Aβ	amyloid-beta
AD	Alzheimer’s disease
AMBRA1	activating molecule in Beclin 1-regulated autophagy protein 1
AMPK	AMP-activated protein kinase
Atg	autophagy-related protein
BFP	blue fluorescent protein
CMA	chaperone-mediated autophagy
ECFP	enhanced cyan fluorescent proteins
EYFP	enhanced yellow fluorescent protein
FIP200	focal adhesion kinase family interacting protein of 200-kDa
FP	fluorescent protein
FRET	fluorescence resonance energy transfer
GFP	green fluorescent protein
HD	Huntington’s Disease
Hsc70	heat shock cognate protein of 70 kDa
Htt	huntingtin
HyD	hydrophobic domain
LAMP2A	lysosomal-associated membrane protein 2A
LC3	microtubule-associated protein light chain 3
LDH	lactate dehydrogenase
LD	lipid droplet
LID	light-induced dimer
LIR	LC3 interacting region
mTOR	mechanistic target of rapamycin
NBR1	neighbor of BRCA1 gene 1
NDP52	nuclear dot protein 52 kDa
PD	Parkinson’s disease
PE	phosphatidylethanolamine
PINK1	PTEN-induced kinase 1
PI3P	phosphatidylinositol 3-phosphate
PolyQ	polyglutamine
PS-CFP2	photoconvertible cyan FP
PS-1	presenilin 1
RFP	red fluorescent protein
SEP	superecliptic pHluourin
SF44	Seoul-Fluor 44
SILAC	stable isotope labeling by amino acid in cell culture
SNARE	soluble NSF (N-Ethylmaleimide-Sensitive Factor) Attachment Protein Receptor
SRAI	signal-retaining autophagy indicator
TEM	transmission electron microscope
TOLLES	TOLerance of Lysosomal EnvironmentS
ULK1	Unc-51 like kinase 1
Vps34	vacuolar protein sorting 34
WIPI	WD-repeat protein interacting with phosphoinositide