What does fixation do to your cells’ morphology?

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All in all, these observations strongly question the use of fixed samples in research involving membrane dependent systems.

A concentration as low as 0.2% PFA already induces very strong cellular changes at the molecular level, which are translated in an observation that does not meet the characteristics of living cells. These modifications are much more accentuated amongst membranes (mitochondrial, nuclear and plasma).

These conclusions correlate with previous research on the subject[1], [2]. PFA fixation has been shown to induce strong perturbations of cellular nanostructures[2], and inefficiently fix glycosylphosphatidylinositol-anchored, phospholipid-anchored or cholesterol-anchored membrane proteins, leading to observation of aberrant clustering of proteins observed by subsequent immune-staining[1].

Source: https://www.nanolive.ch/technology/live-cell-imaging/nanolive-imaging/fixation/