Monitoring the clearance of apoptotic and necrotic cells in the nematode caenorhabditis elegans

Methods in Molecular Biology

Volumn 1004, Issue , 2013, Pages 183-202

  Li, Zao ^a   Lu, Nan ^a   He, Xiangwei ^a   Zhou, Zheng ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Apoptosis; C. elegans; CED 1; CTNS 1; Deconvolution; Differential interference contrast microscope (DIC); DYN 1; Early endosomes; Engulfment; GFP; HGRS 1; ImageJ; Lysosomes; mCherry; mRFP; Necrosis; Phagosome maturation; Programmed cell death; PtdIns(3)P; RAB 2; RAB 5; RAB 7; Time lapse recording

Indexed keywords

GREEN FLUORESCENT PROTEIN;

APOPTOSIS; ARTICLE; BACTERIAL CLEARANCE; CAENORHABDITIS ELEGANS; CELL DEATH; CELL MATURATION; DIFFERENTIAL INTERFERENCE CONTRAST MICROSCOPY; FLUORESCENCE MICROSCOPY; LARVA; MICROSCOPY; MONITORING; NONHUMAN; PHAGOSOME; PRIORITY JOURNAL; CONTROLLED STUDY; PARASITE CLEARANCE; PARASITE DEVELOPMENT;

ANIMALIA; CAENORHABDITIS ELEGANS;

EID: 84926006014     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-383-1_14     Document Type: Article

References (50)

1. Savill J, Fadok V (2000) Corpse clearance de fi nes the meaning of cell death. Nature 407(6805):784-788
2. Jacobson MD, Weil M, Raff MC (1997) Programmed cell death in animal development. Cell 88(3):347-354
3. Elliott MR, Ravichandran KS (2010) Clearance of apoptotic cells: Implications in health and disease. J Cell Biol 189(7):1059-1070
4. Golstein P, Kroemer G (2007) Cell death by necrosis: Towards a molecular definition. Trends Biochem Sci 32(1):37-43
5. Kroemer G, Galluzzi L, Vandenabeele P, Abrams J, Alnemri ES, Baehrecke EH, Blagosklonny MV, El-Deiry WS, Golstein P, Green DR, Hengartner M, Knight RA, Kumar S, Lipton SA, Malorni W, Nunez G, Peter ME, Tschopp J, Yuan J, Piacentini M, Zhivotovsky B, Melino G (2009) Classification of cell death: Recommendations of the Nomenclature Committee on Cell Death 2009. Cell Death Differ 16(1):3-11
6. Jacobson MD, Bergeron L (2002) Cell death in the nervous system. In: Jacobson MD, McCarthy N (eds) Apoptosis, the molecular biology of programmed cell death. Oxford University Press, Oxford, pp 278-301
7. Yamashima T (2004) Ca 2+ -dependent proteases in ischemic neuronal death: A conserved 'calpain-cathepsin cascade' from nematodes to primates. Cell Calcium 36(3-4):285-293
8. Noch E, Khalili K (2009) Molecular mechanisms of necrosis in glioblastoma: The role of glutamate excitotoxicity. Cancer Biol Ther 8(19):1791-1797
9. Challa S, Chan FK (2010) Going up in fl ames: Necrotic cell injury and in flammatory diseases. Cell Mol Life Sci 67(19):3241-3253
10. Fujimoto K, Chen Y, Polonsky KS, Dorn GW II (2010) Targeting cyclophilin D and the mitochondrial permeability transition enhances beta-cell survival and prevents diabetes in Pdx1 deficiency. Proc Natl Acad Sci U S A 107(22): 10214-10219
11. Whelan RS, Kaplinskiy V, Kitsis RN (2010) Cell death in the pathogenesis of heart disease: Mechanisms and signi ficance. Annu Rev Physiol 72:19-44
12. Christofferson DE, Yuan J (2010) Necroptosis as an alternative form of programmed cell death. Curr Opin Cell Biol 22(2):263-268
13. McCall K (2010) Genetic control of necrosis - Another type of programmed cell death. Curr Opin Cell Biol 22(6):882-888
14. Moquin D, Chan FK (2010) The molecular regulation of programmed necrotic cell injury. Trends Biochem Sci 35(8):434-441
15. Vlachos M, Tavernarakis N (2010) Nonapoptotic cell death in Caenorhabditis elegans . Dev Dyn 239(5):1337-1351
16. Krysko DV, D'Herde K, Vandenabeele P (2006) Clearance of apoptotic and necrotic cells and its immunological consequences. Apoptosis 11(10):1709-1726
17. Poon IK, Hulett MD, Parish CR (2010) Molecular mechanisms of late apoptotic/ necrotic cell clearance. Cell Death Differ 17(3):381-397
18. Metzstein MM, Stan fi eld GM, Horvitz HR (1998) Genetics of programmed cell death in C. elegans : Past, present and future. Trends Genet 14:410-416
19. Reddien PW, Horvitz HR (2004) The engulfment process of programmed cell death in Caenorhabditis elegans . Annu Rev Cell Dev Biol 20:193-221
20. Sulston JE, Horvitz HR (1977) Post-embryonic cell lineages of the nematode, Caenorhabditis elegans . Dev Biol 56(1):110-156
21. Sulston JE, Schierenberg E, White JG, Thomson JN (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100(1):64-119
22. Gumienny TL, Lambie E, Hartwieg E, Horvitz HR, Hengartner MO (1999) Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. Development 126:1011-1022
23. Zhou Z, Hartwieg E, Horvitz HR (2001) CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. Cell 104(1):43-56
24. Zhou Z, Mangahas PM, Yu X (2004) The genetics of hiding the corpse: Engulfment and degradation of apoptotic cells in C. elegans and D. melanogaster. Curr Top Dev Biol 63:91-143
25. Driscoll M, Chal fi e M (1991) The mec-4 gene is a member of a family of Caenorhabditis elegans genes that can mutate to induce neuronal degeneration. Nature 349(6310):588-593
26. Driscoll M, Gerstbrein B (2003) Dying for a cause: Invertebrate genetics takes on human neurodegeneration. Nat Rev Genet 4(3): 181-194
27. Bianchi L, Gerstbrein B, Frokjaer-Jensen C, Royal DC, Mukherjee G, Royal MA, Xue J, Schafer WR, Driscoll M (2004) The neurotoxic MEC-4(d) DEG/ENaC sodium channel conducts calcium: Implications for necrosis initiation. Nat Neurosci 7(12):1337-1344
28. Treinin M, Chal fi e M (1995) A mutated acetylcholine receptor subunit causes neuronal degeneration in C. elegans. Neuron 14(4):871-877
29. Hall DH, Gu G, Garcia-Anoveros J, Gong L, Chal fi e M, Driscoll M (1997) Neuropathology of degenerative cell death in Caenorhabditis elegans. J Neurosci 17(3):1033-1045
30. Xu K, Tavernarakis N, Driscoll M (2001) Necrotic cell death in C. elegans requires the function of calreticulin and regulators of Ca(2+) release from the endoplasmic reticulum. Neuron 31(6):957-971
31. Chung S, Gumienny TL, Hengartner MO, Driscoll M (2000) A common set of engulfment genes mediates removal of both apoptotic and necrotic cell corpses in C. elegans. Nat Cell Biol 2(12):931-937
32. Schwartz HT (2007) A protocol describing pharynx counts and a review of other assays of apoptotic cell death in the nematode worm Caenorhabditis elegans. Nat Protoc 2(3): 705-714
33. Venegas V, Zhou Z (2007) Two alternative mechanisms that regulate the presentation of apoptotic cell engulfment signal in Caenorhabditis elegans. Mol Biol Cell 18(8):3180-3192
34. Wang X, Wang J, Gengyo-Ando K, Gu L, Sun CL, Yang C, Shi Y, Kobayashi T, Mitani S, Xie XS, Xue D (2007) C. elegans mitochondrial factor WAH-1 promotes phosphatidylserine externalization in apoptotic cells through phospholipid scramblase SCRM-1. Nat Cell Biol 9(5):541-549
35. Zullig S, Neukomm LJ, Jovanovic M, Charette SJ, Lyssenko NN, Halleck MS, Reutelingsperger CP, Schlegel RA, Hengartner MO (2007) Aminophospholipid translocase TAT-1 promotes phosphatidylserine exposure during C. elegans apoptosis. Curr Biol 17(11):994-999
36. Ooi SL, Priess JR, Henikoff S (2006) Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. PLoS Genet 2(6):e97
37. Mangahas PM, Yu X, Miller KG, Zhou Z (2008) The small GTPase Rab2 functions in the removal of apoptotic cells in Caenorhabditis elegans. J Cell Biol 180(2):357-373
38. Yu X, Odera S, Chuang CH, Lu N, Zhou Z (2006) C. elegans Dynamin mediates the signaling of phagocytic receptor CED-1 for the engulfment and degradation of apoptotic cells. Dev Cell 10(6):743-757
39. Yu X, Lu N, Zhou Z (2008) Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. PLoS Biol 6(3):e61
40. He B, Yu X, Margolis M, Liu X, Leng X, Etzion Y, Zheng F, Lu N, Quiocho FA, Danino D, Zhou Z (2010) Live-cell imaging in Caenorhabditis elegans reveals the distinct roles of dynamin self-assembly and guanosine triphosphate hydrolysis in the removal of apoptotic cells. Mol Biol Cell 21(4):610-629
41. Lu N, Shen Q, Mahoney TR, Liu X, Zhou Z (2011) Three sorting nexins drive the degradation of apoptotic cells in response to PtdIns(3) P signaling. Mol Biol Cell 22(3):354-374
42. Lu N, Shen Q, Mahoney TR, Neukomm LJ, Wang Y, Zhou Z (2012) Two PI 3-kinases and one PI 3-phosphatase together establish the cyclic waves of phagosomal PtdIns(3)P critical for the degradation of apoptotic cells. PLoS Biol 10(1):e1001245
43. Ellis RE, Jacobson DM, Horvitz HR (1991) Genes required for the engulfment of cell corpses during programmed cell death in Caenorhabditis elegans. Genetics 129(1): 79-94
44. Zhou Z, Caron E, Hartwieg E, Hall A, Horvitz HR (2001) The C. elegans PH domain protein CED-12 regulates cytoskeletal reorganization via a Rho/Rac GTPase signaling pathway. Dev Cell 1(4):477-489
45. Hamelin M, Scott IM, Way JC, Culotti JG (1992) The mec-7 beta-tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons. EMBO J 11(8): 2885-2893
46. Wood WB, Researchers of the C. elegans Community (1988) The nematode Caenorhabditis elegans. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
47. Shaham S (2005) Methods in cell biology, WormBook . In: C. elegans (ed) Research Community, WormBook, doi/10.1895/ wormbook.1.7.1, http://www.wormbook. org
48. Lu N, Zhou Z (2012) Membrane traf ficking and phagosome maturation during the clearance of apoptotic cells. Int Rev Cell Mol Biol 293:269-309
49. Gartner A, Milstein S, Ahmed S, Hodgkin J, Hengartner MO (2000) A conserved checkpoint pathway mediates DNA damage-induced apoptosis and cell cycle arrest in C. elegans. Mol Cell 5(3):435-443
50. Sibarita JB (2005) Deconvolution microscopy. Adv Biochem Eng Biotechnol 95:201-243