Autophagy (macroautophagy) is a dynamic process for degradation of cytosolic 
components. Autophagy has intracellular anti-viral and anti-bacterial functions, 
and plays a role in the initiation of innate and adaptive immune system 
responses to viral and bacterial infections. Some viruses encode virulence 
factors for blocking autophagy, whereas others utilize some autophagy components 
for their intracellular growth or cellular budding. The "core" autophagy-related 
(Atg) complexes in mammals are ULK1 protein kinase, Atg9-WIPI-1 and 
Vps34-beclin1 class III PI3-kinase complexes, and the Atg12 and LC3 conjugation 
systems. In addition, PI(3)-binding proteins, PI3-phosphatases, and Rab proteins 
contribute to autophagy. The autophagy process consists of continuous dynamic 
membrane formation and fusion. In this review, the relationships between these 
Atg complexes and each process are described. Finally, the critical points for 
monitoring autophagy, including the use of GFP-LC3 and GFP-Atg5, are discussed.