells, proteins (such as GFP), and generally any material?
My opinion is that autofluorescence refers to the natural fluorescence of cells or tissue in fluorescence microscopy, which is usually an undesirable background.
Fluorescence includes autofluorescence, but the fluorescence of interest is usually an extrinsic probe, such as an engineered GFP or similar fluorescent protein, or a chemical fluorophore, that is not naturally intrinsic to the cell or tissue.
Thanks Adam B Shapiro !
From what I understood, if we look at a non-cellular material (for example, plastic) in a fluorescence microscope, its natural fluorescence should be called autofluorescence.
Let's imagine we cultured cells on a plastic scaffold, and we see that the scaffold emits light at a certain wavelength, what should this emission be called? Is it the scaffold's fluorescence or autofluorescence?
Hello Hanie Kavand
There should be no confusion whatsoever between fluorescence and autofluorescence.
Autofluorescence is something that is natural or fixative-induced. If you need to use the term “autofluorescence” it will refer to the intrinsic natural fluorescence exhibited by all prokaryotic and eukaryotic cells due to the presence of different fluorescent cellular structural components and metabolites, such as flavins, nicotinamide-adenine dinucleotide (NAD), aromatic amino acids, lipofuscins, advanced glycation end products, and collagen.
If you need to use the term “fluorescence” in context of staining then it will refer to the conventional stains typically using antibodies conjugated to a fluorescent moiety such as an organic dye like fluorescein isothiocyanate (FITC), etc.
Autofluorescence during fluorescent staining could be a problem as it could interfere with detection of specific fluorescent signals, especially when the signal of interest is very dim. This problem of autofluorescence is often regarded as a nuisance in immunofluorescence, masking the specific fluorescence of introduced substances and it must be addressed, but at the same time it usually provides a guide to the morphology of the tissue, and is also worthy of study in its own right.
Best.
Fluorescence coming from the glass or plastic scaffold I would term background fluorescence, not autofluorescence. If you are seeing much of it, you should change to a different material that does not have it, if possible, or use wavelengths at which it is negligible.
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