Morphological Analysis of Autophagy

Autophagy is a bulk intracellular degradation process that is ubiquitous in eukaryotic cells and helps to recycle nutrients from catabolites by degrading proteins, lipids, and glycans, including organelles. Since autophagy has divergent physiological roles in cancer, infection, immunity, and other processes, it is important to accurately analyze autophagic activity. In this chapter, we describe methods that can be used to monitor autophagy in cultured mammalian cells by immunostaining and using fluorescently tagged autophagy-related proteins such as GFP- or mRFP-GFP-tandem-tagged proteins as well as electron microscopic methods, including electron tomography and immuno-electron microscopy.