References

1. Mizushima, N.; Levine, B. Autophagy in Human Diseases. N. Engl. J. Med. 2020, 383, 15641576.
2. Bar-Yosef, T.; Damri, O.; Agam, G. Dual Role of Autophagy in Diseases of the Central Nervous System. Front. Cell Neurosci. 2019, 13, 196.
3. Mulcahy Levy, J.M.; Thorburn, A. Autophagy in cancer: Moving from understanding mechanism to improving therapy responses in patients. Cell Death Differ. 2020, 27, 843–857.
4. Yim, W.W.; Mizushima, N. Lysosome biology in autophagy. Cell Discov. 2020, 6, 6.
5. Rubinsztein, D.C.; Shpilka, T.; Elazar, Z. Mechanisms of autophagosome biogenesis. Curr. Biol. 2012, 22, R29–R34.
6. Reggiori, F.; Komatsu, M.; Finley, K.; Simonsen, A. Autophagy: More than a nonselective pathway. Int J. Cell Biol. 2012, 2012, 219625.
7. Palikaras, K.; Lionaki, E.; Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 2018, 20, 1013–1022.
8. Klionsky, D.J.; Cuervo, A.M.; Dunn, W.A., Jr.; Levine, B.; van der Klei, I.; Seglen, P.O. How shall I eat thee? Autophagy 2007, 3, 413–416.
9. Schuck, S. Microautophagy—Distinct molecular mechanisms handle cargoes of many sizes. J. Cell Sci. 2020, 133, 17.
10. Kaushik, S.; Cuervo, A.M. The coming of age of chaperone-mediated autophagy. Nat. Rev. Mol. Cell Biol. 2018, 19, 365–381.
11. Kaushik, S.; Cuervo, A.M. Chaperone-mediated autophagy: A unique way to enter the lysosome world. Trends Cell Biol. 2012, 22, 407–417.
12. Kaushik, S.; Bandyopadhyay, U.; Sridhar, S.; Kiffin, R.; Martinez-Vicente, M.; Kon, M.; Orenstein, S.J.; Wong, E.; Cuervo, A.M. Chaperone-mediated autophagy at a glance. J. Cell Sci. 2011, 124, 495–499.
13. Feng, Y.; He, D.; Yao, Z.; Klionsky, D.J. The machinery of macroautophagy. Cell Res. 2014, 24, 24–41.
14. Mehrpour, M.; Esclatine, A.; Beau, I.; Codogno, P. Overview of macroautophagy regulation in mammalian cells. Cell Res. 2010, 20, 748–762.
15. Hardie, D.G. AMPK and autophagy get connected. EMBO J. 2011, 30, 634–635.
16. Kim, Y.C.; Guan, K.L. mTOR: A pharmacologic target for autophagy regulation. J. Clin. Invest. 2015, 125, 25–32.
17. Zachari, M.; Ganley, I.G. The mammalian ULK1 complex and autophagy initiation. Essays Biochem. 2017, 61, 585–596.
18. Feng, Y.; Klionsky, D.J. Autophagic membrane delivery through ATG9. Cell Res. 2017, 27, 161–162.
19. Mack, H.I.; Zheng, B.; Asara, J.M.; Thomas, S.M. AMPK-dependent phosphorylation of ULK1 regulates ATG9 localization. Autophagy 2012, 8, 1197–1214.
20. Burman, C.; Ktistakis, N.T. Regulation of autophagy by phosphatidylinositol 3-phosphate. FEBS Lett. 2010, 584, 1302–1312.
21. Proikas-Cezanne, T.; Takacs, Z.; Donnes, P.; Kohlbacher, O. WIPI proteins: Essential PtdIns3P effectors at the nascent autophagosome. J. Cell Sci. 2015, 128, 207–217.
22. Walczak, M.; Martens, S. Dissecting the role of the Atg12-Atg5-Atg16 complex during autophagosome formation. Autophagy 2013, 9, 424–425.
23. Agrotis, A.; von Chamier, L.; Oliver, H.; Kiso, K.; Singh, T.; Ketteler, R. Human ATG4 autophagy proteases counteract attachment of ubiquitin-like LC3/GABARAP proteins to other cellular proteins. J. Biol. Chem. 2019, 294, 12610–12621.
24. Khaminets, A.; Behl, C.; Dikic, I. Ubiquitin-Dependent And Independent Signals In Selective Autophagy. Trends Cell Biol. 2016, 26, 6–16.
25. Kirkin, V.; Lamark, T.; Sou, Y.S.; Bjorkoy, G.; Nunn, J.L.; Bruun, J.A.; Shvets, E.; McEwan, D.G.; Clausen, T.H.; Wild, P.; et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol. Cell 2009, 33, 505–516.
26. Kirkin, V.; Rogov, V.V. A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway. Mol. Cell 2019, 76, 268–285.
27. Pankiv, S.; Clausen, T.H.; Lamark, T.; Brech, A.; Bruun, J.A.; Outzen, H.; Overvatn, A.; Bjorkoy, G.; Johansen, T. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J. Biol. Chem. 2007, 282, 24131–24145.
28. Maruyama, T.; Noda, N.N. Autophagy-regulating protease Atg4: Structure, function, regulation and inhibition. J. Antibiot. (Tokyo) 2018, 71, 72–78.
29. Ao, X.; Zou, L.; Wu, Y. Regulation of autophagy by the Rab GTPase network. Cell Death Differ. 2014, 21, 348–358.
30. Wang, Y.; Li, L.; Hou, C.; Lai, Y.; Long, J.; Liu, J.; Zhong, Q.; Diao, J. SNARE-mediated membrane fusion in autophagy. Semin Cell Dev. Biol. 2016, 60, 97–104.
31. Nixon, R.A. The role of autophagy in neurodegenerative disease. Nat. Med. 2013, 19, 983–997.
32. Tanida, I.; Ueno, T.; Kominami, E. LC3 conjugation system in mammalian autophagy. Int J. Biochem. Cell Biol. 2004, 36, 2503–2518.
33. Chung, C.G.; Lee, H.; Lee, S.B. Mechanisms of protein toxicity in neurodegenerative diseases. Cell Mol. Life Sci. 2018, 75, 3159–3180.
34. Harjes, P.; Wanker, E.E. The hunt for huntingtin function: Interaction partners tell many different stories. Trends Biochem. Sci. 2003, 28, 425–433.
35. Martinez-Vicente, M.; Talloczy, Z.; Wong, E.; Tang, G.; Koga, H.; Kaushik, S.; de Vries, R.; Arias, E.; Harris, S.; Sulzer, D.; et al. Cargo recognition failure is responsible for inefficient autophagy in Huntington’s disease. Nat. Neurosci. 2010, 13, 567–576.
36. Wong, Y.C.; Holzbaur, E.L. The regulation of autophagosome dynamics by huntingtin and HAP1 is disrupted by expression of mutant huntingtin, leading to defective cargo degradation. J. Neurosci. 2014, 34, 1293–1305.
37. Koga, H.; Martinez-Vicente, M.; Arias, E.; Kaushik, S.; Sulzer, D.; Cuervo, A.M. Constitutive upregulation of chaperone-mediated autophagy in Huntington’s disease. J. Neurosci. 2011, 31, 18492–18505.
38. Nixon, R.A. Autophagy, amyloidogenesis and Alzheimer disease. J. Cell Sci. 2007, 120, 4081–4091.
39. Boland, B.; Kumar, A.; Lee, S.; Platt, F.M.; Wegiel, J.; Yu, W.H.; Nixon, R.A. Autophagy induction and autophagosome clearance in neurons: Relationship to autophagic pathology in Alzheimer’s disease. J. Neurosci. 2008, 28, 6926–6937.
40. Neely, K.M.; Green, K.N.; LaFerla, F.M. Presenilin is necessary for efficient proteolysis through the autophagy-lysosome system in a gamma-secretase-independent manner. J. Neurosci 2011, 31, 2781–2791.
41. Guglielmotto, M.; Monteleone, D.; Piras, A.; Valsecchi, V.; Tropiano, M.; Ariano, S.; Fornaro, M.; Vercelli, A.; Puyal, J.; Arancio, O.; et al. Abeta1-42 monomers or oligomers have different effects on autophagy and apoptosis. Autophagy 2014, 10, 1827–1843.
42. Iqbal, K. Tau in Alzheimer Disease and Related Tauopathies. Curr Alzheimer Res. 2010, 7, 656–664.
43. Jiang, S.; Bhaskar, K. Degradation and Transmission of Tau by Autophagic-Endolysosomal Networks and Potential Therapeutic Targets for Tauopathy. Front. Mol. Neurosci. 2020, 13, 586731.
44. Menzies, F.M.; Fleming, A.; Caricasole, A.; Bento, C.F.; Andrews, S.P.; Ashkenazi, A.; Fullgrabe, J.; Jackson, A.; Jimenez Sanchez, M.; Karabiyik, C.; et al. Autophagy and Neurodegeneration: Pathogenic Mechanisms and Therapeutic Opportunities. Neuron 2017, 93, 1015–1034.
45. Stefanis, L. alpha-Synuclein in Parkinson’s disease. Cold Spring Harb Perspect Med. 2012, 2, a009399.
46. Cuervo, A.M. Impaired Degradation of mutant alpha synuclein of chaperone-mediated autophagy. Science 2004, 305, 1292–1295.
47. Vogiatzi, T.; Xilouri, M.; Vekrellis, K.; Stefanis, L. Wild type alpha-synuclein is degraded by chaperone-mediated autophagy and macroautophagy in neuronal cells. J. Biol Chem. 2008, 283, 23542–23556.
48. Winslow, A.R.; Chen, C.W.; Corrochano, S.; Acevedo-Arozena, A.; Gordon, D.E.; Peden, A.A.; Lichtenberg, M.; Menzies, F.M.; Ravikumar, B.; Imarisio, S.; et al. alpha-Synuclein impairs macroautophagy: Implications for Parkinson’s disease. J. Cell Biol. 2010, 190, 1023–1037.
49. Coune, P.G.; Bensadoun, J.C.; Aebischer, P.; Schneider, B.L. Rab1A over-expression prevents Golgi apparatus fragmentation and partially corrects motor deficits in an alpha-synuclein based rat model of Parkinson’s disease. J. Parkinsons Dis. 2011, 1, 373–387.
50. Tanik, S.A.; Schultheiss, C.E.; Volpicelli-Daley, L.A.; Brunden, K.R.; Lee, V.M. Lewy body-like alpha-synuclein aggregates resist degradation and impair macroautophagy. J. Biol. Chem. 2013, 288, 15194–15210.
51. Volpicelli-Daley, L.A.; Gamble, K.L.; Schultheiss, C.E.; Riddle, D.M.; West, A.B.; Lee, V.M. Formation of alpha-synuclein Lewy neurite-like aggregates in axons impedes the transport of distinct endosomes. Mol. Biol. Cell 2014, 25, 4010–4023.
52. Malpartida, A.B.; Williamson, M.; Narendra, D.P.; Wade-Martins, R.; Ryan, B.J. Mitochondrial Dysfunction and Mitophagy in Parkinson’s Disease: From Mechanism to Therapy. Trends Biochem. Sci. 2021, 46, 329–343.
53. Pickrell, A.M.; Youle, R.J. The roles of PINK1, parkin, and mitochondrial fidelity in Parkinson’s disease. Neuron 2015, 85, 257–273.
54. Ge, P.; Dawson, V.L.; Dawson, T.M. PINK1 and Parkin mitochondrial quality control: A source of regional vulnerability in Parkinson’s disease. Mol. Neurodegener 2020, 15, 20.
55. Mizushima, N.; Yoshimori, T.; Levine, B. Methods in mammalian autophagy research. Cell 2010, 140, 313–326.
56. Mizushima, N. Methods for monitoring autophagy. Int J. Biochem. Cell Biol. 2004, 36, 2491–2502.
57. du Toit, A.; Hofmeyr, J.S.; Gniadek, T.J.; Loos, B. Measuring autophagosome flux. Autophagy 2018, 14, 1060–1071.
58. Rhodin, J. Correlation of Ultrastructural Organization and Function in Normal and Experimentally Changed Proximal Convoluted Tubule Cells of the Mouse Kidney: An Electron Microscopic Study Including an Experimental Analysis of the Conditions For Fixation of the Renal Tissue For High Reso-Lution Electron Microscopy. Ph.D. Thesis, Karolinska Institutet, Stockholm, Sweden, 1954.
59. Eskelinen, E.L.; Reggiori, F.; Baba, M.; Kovacs, A.L.; Seglen, P.O. Seeing is believing: The impact of electron microscopy on autophagy research. Autophagy 2011, 7, 935–956.
60. Barth, S.; Glick, D.; Macleod, K.F. Autophagy: Assays and artifacts. J. Pathol. 2010, 221, 117–124.
61. Bauvy, C.; Meijer, A.J.; Codogno, P. Chapter 4 Assaying of Autophagic Protein Degradation. Autophagy Mamm. Syst. Part B 2009, 452, 47–61.
62. Zhang, T.; Wolfe, C.; Pierle, A.; Welle, K.A.; Hryhorenko, J.R.; Ghaemmaghami, S. Proteome-wide modulation of degradation dynamics in response to growth arrest. Proc. Natl. Acad. Sci. USA 2017, 114, E10329–E10338.
63. Zhang, T.; Price, J.C.; Nouri-Nigjeh, E.; Li, J.; Hellerstein, M.K.; Qu, J.; Ghaemmaghami, S. Kinetics of precursor labeling in stable isotope labeling in cell cultures (SILAC) experiments. Anal. Chem. 2014, 86, 11334–11341.
64. Luhr, M.; Szalai, P.; Saetre, F.; Gerner, L.; Seglen, P.O.; Engedal, N. A Simple Cargo Sequestration Assay for Quantitative Measurement of Nonselective Autophagy in Cultured Cells. Methods Enzymol. 2017, 587, 351–364.
65. Lamark, T.; Svenning, S.; Johansen, T. Regulation of selective autophagy: The p62/SQSTM1 paradigm. Essays Biochem. 2017, 61, 609–624.
66. Kirisako, T.; Ichimura, Y.; Okada, H.; Kabeya, Y.; Mizushima, N.; Yoshimori, T.; Ohsumi, M.; Takao, T.; Noda, T.; Ohsumi, Y. The Reversible Modification Regulates the Membrane-Binding State of Apg8 Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J. Cell Biol. 2000, 151, 263–275.
67. Wild, P.; McEwan, D.G.; Dikic, I. The LC3 interactome at a glance. J. Cell Sci. 2014, 127, 3–9.
68. Kabeya, Y.; Mizushima, N.; Ueno, T.; Yamamoto, A.; Kirisako, T.; Noda, T.; Kominami, E.; Ohsumi, Y.; Yoshimori, T. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 2000, 19, 5720–5728.
69. Mizushima, N.; Yoshimori, T. How to interpret LC3 immunoblotting. Autophagy 2007, 3, 542–545.
70. Cui, D.; Sun, D.; Wang, X.; Yi, L.; Kulikowicz, E.; Reyes, M.; Zhu, J.; Yang, Z.J.; Jiang, W.; Koehler, R.C. Impaired autophagosome clearance contributes to neuronal death in a piglet model of neonatal hypoxic-ischemic encephalopathy. Cell Death Dis. 2017, 8, e2919.
71. Mauthe, M.; Orhon, I.; Rocchi, C.; Zhou, X.; Luhr, M.; Hijlkema, K.J.; Coppes, R.P.; Engedal, N.; Mari, M.; Reggiori, F. Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion. Autophagy 2018, 14, 1435–1455.
72. Mauvezin, C.; Neufeld, T.P. Bafilomycin A1 disrupts autophagic flux by inhibiting both V-ATPase-dependent acidification and Ca-P60A/SERCA-dependent autophagosome-lysosome fusion. Autophagy 2015, 11, 1437–1438.
73. Kim, E.; Koh, M.; Lim, B.J.; Park, S.B. Emission wavelength prediction of a full-color-tunable fluorescent core skeleton, 9-aryl-1,2-dihydropyrrolo[3,4-b]indolizin-3-one. J. Am. Chem Soc. 2011, 133, 6642–6649.
74. Lee, S.; Kim, E.; Park, S.B. Discovery of autophagy modulators through the construction of a high-content screening platform via monitoring of lipid droplets. Chem. Sci. 2013, 4, 8.
75. Li, S.S.; Zhang, M.; Wang, J.H.; Yang, F.; Kang, B.; Xu, J.J.; Chen, H.Y. Monitoring the Changes of pH in Lysosomes during Autophagy and Apoptosis by Plasmon Enhanced Raman Imaging. Anal. Chem. 2019, 91, 8398–8405.
76. Chudakov, D.M.; Matz, M.V.; Lukyanov, S.; Lukyanov, K.A. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev. 2010, 90, 1103–1163.
77. Shaner, N.C.; Patterson, G.H.; Davidson, M.W. Advances in fluorescent protein technology. J. Cell Sci 2007, 120, 4247–4260.
78. Kim, H.; Ju, J.; Lee, H.N.; Chun, H.; Seong, J. Genetically Encoded Biosensors Based on Fluorescent Proteins. Sensors 2021, 21, 3.
79. Kaizuka, T.; Morishita, H.; Hama, Y.; Tsukamoto, S.; Matsui, T.; Toyota, Y.; Kodama, A.; Ishihara, T.; Mizushima, T.; Mizushima, N. An Autophagic Flux Probe that Releases an Internal Control. Mol. Cell 2016, 64, 835–849.
80. Kim, H.; Kim, H.; Choi, J.; Inn, K.S.; Seong, J. Visualization of Autophagy Progression by a Red-Green-Blue Autophagy Sensor. ACS Sens. 2020, 5, 3850–3861.
81. Kimura, S.; Noda, T.; Yoshimori, T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 2007, 3, 452–460.
82. Maulucci, G.; Chiarpotto, M.; Papi, M.; Samengo, D.; Pani, G.; De Spirito, M. Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates. Autophagy 2015, 11, 1905–1916.
83. Tanida, I.; Ueno, T.; Uchiyama, Y. A super-ecliptic, pHluorin-mKate2, tandem fluorescent protein-tagged human LC3 for the monitoring of mammalian autophagy. PLoS ONE 2014, 9, e110600.
84. Zhou, C.; Zhong, W.; Zhou, J.; Sheng, F.; Fang, Z.; Wei, Y.; Chen, Y.; Deng, X.; Xia, B.; Lin, J. Monitoring autophagic flux by an improved tandem fluorescent-tagged LC3 (mTagRFP-mWasabi-LC3) reveals that high-dose rapamycin impairs autophagic flux in cancer cells. Autophagy 2012, 8, 1215–1226.
85. Koga, H.; Martinez-Vicente, M.; Macian, F.; Verkhusha, V.V.; Cuervo, A.M. A photoconvertible fluorescent reporter to track chaperone-mediated autophagy. Nat. Commun. 2011, 2, 386.
86. D’Acunzo, P.; Strappazzon, F.; Caruana, I.; Meneghetti, G.; Di Rita, A.; Simula, L.; Weber, G.; Del Bufalo, F.; Dalla Valle, L.; Campello, S.; et al. Reversible induction of mitophagy by an optogenetic bimodular system. Nat. Commun. 2019, 10, 1533.
87. Miesenbock, G.; De Angelis, D.A.; Rothman, J.E. Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature 1998, 394, 192–195.
88. Sankaranarayanan, S.; De Angelis, D.; Rothman, J.E.; Ryan, T.A. The Use of pHluorins for Optical Measurements of Presynaptic Activity. Biophys. J. 2000, 79, 2199–2208.
89. Li, Y.; Tsien, R.W. pHTomato, a red, genetically encoded indicator that enables multiplex interrogation of synaptic activity. Nat. Neurosci. 2012, 15, 1047–1053.
90. Shen, Y.; Rosendale, M.; Campbell, R.E.; Perrais, D. pHuji, a pH-sensitive red fluorescent protein for imaging of exo- and endocytosis. J. Cell Biol. 2014, 207, 419–432.
91. Liu, A.; Huang, X.; He, W.; Xue, F.; Yang, Y.; Liu, J.; Chen, L.; Yuan, L.; Xu, P. pHmScarlet is a pH-sensitive red fluorescent protein to monitor exocytosis docking and fusion steps. Nat. Commun. 2021, 12, 1413.
92. Tantama, M.; Hung, Y.P.; Yellen, G. Imaging intracellular pH in live cells with a genetically encoded red fluorescent protein sensor. J. Am. Chem Soc. 2011, 133, 10034–10037.
93. Subach, O.M.; Cranfill, P.J.; Davidson, M.W.; Verkhusha, V.V. An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore. PLoS ONE 2011, 6, e28674.
94. Goedhart, J.; von Stetten, D.; Noirclerc-Savoye, M.; Lelimousin, M.; Joosen, L.; Hink, M.A.; van Weeren, L.; Gadella, T.W., Jr.; Royant, A. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat. Commun 2012, 3, 751.
95. Lambert, T.J. FPbase: A community-editable fluorescent protein database. Nat. Methods. 2019, 16, 277–278.
96. Kogure, T.; Karasawa, S.; Araki, T.; Saito, K.; Kinjo, M.; Miyawaki, A. A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nat. Biotechnol. 2006, 24, 577–581.
97. Shaner, N.C.; Lambert, G.G.; Chammas, A.; Ni, Y.; Cranfill, P.J.; Baird, M.A.; Sell, B.R.; Allen, J.R.; Day, R.N.; Israelsson, M.; et al. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Methods 2013, 10, 407–409.
98. Johnson, D.E.; Ai, H.W.; Wong, P.; Young, J.D.; Campbell, R.E.; Casey, J.R. Red fluorescent protein pH biosensor to detect concentrative nucleoside transport. J. Biol. Chem. 2009, 284, 20499–20511.
99. Gross, L.A.; Baird, G.S.; Hoffman, R.C.; Baldridge, K.K.; Tsien, R.Y. The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. USA 2000, 97, 11990–11995.
100. Subach, F.V.; Patterson, G.H.; Manley, S.; Gillette, J.M.; Lippincott-Schwartz, J.; Verkhusha, V.V. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat. Methods 2009, 6, 153–159.
101. Bindels, D.S.; Haarbosch, L.; van Weeren, L.; Postma, M.; Wiese, K.E.; Mastop, M.; Aumonier, S.; Gotthard, G.; Royant, A.; Hink, M.A.; et al. mScarlet: A bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 2017, 14, 53–56.
102. Shcherbo, D.; Merzlyak, E.M.; Chepurnykh, T.V.; Fradkov, A.F.; Ermakova, G.V.; Solovieva, E.A.; Lukyanov, K.A.; Bogdanova, E.A.; Zaraisky, A.G.; Lukyanov, S.; et al. Bright far-red fluorescent protein for whole-body imaging. Nat. Methods 2007, 4, 741–746.
103. Kabeya, Y.; Mizushima, N.; Yamamoto, A.; Oshitani-Okamoto, S.; Ohsumi, Y.; Yoshimori, T. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J. Cell Sci. 2004, 117, 2805–2812.
104. Leeman, D.S.; Hebestreit, K.; Ruetz, T.; Webb, A.E.; McKay, A.; Pollina, E.A.; Dulken, B.W.; Zhao, X.; Yeo, R.W.; Ho, T.T.; et al. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science 2018, 359, 1277–1283.
105. Lee, I.H.; Cao, L.; Mostoslavsky, R.; Lombard, D.B.; Liu, J.; Bruns, N.E.; Tsokos, M.; Alt, F.W.; Finkel, T. A role for the NAD-dependent deacetylase Sirt1 in the regulation of autophagy. Proc. Natl. Acad. Sci. USA 2008, 105, 3374–3379.
106. Bains, M.; Heidenreich, K.A. Chapter 7 Live-Cell Imaging of Autophagy Induction and Autophagosome-Lysosome Fusion in Primary Cultured Neurons. Autophagy Dis. Clin. Appl. Part C 2009, 453, 145–158.
107. Demarchi, F.; Bertoli, C.; Copetti, T.; Tanida, I.; Brancolini, C.; Eskelinen, E.L.; Schneider, C. Calpain is required for macroautophagy in mammalian cells. J. Cell Biol. 2006, 175, 595–605.
108. Flavin, W.P.; Bousset, L.; Green, Z.C.; Chu, Y.; Skarpathiotis, S.; Chaney, M.J.; Kordower, J.H.; Melki, R.; Campbell, E.M. Endocytic vesicle rupture is a conserved mechanism of cellular invasion by amyloid proteins. Acta Neuropathol. 2017, 134, 629–653.
109. Jahreiss, L.; Menzies, F.M.; Rubinsztein, D.C. The itinerary of autophagosomes: From peripheral formation to kiss-and-run fusion with lysosomes. Traffic 2008, 9, 574–587.
110. Mizushima, N.; Yamamoto, A.; Hatano, M.; Kobayashi, Y.; Kabeya, Y.; Suzuki, K.; Tokuhisa, T.; Ohsumi, Y.; Yoshimori, T. Dissection of autophagosome formation using Apg5-deficient mouse embryonic. J. Cell Biol. 2001, 152, 657–667.
111. Tanida, I.; Yamaji, T.; Ueno, T.; Ishiura, S.; Kominami, E.; Hanada, K. Consideration about negative controls for LC3 and expression vectors for four colored fluorescent protein-LC3 negative controls. Autophagy 2008, 4, 131–134.
112. Erin, M.; Buckingham, J.E.C. Wallen Jackson Charles Grose, Nuclear LC3-positive puncta in stressed cells do not represent autophagosomes. Biotechniques 2018, 57, 241–244.
113. Lee, Y.K.; Jun, Y.W.; Choi, H.E.; Huh, Y.H.; Kaang, B.K.; Jang, D.J.; Lee, J.A. Development of LC3/GABARAP sensors containing a LIR and a hydrophobic domain to monitor autophagy. EMBO J. 2017, 36, 1100–1116.
114. Rosado, C.J.; Mijaljica, D.; Hatzinisiriou, I.; Prescott, M.; Devenish, R.J. Rosella: A fluorescent pH-biosensor for reporting vacuolar turnover of cytosol and organelles in yeast. Autophagy 2008, 4, 205–213.
115. Patterson, G.H.; Knobel, S.M.; Sharif, W.D.; Kain, S.R.; Piston, D.W. Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys. J. 1997, 73, 2782–2790.
116. Ai, H.W.; Olenych, S.G.; Wong, P.; Davidson, M.W.; Campbell, R.E. Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: Identification of the molecular determinants of color and applications in fluorescence imaging. BMC Biol. 2008, 6, 13.
117. Merzlyak, E.M.; Goedhart, J.; Shcherbo, D.; Bulina, M.E.; Shcheglov, A.S.; Fradkov, A.F.; Gaintzeva, A.; Lukyanov, K.A.; Lukyanov, S.; Gadella, T.W.; et al. Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat. Methods 2007, 4, 555–557.
118. Shaner, N.C.; Lin, M.Z.; McKeown, M.R.; Steinbach, P.A.; Hazelwood, K.L.; Davidson, M.W.; Tsien, R.Y. Improving the photostability of bright monomeric orange and red fluorescent proteins. Nat. Methods 2008, 5, 545–551.
119. Esposito, A.; Gralle, M.; Dani, M.A.C.; Lange, D.; Wouters, F.S. pHlameleons: A Family of FRET-Based Protein Sensors for Quantitative pH Imaging. Biochemistry 2008, 47, 13115–13126.
120. Kremers, G.; Goedhart, J.; van Munster, E.B.; Gadella, T.W.J. Cyan and Yellow Super Fluorescent Proteins with Improved Brightness, Protein Folding, and FRET Förster Radius. Biochemistry 2006, 45, 6570–6580.
121. Elsliger, M.; Wachter, R.M.; Hanson, G.T.; Kallio, K.; Remington, S.J. Structural and Spectral Response of Green Fluorescent Protein Variants to Changes in pH. Biochemistry 1999, 38, 5296–5301.
122. Nagai, T.; Ibata, K.; Park, E.S.; Kubota, M.; Mikoshiba, K.; Miyawaki, A. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat. Biotechnol. 2002, 20, 87–90.
123. Shimozono, S.; Hosoi, H.; Mizuno, H.; Fukano, T.; Tahara, T.; Miyawaki, A. Concatenation of Cyan and Yellow Fluorescent Proteins for Efficient Resonance Energy Transfer. Biochemistry 2006, 45, 6267–6271.
124. Burgstaller, S.; Bischof, H.; Gensch, T.; Stryeck, S.; Gottschalk, B.; Ramadani-Muja, J.; Eroglu, E.; Rost, R.; Balfanz, S.; Baumann, A.; et al. pH-Lemon, a Fluorescent Protein-Based pH Reporter for Acidic Compartments. ACS Sens. 2019, 4, 883–891.
125. Katayama, H.; Hama, H.; Nagasawa, K.; Kurokawa, H.; Sugiyama, M.; Ando, R.; Funata, M.; Yoshida, N.; Homma, M.; Nishimura, T.; et al. Visualizing and Modulating Mitophagy for Therapeutic Studies of Neurodegeneration. Cell 2020, 181, 1176–1187.e16.
126. Karasawa, S.; Araki, T.; Yamamoto-Hino, M.; Miyawaki, A. A green-emitting fluorescent protein from Galaxeidae coral and its monomeric version for use in fluorescent labeling. J. Biol. Chem. 2003, 278, 34167–34171.
127. Rudolf, R.; Mongillo, M.; Magalhaes, P.J.; Pozzan, T. In vivo monitoring of Ca(2+) uptake into mitochondria of mouse skeletal muscle during contraction. J. Cell Biol. 2004, 166, 527–536.
128. Gilon, T.; Chomsky, O.; Kulka, R.G. Degradation signals for ubiquitin system proteolysis in Saccharomyces cerevisiae. EMBO J. 1998, 17, 2759–2766.
129. Ghoda, L.; Sidney, D.; Macrae, M.; Coffino, P. Structural elements of Ornithine decarboxylase required for intracellular degradation and polyamine-dependent regulation. Mol. Cell. Biol. 1992, 12, 2178–2185.
130. Chudakov, D.M.; Verkhusha, V.V.; Staroverov, D.B.; Souslova, E.A.; Lukyanov, S.; Lukyanov, K.A. Photoswitchable cyan fluorescent protein for protein tracking. Nat. Biotechnol. 2004, 22, 1435–1439.